Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling

PubMed Central

Du, Jingjing; Liu, Chendong; Wu, Xiaoqian; Pu, Qiang; Fu, Yuhua; Tang, Qianzi; Liu, Yuanrui; Li, Qiang; Yang, Runlin; Li, Xuewei; Tang, Guoqing; Jiang, Yanzhi; Li, Mingzhou; Zhang, Shunhua; Zhu, Li

2015-01-01

Animal growth curves can provide essential information for animal breeders to optimize feeding and management strategies. However, the genetic mechanism underlying the phenotypic differentiation between the inflection point and asymptotic stages of the growth curve is not well characterized. Here, we employed Liangshan pigs in stages of growth at the inflection point (under inflection point: UIP) and the two asymptotic stages (before the inflection point: BIP, after the inflection point: AIP) as models to survey global gene expression in the longissimus dorsi muscle using digital gene expression (DGE) tag profiling. We found Liangshan pigs reached maximum growth rate (UIP) at 163.6 days of age and a weight of 134.6 kg. The DGE libraries generated 117 million reads of 5.89 gigabases in length. 21,331, 20,996 and 20,139 expressed transcripts were identified BIP, UIP and AIP, respectively. Among them, we identified 757 differentially expressed genes (DEGs) between BIP and UIP, and 271 DEGs between AIP and UIP. An enrichment analysis of DEGs proved the immune system was strengthened in the AIP stage. Energy metabolism rate, global transcriptional activity and bone development intensity were highest UIP. Meat from Liangshan pigs had the highest intramuscular fat content and most favorable fatty acid composition in the AIP. Three hundred eighty (27.70%) specific expression genes were highly enriched in QTL regions for growth and meat quality traits. This study completed a comprehensive analysis of diverse genetic mechanisms underlying the inflection point and asymptotic stages of growth. Our findings will serve as an important resource in the understanding of animal growth and development in indigenous pig breeds. PMID:26292092

Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling.

PubMed

Shen, Linyuan; Luo, Jia; Du, Jingjing; Liu, Chendong; Wu, Xiaoqian; Pu, Qiang; Fu, Yuhua; Tang, Qianzi; Liu, Yuanrui; Li, Qiang; Yang, Runlin; Li, Xuewei; Tang, Guoqing; Jiang, Yanzhi; Li, Mingzhou; Zhang, Shunhua; Zhu, Li

2015-01-01

Animal growth curves can provide essential information for animal breeders to optimize feeding and management strategies. However, the genetic mechanism underlying the phenotypic differentiation between the inflection point and asymptotic stages of the growth curve is not well characterized. Here, we employed Liangshan pigs in stages of growth at the inflection point (under inflection point: UIP) and the two asymptotic stages (before the inflection point: BIP, after the inflection point: AIP) as models to survey global gene expression in the longissimus dorsi muscle using digital gene expression (DGE) tag profiling. We found Liangshan pigs reached maximum growth rate (UIP) at 163.6 days of age and a weight of 134.6 kg. The DGE libraries generated 117 million reads of 5.89 gigabases in length. 21,331, 20,996 and 20,139 expressed transcripts were identified BIP, UIP and AIP, respectively. Among them, we identified 757 differentially expressed genes (DEGs) between BIP and UIP, and 271 DEGs between AIP and UIP. An enrichment analysis of DEGs proved the immune system was strengthened in the AIP stage. Energy metabolism rate, global transcriptional activity and bone development intensity were highest UIP. Meat from Liangshan pigs had the highest intramuscular fat content and most favorable fatty acid composition in the AIP. Three hundred eighty (27.70%) specific expression genes were highly enriched in QTL regions for growth and meat quality traits. This study completed a comprehensive analysis of diverse genetic mechanisms underlying the inflection point and asymptotic stages of growth. Our findings will serve as an important resource in the understanding of animal growth and development in indigenous pig breeds.

Delayed gastric emptying following pancreatoduodenectomy with alimentary reconstruction according to Roux-en-Y or Billroth-II.

PubMed

Glowka, Tim R; Webler, Markus; Matthaei, Hanno; Schäfer, Nico; Schmitz, Volker; Kalff, Jörg C; Standop, Jens; Manekeller, Steffen

2017-03-20

Delayed gastric emptying (DGE) remains the most frequent complication following pancreatoduodenectomy (PD) with published incidences as high as 61%. The present study investigates the impact of bowel reconstruction techniques on DGE following classic PD (Whipple-Kausch procedure) with pancreatogastrostomy (PG). We included 168 consecutive patients who underwent PD with PG with either Billroth II type (BII, n = 78) or Roux-en-Y type reconstruction (ReY, n = 90) between 2004 and 2015. Excluded were patients with conventional single loop reconstruction after pylorus preserving procedures. DGE was classified according to the 2007 International Study Group of Pancreatic Surgery definition. Patients were analyzed regarding severity of DGE, morbidity and mortality, length of hospital stay and demographic factors. No difference was observed between BII and ReY regarding frequency of DGE. Overall rate for clinically relevant DGE was 30% (ReY) and 26% (BII). BII and ReY did not differ in terms of demographics, morbidity or mortality. DGE significantly prolongs ICU (four vs. two days) and hospital stay (20.5 vs. 14.5 days). Risk factors for DGE development are advanced age, retrocolic reconstruction, postoperative hemorrhage and major complications. The occurrence of DGE can not be influenced by the type of alimentary reconstruction (ReY vs. BII) following classic PD with PG. Old age and major complications could be identified as important risk factors in multivariate analysis. German Clinical Trials Register (DRKS) DRKS00011860 . Registered 14 March 2017.

Flavonoid constituents of Dobera glabra leaves: amelioration impact against CCl4-induced changes in the genetic materials in male rats.

PubMed

Elkhateeb, Ahmed; Abdel Latif, Rasha R; Marzouk, Mona M; Hussein, Sameh R; Kassem, Mona E S; Khalil, Wagdy K B; El-Ansari, Mohamed A

2017-12-01

Dobera glabra (Forssk.) Poir (Salvadoraceae) is a highly valued tree with diverse importance as special mineral sourced feed and a folkloric tool for forecasting droughts. However, there are no reports on its phytochemical and biological investigations. Phytochemical investigation of D. glabra leaves and its protective potential against CCl 4 inducing changes in the genetic materials. D. glabra extract, DGE (70% MeOH/H 2 O), was applied to polyamide column chromatography, eluting with MeOH/H 2 O of decreasing polarities, followed by preparative chromatographic tools, yielded seven compounds. Three DGE doses (50, 100 and 200 mg/kg bw/d) were administrated for 8 weeks intragastrically to male albino rats prior treated with CCl 4 (0.5 mL/kg/bw). The reactive oxygen species (ROS) levels, expression changes of glutamate transporters (GLAST, GLT-1 and SNAT3) mRNA, DNA fragmentation and glutathione peroxidase (GPx) activity were investigated in the liver tissues of these rats. Isorhamnetin-3-O-β-glucopyranoside-7-O-α-rhamnopyranoside, isorhamnetin-3-O-α-rhamnopyranoside-7-O-β-glucopyranoside, kaempferol-3,7-di-O-α-rhamnopyranoside, isorhamnetin-3-O-β-glucopyranoside, kaempferol-3-O-β-glucopyranoside, isorhamnetin and kaempferol were identified. DGE (200 mg/kg bw) + CCl 4 exhibited the most significant reduction in ROS levels and DNA fragmentation with 251.3% and141% compared to 523.1% and 273.2% for CCl 4 , respectively. Additionally, it increased significantly the mRNA expression of GLAST, GLT-1 and SNAT3 to 2.16-, 1.72- and 2.09-fold, respectively. Also, GPx activity was increased to 4.8 U/mg protein/min compared to CCl 4 (1.8 U/mg protein/min). Flavonoid constituents, antioxidant effect and genotoxic protection activity of D. glabra were first reported. DGE may be valuable in the treatment and hindrance of hepatic oxidative stress and genotoxicity.

Transcript and Protein Profiling Analysis of the Destruxin A-Induced Response in Larvae of Plutella xylostella

PubMed Central

Dong, Xiaolin; Fan, Jiqiao; Qiu, Baoli; Ren, Shunxiang

2013-01-01

Background Destruxins (dtxs) are the mycotoxin produced by certain entomopathogenic fungi, such as Metarhizium anisopliae, Aschersonia sp, Alternaria brassicae and Ophiosphaerella herpotrichae. It can affect a wide variety of biological processes in insects, including innate immune, Ca2+ channel in cells, and apoptosis in a dose-dependent manner. Dtxs have been used as biological control agent for a long time, however, their molecular mechanism of action is still unknown. Principal Findings In this study, both digital gene expression (DGE) and two-dimensional electrophoresis (2-DE) approaches were adopted to examine the effects of dtx A on Plutella xyllostella (L.) larvae. By using DGE and 2-DE analyses, 1584 genes and 42 protein points were identified as being up- or down regulated at least 2-fold in response to dtx A. Firstly, injection of dtx A to larvae accelerated the increase of peptidoglycan recognition protein (PGRP), which could activate the Toll signal pathway inducing production of antibacterial substances such as cecropin and gloverin. Dtx A also stimulated prophenoloxidase (proPO) system which plays an important role in innate immunity and leads to melanization of external organisms. Secondly, dtx A suppressed the expression of genes related to the Toll pathway, and induced expression of serine proteinase inhibitors (serpins), especially the serpin 2 that blocked process of the proPO system. Finally, other physiological process like xenobiotics detoxification, apoptosis, calcium signaling pathway and insect hormone biosynthesis, were also mediated in response to dtx A toxicity. Conclusions Transcript and protein profiling analyses will provide an insight into the potential molecular mechanism of action in P. xylostella larvae in response to dtx A. PMID:23585848

Delayed Gastric Emptying in Side-to-Side Gastrojejunostomy in Pancreaticoduodenectomy: Result of a Propensity Score Matching.

PubMed

Tsutaho, Akio; Nakamura, Toru; Asano, Toshimichi; Okamura, Keisuke; Tsuchikawa, Takahiro; Noji, Takehiro; Nakanishi, Yoshitsugu; Tanaka, Kimitaka; Murakami, Soichi; Kurashima, Yo; Ebihara, Yuma; Shichinohe, Toshiaki; Ito, Yoichi M; Hirano, Satoshi

2017-10-01

Delayed gastric emptying (DGE) is one of the most common morbidities of pancreaticoduodenectomy (PD). The aim of this study was to clarify whether the incidence of DGE can be reduced by side-to-side gastric greater curvature-to-jejunal anastomosis in subtotal stomach-preserving pancreaticoduodenectomy (SSPPD). The clinical data of 253 patients who had undergone PD were examined. Of a total of 188 patients who had undergone SSPPD, a gastrojejunostomy (GJ) was performed with end-to-side anastomosis in 87 patients (SSPPD-ETS group), and a GJ was performed with a greater curvature side-to-jejunal side anastomosis in 101 patients (SSPPD-STS group). After propensity score matching, the matched cohort consisted of 74 patients in each group. The postoperative data were evaluated according to the International Study Group of Pancreatic Surgery grade of DGE. The total incidence of DGE was 9.4% in the SSPPD-ETS group and 4% in the SSPPD-STS group, with no significant difference (p = 0.1902). A significant difference was observed between the two groups in the incidence of DGE grade C (p = 0.0426). The incidence of total DGE was not reduced statistically in the STS group compared with the ETS group, but reduced DGE grade C. Side-to-side anastomosis might be associated with a reduced incidence of DGE grade C.

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

PubMed Central

2010-01-01

Background Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE) are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish. Results RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution. Conclusion This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host-pathogen interactions and evolutionary history of immunogenetics from fish to mammals. PMID:20707909

Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing.

PubMed

Sun, Quan; Zhou, Guanfan; Cai, Yingfan; Fan, Yonghong; Zhu, Xiaoyan; Liu, Yihua; He, Xiaohong; Shen, Jinjuan; Jiang, Huaizhong; Hu, Daiwen; Pan, Zheng; Xiang, Liuxin; He, Guanghua; Dong, Daiwen; Yang, Jianping

2012-04-21

Tumourous stem mustard (Brassica juncea var. tumida Tsen et Lee) is an economically and nutritionally important vegetable crop of the Cruciferae family that also provides the raw material for Fuling mustard. The genetics breeding, physiology, biochemistry and classification of mustards have been extensively studied, but little information is available on tumourous stem mustard at the molecular level. To gain greater insight into the molecular mechanisms underlying stem swelling in this vegetable and to provide additional information for molecular research and breeding, we sequenced the transcriptome of tumourous stem mustard at various stem developmental stages and compared it with that of a mutant variety lacking swollen stems. Using Illumina short-read technology with a tag-based digital gene expression (DGE) system, we performed de novo transcriptome assembly and gene expression analysis. In our analysis, we assembled genetic information for tumourous stem mustard at various stem developmental stages. In addition, we constructed five DGE libraries, which covered the strains Yong'an and Dayejie at various development stages. Illumina sequencing identified 146,265 unigenes, including 11,245 clusters and 135,020 singletons. The unigenes were subjected to a BLAST search and annotated using the GO and KO databases. We also compared the gene expression profiles of three swollen stem samples with those of two non-swollen stem samples. A total of 1,042 genes with significantly different expression levels occurring simultaneously in the six comparison groups were screened out. Finally, the altered expression levels of a number of randomly selected genes were confirmed by quantitative real-time PCR. Our data provide comprehensive gene expression information at the transcriptional level and the first insight into the understanding of the molecular mechanisms and regulatory pathways of stem swelling and development in this plant, and will help define new mechanisms of stem development in non-model plant organisms.

Allelic analysis of low molecular weight glutenin subunits using 2-DGE in Korean wheat cultivars

USDA-ARS?s Scientific Manuscript database

Two-dimensional gel electrophoresis (2-DGE) was used to determine the allelic compositions of LMW-GS in 32 Korean wheat cultivars. Protein patterns generated by 2-DGE from each cultivar were compared to patterns from standard wheat cultivars for each allele. At the Glu-A3 locus, thirteen c, twelve ...

Molecular and Cellular Mechanisms of Apoptosis during Dissociated Spermatogenesis

PubMed Central

Liu, Tengfei; Wang, Lingling; Chen, Hong; Huang, Yufei; Yang, Ping; Ahmed, Nisar; Wang, Taozhi; Liu, Yi; Chen, Qiusheng

2017-01-01

Apoptosis is a tightly controlled process by which tissues eliminate unwanted cells. Spontaneous germ cell apoptosis in testis has been broadly investigated in mammals that have an associated spermatogenesis pattern. However, the mechanism of germ cell apoptosis in seasonally breeding reptiles following a dissociated spermatogenesis has remained enigmatic. In the present study, morphological evidence has clearly confirmed the dissociated spermatogenesis pattern in Pelodiscus sinensis. TUNEL and TEM analyses presented dynamic changes and ultrastructural characteristics of apoptotic germ cells during seasonal spermatogenesis, implying that apoptosis might be one of the key mechanisms to clear degraded germ cells. Furthermore, using RNA-Seq and digital gene expression (DGE) profiling, a large number of apoptosis-related differentially expressed genes (DEGs) at different phases of spermatogenesis were identified and characterized in the testis. DGE and RT-qPCR analysis revealed that the critical anti-apoptosis genes, such as Bcl-2, BAG1, and BAG5, showed up-regulated patterns during intermediate and late spermatogenesis. Moreover, the increases in mitochondrial transmembrane potential in July and October were detected by JC-1 staining. Notably, the low protein levels of pro-apoptotic cleaved caspase-3 and CytC in cytoplasm were detected by immunohistochemistry and western blot analyses, indicating that the CytC-Caspase model might be responsible for the effects of germ cell apoptosis on seasonal spermatogenesis. These results facilitate understanding the regulatory mechanisms of apoptosis during spermatogenesis and uncovering the biological process of the dissociated spermatogenesis system in reptiles. PMID:28424629

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.

PubMed

Liu, Guo-hua; Rajendran, Narasimmalu; Amemiya, Takashi; Itoh, Kiminori

2011-11-01

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression.

USDA-ARS?s Scientific Manuscript database

An essential step to understanding the genomic biology of any organism is to comprehensively survey its transcriptome. We present the Bovine Gene Atlas (BGA) a compendium of over 7.2 million unique 20 base Illumina DGE tags representing 100 tissue transcriptomes collected primarily from L1 Dominette...

Registration of DGE-2, a durum wheat disomic alien substitution line 1E(1A) involving a diploid wheatgrass chromosome

USDA-ARS?s Scientific Manuscript database

The durum wheat (Triticum turgidum L., 2n = 2x = 28; AABB genomes) alien disomic substitution 1E(1A) line DGE-2 (PI 663216) was developed by the USDA–ARS, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, North Dakota and released in 2011. DGE-2 has 2n = 28 chromosomes, which are...

Characterization of the immune response of domestic fowl following immunization with proteins extracted from Dermanyssus gallinae.

PubMed

Harrington, David; Din, Hatem Mohi El; Guy, Jonathan; Robinson, Karen; Sparagano, Olivier

2009-03-23

Dermanyssus gallinae is the most significant ectoparasite of European poultry egg laying production systems due to high costs of control and associated production losses as well as adverse effects on bird welfare. In this study, soluble proteins were extracted from unfed D. gallinae (DGE) using a urea-based detergent and ultra-filtration, passed through a 0.22 microm filter and blended aseptically with adjuvant. One group of laying hens was immunized with DGE and adjuvant (Montanide ISA 50 V) whilst another group (Control) received physiological saline and adjuvant. All birds were immunized on two occasions, 21 days apart. Antibody response to immunization was determined by ELISA and western blotting using immunoglobulins (Igs) extracted from egg yolk. DGE immunization of hens resulted in a significant (P<0.05) IgY response compared to controls, although there was no significant difference in IgM response between treatments. A number of proteins were identified by western blotting using IgY antibodies from DGE immunized birds, most prominently at 40 and 230kDa. Analysis of proteins from approximately corresponding bands on SDS-PAGE confirmed the identity of tropomyosin, whilst other proteins showed high sequence homology with myosin and actin from other arachnid and insect species. Immunization of hens with DGE resulted in a 50.6% increase in mite mortality (P<0.001) 17h after feeding when tested by an in vitro mite feeding model. Data in this study demonstrate that somatic antigens from D. gallinae can be used to stimulate a protective immune response in laying hens. Further work is needed to identify other proteins of interest that could confer higher protection against D. gallinae, as well as optimization of the vaccination and in vitro testing protocol.

An experimental evolution study confirms that discontinuous gas exchange does not contribute to body water conservation in locusts.

PubMed

Talal, Stav; Ayali, Amir; Gefen, Eran

2016-12-01

The adaptive nature of discontinuous gas exchange (DGE) in insects is contentious. The classic 'hygric hypothesis', which posits that DGE serves to reduce respiratory water loss (RWL), is still the best supported. We thus focused on the hygric hypothesis in this first-ever experimental evolution study of any of the competing adaptive hypotheses. We compared populations of the migratory locust (Locusta migratoria) that underwent 10 consecutive generations of selection for desiccation resistance with control populations. Selected locusts survived 36% longer under desiccation stress but DGE prevalence did not differ between these and control populations (approx. 75%). Evolved changes in DGE properties in the selected locusts included longer cycle and interburst durations. However, in contrast with predictions of the hygric hypothesis, these changes were not associated with reduced RWL rates. Other responses observed in the selected locusts were higher body water content when hydrated and lower total evaporative water loss rates. Hence, our data suggest that DGE cycle properties in selected locusts are a consequence of an evolved increased ability to store water, and thus an improved capacity to buffer accumulated CO 2 , rather than an adaptive response to desiccation. We conclude that DGE is unlikely to be an evolutionary response to dehydration challenge in locusts. © 2016 The Author(s).

Dynamic glucose enhanced (DGE) MRI for combined imaging of blood-brain barrier break down and increased blood volume in brain cancer.

PubMed

Xu, Xiang; Chan, Kannie W Y; Knutsson, Linda; Artemov, Dmitri; Xu, Jiadi; Liu, Guanshu; Kato, Yoshinori; Lal, Bachchu; Laterra, John; McMahon, Michael T; van Zijl, Peter C M

2015-12-01

Recently, natural d-glucose was suggested as a potential biodegradable contrast agent. The feasibility of using d-glucose for dynamic perfusion imaging was explored to detect malignant brain tumors based on blood brain barrier breakdown. Mice were inoculated orthotopically with human U87-EGFRvIII glioma cells. Time-resolved glucose signal changes were detected using chemical exchange saturation transfer (glucoCEST) MRI. Dynamic glucose enhanced (DGE) MRI was used to measure tissue response to an intravenous bolus of d-glucose. DGE images of mouse brains bearing human glioma showed two times higher and persistent changes in tumor compared with contralateral brain. Area-under-curve (AUC) analysis of DGE delineated blood vessels and tumor and had contrast comparable to the AUC determined using dynamic contrast enhanced (DCE) MRI with GdDTPA, both showing a significantly higher AUC in tumor than in brain (P < 0.005). Both CEST and relaxation effects contribute to the signal change. DGE MRI is a feasible technique for studying brain tumor enhancement reflecting differences in tumor blood volume and permeability with respect to normal brain. We expect DGE will provide a low-risk and less expensive alternative to DCE MRI for imaging cancer in vulnerable populations, such as children and patients with renal impairment. © 2015 Wiley Periodicals, Inc.

Dynamic Glucose Enhanced (DGE) MRI for Combined Imaging of Blood Brain Barrier Break Down and Increased Blood Volume in Brain Cancer

PubMed Central

Xu, Xiang; Chan, Kannie WY; Knutsson, Linda; Artemov, Dmitri; Xu, Jiadi; Liu, Guanshu; Kato, Yoshinori; Lal, Bachchu; Laterra, John; McMahon, Michael T.; van Zijl, Peter C.M.

2015-01-01

Purpose Recently, natural d-glucose was suggested as a potential biodegradable contrast agent. The feasibility of using d-glucose for dynamic perfusion imaging was explored to detect malignant brain tumors based on blood brain barrier breakdown. Methods Mice were inoculated orthotopically with human U87-EGFRvIII glioma cells. Time-resolved glucose signal changes were detected using chemical exchange saturation transfer (glucoCEST) MRI. Dynamic glucose enhanced (DGE) MRI was used to measure tissue response to an intravenous bolus of d-glucose. Results DGE images of mouse brains bearing human glioma showed two times higher and persistent changes in tumor compared to contralateral brain. Area-under-curve (AUC) analysis of DGE delineated blood vessels and tumor and had contrast comparable to the AUC determined using dynamic contrast enhanced (DCE) MRI with GdDTPA, both showing a significantly higher AUC in tumor than in brain (p<0.005). Both CEST and relaxation effects contribute to the signal change. Conclusion DGE MRI is a feasible technique for studying brain tumor enhancement reflecting differences in tumor blood volume and permeability with respect to normal brain. We expect DGE will provide a low-risk and less expensive alternative to DCE MRI for imaging cancer in vulnerable populations, such as children and patients with renal impairment. PMID:26404120

Gastric emptying and gastro-oesophageal reflux in children with cystic fibrosis.

PubMed

Hauser, Bruno; De Schepper, Jean; Malfroot, Anne; De Wachter, Elke; De Schutter, Iris; Keymolen, Kathelijn; Vandenplas, Yvan

2016-07-01

Gastro-oesophageal reflux (GOR) is common in patients with cystic fibrosis (CF). The aim of this study was to investigate the relationship between gastric emptying (GE) and GOR in children with CF. Multichannel intraluminal impedance-pH monitoring (MII-pH) to measure GOR and GE breath test (GEBT) to measure GE were performed in 28 children with symptoms suggestive for GOR disease (GORD) (group 1). GEBT was performed in another 28 children with/without GOR symptoms who agreed to undergo GEBT but not MII-pH (group 2). In group 1, we found increased acid GOR (AGOR) in 46.4% and delayed GE (DGE) in 21.4% but no relationship between increased AGOR and DGE. There was no DGE in group 2. We found DGE in 10.7% and rapid GE in 12.5% of the whole group. Almost half of the children with CF and symptoms suggestive for GORD have increased AGOR and almost a quarter has DGE. However, there was no relation between GOR and GE. Copyright © 2015 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Transcriptomic Analysis of Paulownia Infected by Paulownia Witches'-Broom Phytoplasma

PubMed Central

Zhu, Shui-Fang; Lin, Cai-Li; Tian, Guo-Zhong; Xu, Xia; Zhao, Wen-Jun

2013-01-01

Phytoplasmas are plant pathogenic bacteria that have no cell wall and are responsible for major crop losses throughout the world. Phytoplasma-infected plants show a variety of symptoms and the mechanisms they use to physiologically alter the host plants are of considerable interest, but poorly understood. In this study we undertook a detailed analysis of Paulownia infected by Paulownia witches’-broom (PaWB) Phytoplasma using high-throughput mRNA sequencing (RNA-Seq) and digital gene expression (DGE). RNA-Seq analysis identified 74,831 unigenes, which were subsequently used as reference sequences for DGE analysis of diseased and healthy Paulownia in field grown and tissue cultured plants. Our study revealed that dramatic changes occurred in the gene expression profile of Paulownia after PaWB Phytoplasma infection. Genes encoding key enzymes in cytokinin biosynthesis, such as isopentenyl diphosphate isomerase and isopentenyltransferase, were significantly induced in the infected Paulownia. Genes involved in cell wall biosynthesis and degradation were largely up-regulated and genes related to photosynthesis were down-regulated after PaWB Phytoplasma infection. Our systematic analysis provides comprehensive transcriptomic data about plants infected by Phytoplasma. This information will help further our understanding of the detailed interaction mechanisms between plants and Phytoplasma. PMID:24130859

Transcriptome and gene expression analysis during flower blooming in Rosa chinensis 'Pallida'.

PubMed

Yan, Huijun; Zhang, Hao; Chen, Min; Jian, Hongying; Baudino, Sylvie; Caissard, Jean-Claude; Bendahmane, Mohammed; Li, Shubin; Zhang, Ting; Zhou, Ningning; Qiu, Xianqin; Wang, Qigang; Tang, Kaixue

2014-04-25

Rosa chinensis 'Pallida' (Rosa L.) is one of the most important ancient rose cultivars originating from China. It contributed the 'tea scent' trait to modern roses. However, little information is available on the gene regulatory networks involved in scent biosynthesis and metabolism in Rosa. In this study, the transcriptome of R. chinensis 'Pallida' petals at different developmental stages, from flower buds to senescent flowers, was investigated using Illumina sequencing technology. De novo assembly generated 89,614 clusters with an average length of 428bp. Based on sequence similarity search with known proteins, 62.9% of total clusters were annotated. Out of these annotated transcripts, 25,705 and 37,159 sequences were assigned to gene ontology and clusters of orthologous groups, respectively. The dataset provides information on transcripts putatively associated with known scent metabolic pathways. Digital gene expression (DGE) was obtained using RNA samples from flower bud, open flower and senescent flower stages. Comparative DGE and quantitative real time PCR permitted the identification of five transcripts encoding proteins putatively associated with scent biosynthesis in roses. The study provides a foundation for scent-related gene discovery in roses. Copyright © 2014. Published by Elsevier B.V.

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review.

PubMed

Goez, Manuel Mauricio; Torres-Madroñero, Maria Constanza; Röthlisberger, Sarah; Delgado-Trejos, Edilson

2018-02-01

Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images: Gaussian, Rayleigh, and exponential, with signal-to-noise ratios (SNRs) ranging 8-20 decibels (dB). We compared the performance of wavelet, contourlet, total variation (TV), and wavelet-total variation (WTTV) techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sensitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10-20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best performance with any level of Gaussian noise and low levels (20-14 dB) of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image. Copyright © 2018 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Production and hosting by Elsevier B.V. All rights reserved.

Identification of Equine Lactadherin-derived Peptides That Inhibit Rotavirus Infection via Integrin Receptor Competition.

PubMed

Civra, Andrea; Giuffrida, Maria Gabriella; Donalisio, Manuela; Napolitano, Lorenzo; Takada, Yoshikazu; Coulson, Barbara S; Conti, Amedeo; Lembo, David

2015-05-08

Human rotavirus is the leading cause of severe gastroenteritis in infants and children under the age of 5 years in both developed and developing countries. Human lactadherin, a milk fat globule membrane glycoprotein, inhibits human rotavirus infection in vitro, whereas bovine lactadherin is not active. Moreover, it protects breastfed infants against symptomatic rotavirus infections. To explore the potential antiviral activity of lactadherin sourced by equines, we undertook a proteomic analysis of milk fat globule membrane proteins from donkey milk and elucidated its amino acid sequence. Alignment of the human, bovine, and donkey lactadherin sequences revealed the presence of an Asp-Gly-Glu (DGE) α2β1 integrin-binding motif in the N-terminal domain of donkey sequence only. Because integrin α2β1 plays a critical role during early steps of rotavirus host cell adhesion, we tested a minilibrary of donkey lactadherin-derived peptides containing DGE sequence for anti-rotavirus activity. A 20-amino acid peptide containing both DGE and RGD motifs (named pDGE-RGD) showed the greatest activity, and its mechanism of antiviral action was characterized; pDGE-RGD binds to integrin α2β1 by means of the DGE motif and inhibits rotavirus attachment to the cell surface. These findings suggest the potential anti-rotavirus activity of equine lactadherin and support the feasibility of developing an anti-rotavirus peptide that acts by hindering virus-receptor binding. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Alternative Fuels Data Center

Science.gov Websites

: CNG: $0.08 per gasoline gallon equivalent (GGE) until September 30, 2023; $0.13 per GGE from October 1 diesel gallon equivalent (DGE) until September 30, 2023; $0.13 per DGE from October 1, 2023, until

Alternative Fuels Data Center

Science.gov Websites

Tax Compressed natural gas (CNG) used as a vehicle fuel is taxed on a gasoline gallon equivalent ) used as a vehicle fuel is taxed on a diesel gallon equivalent (DGE) basis as follows: $0.05 per DGE

Intricate but tight coupling of spiracular activity and abdominal ventilation during locust discontinuous gas exchange cycles.

PubMed

Talal, Stav; Gefen, Eran; Ayali, Amir

2018-03-15

Discontinuous gas exchange (DGE) is the best studied among insect gas exchange patterns. DGE cycles comprise three phases, which are defined by their spiracular state: closed, flutter and open. However, spiracle status has rarely been monitored directly; rather, it is often assumed based on CO 2 emission traces. In this study, we directly recorded electromyogram (EMG) signals from the closer muscle of the second thoracic spiracle and from abdominal ventilation muscles in a fully intact locust during DGE. Muscular activity was monitored simultaneously with CO 2 emission, under normoxia and under various experimental oxic conditions. Our findings indicate that locust DGE does not correspond well with the commonly described three-phase cycle. We describe unique DGE-related ventilation motor patterns, coupled to spiracular activity. During the open phase, when CO 2 emission rate is highest, the thoracic spiracles do not remain open; rather, they open and close rapidly. This fast spiracle activity coincides with in-phase abdominal ventilation, while alternating with the abdominal spiracle and thus facilitating a unidirectional air flow along the main trachea. A change in the frequency of rhythmic ventilation during the open phase suggests modulation by intra-tracheal CO 2 levels. A second, slow ventilatory movement pattern probably serves to facilitate gas diffusion during spiracle closure. Two flutter-like patterns are described in association with the different types of ventilatory activity. We offer a modified mechanistic model for DGE in actively ventilating insects, incorporating ventilatory behavior and changes in spiracle state. © 2018. Published by The Company of Biologists Ltd.

Integrin-Using Rotaviruses Bind α2β1 Integrin α2 I Domain via VP4 DGE Sequence and Recognize αXβ2 and αVβ3 by Using VP7 during Cell Entry

PubMed Central

Graham, Kate L.; Halasz, Peter; Tan, Yan; Hewish, Marilyn J.; Takada, Yoshikazu; Mackow, Erich R.; Robinson, Martyn K.; Coulson, Barbara S.

2003-01-01

Integrins α2β1, αXβ2, and αVβ3 have been implicated in rotavirus cell attachment and entry. The virus spike protein VP4 contains the α2β1 ligand sequence DGE at amino acid positions 308 to 310, and the outer capsid protein VP7 contains the αXβ2 ligand sequence GPR. To determine the viral proteins and sequences involved and to define the roles of α2β1, αXβ2, and αVβ3, we analyzed the ability of rotaviruses and their reassortants to use these integrins for cell binding and infection and the effect of peptides DGEA and GPRP on these events. Many laboratory-adapted human, monkey, and bovine viruses used integrins, whereas all porcine viruses were integrin independent. The integrin-using rotavirus strains each interacted with all three integrins. Integrin usage related to VP4 serotype independently of sialic acid usage. Analysis of rotavirus reassortants and assays of virus binding and infectivity in integrin-transfected cells showed that VP4 bound α2β1, and VP7 interacted with αXβ2 and αVβ3 at a postbinding stage. DGEA inhibited rotavirus binding to α2β1 and infectivity, whereas GPRP binding to αXβ2 inhibited infectivity but not binding. The truncated VP5* subunit of VP4, expressed as a glutathione S-transferase fusion protein, bound the expressed α2 I domain. Alanine mutagenesis of D308 and G309 in VP5* eliminated VP5* binding to the α2 I domain. In a novel process, integrin-using viruses bind the α2 I domain of α2β1 via DGE in VP4 and interact with αXβ2 (via GPR) and αVβ3 by using VP7 to facilitate cell entry and infection. PMID:12941907

Nutrigenomics in honey bees: digital gene expression analysis of pollen's nutritive effects on healthy and varroa-parasitized bees

PubMed Central

2011-01-01

Background Malnutrition is a major factor affecting animal health, resistance to disease and survival. In honey bees (Apis mellifera), pollen, which is the main dietary source of proteins, amino acids and lipids, is essential to adult bee physiological development while reducing their susceptibility to parasites and pathogens. However, the molecular mechanisms underlying pollen's nutritive impact on honey bee health remained to be determined. For that purpose, we investigated the influence of pollen nutrients on the transcriptome of worker bees parasitized by the mite Varroa destructor, known for suppressing immunity and decreasing lifespan. The 4 experimental groups (control bees without a pollen diet, control bees fed with pollen, varroa-parasitized bees without a pollen diet and varroa-parasitized bees fed with pollen) were analyzed by performing a digital gene expression (DGE) analysis on bee abdomens. Results Around 36, 000 unique tags were generated per DGE-tag library, which matched about 8, 000 genes (60% of the genes in the honey bee genome). Comparing the transcriptome of bees fed with pollen and sugar and bees restricted to a sugar diet, we found that pollen activates nutrient-sensing and metabolic pathways. In addition, those nutrients had a positive influence on genes affecting longevity and the production of some antimicrobial peptides. However, varroa parasitism caused the development of viral populations and a decrease in metabolism, specifically by inhibiting protein metabolism essential to bee health. This harmful effect was not reversed by pollen intake. Conclusions The DGE-tag profiling methods used in this study proved to be a powerful means for analyzing transcriptome variation related to nutrient intake in honey bees. Ultimately, with such an approach, applying genomics tools to nutrition research, nutrigenomics promises to offer a better understanding of how nutrition influences body homeostasis and may help reduce the susceptibility of bees to (less virulent) pathogens. PMID:21985689

Digital gene expression analysis in the gills of Ruditapes philippinarum exposed to short- and long-term exposures of ammonia nitrogen.

PubMed

Cong, Ming; Wu, Huifeng; Cao, Tengfei; Lv, Jiasen; Wang, Qing; Ji, Chenglong; Li, Chenghua; Zhao, Jianmin

2018-01-01

Previous study revealed severe toxic effects of ammonia nitrogen on Ruditapes philippinarum including lysosomal instability, disturbed metabolic profiles, gill tissues with damaged structure, and variation of neurotransmitter concentrations. However, the underlying molecular mechanism was not fully understood yet. In the present study, digital gene expression technology (DGE) was applied to globally screen the key genes and pathways involved in the responses to short- and long-term exposures of ammonia nitrogen. Results of DGE analysis indicated that short-term duration of ammonia exposure affected pathways in Dorso-ventral axis formation, Notch signaling, thyroid hormone signaling and protein processing in endoplasmic reticulum. The long-term exposure led to DEGs significantly enriched in gap junction, immunity, signal and hormone transduction, as well as key substance metabolism pathways. Functional research of significantly changed DEGs suggested that the immunity of R. philippinarum was weakened heavily by toxic effects of ammonia nitrogen, as well as neuro-transduction and metabolism of important substances. Taken together, the present study provides a molecular support for the previous results of the detrimental toxicity of ammonia exposure in R. philippinarum, further work will be performed to investigate the specific genes and their certain functions involved in ammonia toxicity to molluscs. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization and Comparative Expression Profiling of Browning Response in Medinilla formosana after Cutting.

PubMed

Wang, Yan; Wang, Yiting; Li, Kunfeng; Song, Xijiao; Chen, Jianping

2016-01-01

Plant browning is a recalcitrant problem for in vitro culture and often leads to poor growth of explants and even failure of tissue culture. However, the molecular mechanisms underlying browning-induced physiological processes remain unclear. Medinilla is considered one of the most difficult genera for tissue culture owning to its severe browning. In the present study, intact aseptic plantlets of Medinilla formosana Hayata previously obtained by ovary culture, were used to explore the characteristics and molecular mechanism of the browning response. Successive morphological and anatomical observations after cutting showed that the browning of M. formosana was not lethal but adaptive. De novo transcriptome and digital gene expression (DGE) profiling using Illumina high-throughput sequencing were then used to explore molecular regulation after cutting. About 7.5 million tags of de novo transcriptome were obtained and 58,073 unigenes were assembled and annotated. A total of 6,431 differentially expressed genes (DEGs) at three stages after cutting were identified, and the expression patterns of these browning-related genes were clustered and analyzed. A number of putative DEGs involved in signal transduction and secondary metabolism were particularly studied and the potential roles of these cutting-responsive mRNAs in plant defense to diverse abiotic stresses are discussed. The DGE profiling data were also validated by quantitative RT-PCR analysis. The data obtained in this study provide an excellent resource for unraveling the molecular mechanisms of browning processes during in vitro tissue culture, and lay a foundation for future studies to inhibit and eliminate browning damage.

Characterization and Comparative Expression Profiling of Browning Response in Medinilla formosana after Cutting

PubMed Central

Wang, Yan; Wang, Yiting; Li, Kunfeng; Song, Xijiao; Chen, Jianping

2016-01-01

Plant browning is a recalcitrant problem for in vitro culture and often leads to poor growth of explants and even failure of tissue culture. However, the molecular mechanisms underlying browning-induced physiological processes remain unclear. Medinilla is considered one of the most difficult genera for tissue culture owning to its severe browning. In the present study, intact aseptic plantlets of Medinilla formosana Hayata previously obtained by ovary culture, were used to explore the characteristics and molecular mechanism of the browning response. Successive morphological and anatomical observations after cutting showed that the browning of M. formosana was not lethal but adaptive. De novo transcriptome and digital gene expression (DGE) profiling using Illumina high-throughput sequencing were then used to explore molecular regulation after cutting. About 7.5 million tags of de novo transcriptome were obtained and 58,073 unigenes were assembled and annotated. A total of 6,431 differentially expressed genes (DEGs) at three stages after cutting were identified, and the expression patterns of these browning-related genes were clustered and analyzed. A number of putative DEGs involved in signal transduction and secondary metabolism were particularly studied and the potential roles of these cutting-responsive mRNAs in plant defense to diverse abiotic stresses are discussed. The DGE profiling data were also validated by quantitative RT-PCR analysis. The data obtained in this study provide an excellent resource for unraveling the molecular mechanisms of browning processes during in vitro tissue culture, and lay a foundation for future studies to inhibit and eliminate browning damage. PMID:28066460

Numerical analysis of the reverse blocking enhancement in High-K passivation AlGaN/GaN Schottky barrier diodes with gated edge termination

NASA Astrophysics Data System (ADS)

Bai, Zhiyuan; Du, Jiangfeng; Xin, Qi; Li, Ruonan; Yu, Qi

2018-02-01

We conducted a numerical analysis on high-K dielectric passivated AlGaN/GaN Schottky barrier diodes (HPG-SBDs) with a gated edge termination (GET). The reverse blocking characteristics were significantly enhanced without the stimulation of any parasitic effect by varying the dielectric thickness dge under the GET, thickness TP, and dielectric constant εr of the high-K passivation layer. The leakage current was reduced by increasing εr and decreasing dge. The breakdown voltage of the device was enhanced by increasing εr and TP. The highest breakdown voltage of 970 V and the lowest leakage current of 0.5 nA/mm were achieved under the conditions of εr = 80, TP = 800 nm, and dge = 10 nm. C-V simulation revealed that the HPG-SBDs induced no parasitic capacitance by comparing the integrated charges of the devices with different high-K dielectrics and different dge.

Comparative Digital Gene Expression Analysis of the Arabidopsis Response to Volatiles Emitted by Bacillus amyloliquefaciens

PubMed Central

Hao, Hai-Ting; Zhao, Xia; Shang, Qian-Han; Wang, Yun; Guo, Zhi-Hong; Zhang, Yu-Bao; Xie, Zhong-Kui; Wang, Ruo-Yu

2016-01-01

Some plant growth-promoting rhizobacteria (PGPR) regulated plant growth and elicited plant basal immunity by volatiles. The response mechanism to the Bacillus amyloliquefaciens volatiles in plant has not been well studied. We conducted global gene expression profiling in Arabidopsis after treatment with Bacillus amyloliquefaciens FZB42 volatiles by Illumina Digital Gene Expression (DGE) profiling of different growth stages (seedling and mature) and tissues (leaves and roots). Compared with the control, 1,507 and 820 differentially expressed genes (DEGs) were identified in leaves and roots at the seedling stage, respectively, while 1,512 and 367 DEGs were identified in leaves and roots at the mature stage. Seventeen genes with different regulatory patterns were validated using quantitative RT-PCR. Numerous DEGs were enriched for plant hormones, cell wall modifications, and protection against stress situations, which suggests that volatiles have effects on plant growth and immunity. Moreover, analyzes of transcriptome difference in tissues and growth stage using DGE profiling showed that the plant response might be tissue-specific and/or growth stage-specific. Thus, genes encoding flavonoid biosynthesis were downregulated in leaves and upregulated in roots, thereby indicating tissue-specific responses to volatiles. Genes related to photosynthesis were downregulated at the seedling stage and upregulated at the mature stage, respectively, thereby suggesting growth period-specific responses. In addition, the emission of bacterial volatiles significantly induced killing of cells of other organism pathway with up-regulated genes in leaves and the other three pathways (defense response to nematode, cell morphogenesis involved in differentiation and trichoblast differentiation) with up-regulated genes were significantly enriched in roots. Interestingly, some important alterations in the expression of growth-related genes, metabolic pathways, defense response to biotic stress and hormone-related genes were firstly founded response to FZB42 volatiles. PMID:27513952

Mining genes involved in insecticide resistance of Liposcelis bostrychophila Badonnel by transcriptome and expression profile analysis.

PubMed

Dou, Wei; Shen, Guang-Mao; Niu, Jin-Zhi; Ding, Tian-Bo; Wei, Dan-Dan; Wang, Jin-Jun

2013-01-01

Recent studies indicate that infestations of psocids pose a new risk for global food security. Among the psocids species, Liposcelis bostrychophila Badonnel has gained recognition in importance because of its parthenogenic reproduction, rapid adaptation, and increased worldwide distribution. To date, the molecular data available for L. bostrychophila is largely limited to genes identified through homology. Also, no transcriptome data relevant to psocids infection is available. In this study, we generated de novo assembly of L. bostrychophila transcriptome performed through the short read sequencing technology (Illumina). In a single run, we obtained more than 51 million sequencing reads that were assembled into 60,012 unigenes (mean size = 711 bp) by Trinity. The transcriptome sequences from different developmental stages of L. bostrychophila including egg, nymph and adult were annotated with non-redundant (Nr) protein database, gene ontology (GO), cluster of orthologous groups of proteins (COG), and KEGG orthology (KO). The analysis revealed three major enzyme families involved in insecticide metabolism as differentially expressed in the L. bostrychophila transcriptome. A total of 49 P450-, 31 GST- and 21 CES-specific genes representing the three enzyme families were identified. Besides, 16 transcripts were identified to contain target site sequences of resistance genes. Furthermore, we profiled gene expression patterns upon insecticide (malathion and deltamethrin) exposure using the tag-based digital gene expression (DGE) method. The L. bostrychophila transcriptome and DGE data provide gene expression data that would further our understanding of molecular mechanisms in psocids. In particular, the findings of this investigation will facilitate identification of genes involved in insecticide resistance and designing of new compounds for control of psocids.

Mining Genes Involved in Insecticide Resistance of Liposcelis bostrychophila Badonnel by Transcriptome and Expression Profile Analysis

PubMed Central

Dou, Wei; Shen, Guang-Mao; Niu, Jin-Zhi; Ding, Tian-Bo; Wei, Dan-Dan; Wang, Jin-Jun

2013-01-01

Background Recent studies indicate that infestations of psocids pose a new risk for global food security. Among the psocids species, Liposcelis bostrychophila Badonnel has gained recognition in importance because of its parthenogenic reproduction, rapid adaptation, and increased worldwide distribution. To date, the molecular data available for L. bostrychophila is largely limited to genes identified through homology. Also, no transcriptome data relevant to psocids infection is available. Methodology and Principal Findings In this study, we generated de novo assembly of L. bostrychophila transcriptome performed through the short read sequencing technology (Illumina). In a single run, we obtained more than 51 million sequencing reads that were assembled into 60,012 unigenes (mean size = 711 bp) by Trinity. The transcriptome sequences from different developmental stages of L. bostrychophila including egg, nymph and adult were annotated with non-redundant (Nr) protein database, gene ontology (GO), cluster of orthologous groups of proteins (COG), and KEGG orthology (KO). The analysis revealed three major enzyme families involved in insecticide metabolism as differentially expressed in the L. bostrychophila transcriptome. A total of 49 P450-, 31 GST- and 21 CES-specific genes representing the three enzyme families were identified. Besides, 16 transcripts were identified to contain target site sequences of resistance genes. Furthermore, we profiled gene expression patterns upon insecticide (malathion and deltamethrin) exposure using the tag-based digital gene expression (DGE) method. Conclusion The L. bostrychophila transcriptome and DGE data provide gene expression data that would further our understanding of molecular mechanisms in psocids. In particular, the findings of this investigation will facilitate identification of genes involved in insecticide resistance and designing of new compounds for control of psocids. PMID:24278202

Dragging in a Dynamic Geometry Environment through the Lens of Variation

ERIC Educational Resources Information Center

Leung, Allen

2008-01-01

What makes Dynamic Geometry Environment (DGE) a powerful mathematical knowledge acquisition microworld is its ability to visually make explicit the implicit dynamism of thinking about mathematical geometrical concepts. One of DGE's powers is to equip us with the ability to retain the background of a geometrical configuration while we can…

The Dynamic Geometrisation of Computer Programming

ERIC Educational Resources Information Center

Sinclair, Nathalie; Patterson, Margaret

2018-01-01

The goal of this paper is to explore dynamic geometry environments (DGE) as a type of computer programming language. Using projects created by secondary students in one particular DGE, we analyse the extent to which the various aspects of computational thinking--including both ways of doing things and particular concepts--were evident in their…

Application of a label-free, gel-free quantitative proteomics method for ecotoxicological studies of small fish species

EPA Science Inventory

Although two-dimensional electrophoresis (2D-GE) remains the basis for many ecotoxicoproteomic analyses, new, non gel-based methods are beginning to be applied to overcome throughput and coverage limitations of 2D-GE. The overall objective of our research was to apply a comprehe...

Trans-3,4-dideoxyglucone-3-ene (trans-3,4-DGE), a most reactive glucose degradation product in freshly heat sterilized glucose solutions.

PubMed

Chen, Ke; Prabel, Jason; Dutton, Johanna; Gotoda, Masaharu; Asai, Yumi; Grobin, Adam

2015-12-11

In our study, one or more glucose degradation products (GDPs) in freshly heat sterilized dextrose 5% in water (D5W) were found to react with a drug candidate having a β-keto amide group (Compound A) to form several drug related compounds with the same molecular weight. However the previously identified GDPs did not react with Compound A to produce the observed adducts, indicating that unidentified GDP(s) reacted with Compound A to form these adducts. Our investigation by reaction-directed fractionation of the reactive D5W with HPLC led to the identification of the reactive GDP, trans-3,4-dideoxyglucosone-3-ene (trans-3,4-DGE), responsible for producing these reaction products. The trans-3,4-DGE was identified from its derivatives of dinitrophenylhydrazine (DNPH) and acetoacetanilide and confirmed by (1) admixing Compound A with authentic trans-3,4-DGE to produce the identical impurities as admixing with freshly heat sterilized D5W, and (2) NMR analysis of the reactive fraction of glucose solutions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Transcriptome profiling and digital gene expression analysis of sweet potato for the identification of putative genes involved in the defense response against Fusarium oxysporum f. sp. batatas.

PubMed

Lin, Yuli; Zou, Weikun; Lin, Shiqiang; Onofua, Dennis; Yang, Zhijian; Chen, Haizhou; Wang, Songliang; Chen, Xuanyang

2017-01-01

Sweet potato production is constrained by Fusarium wilt, which is caused by Fusarium oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute to improving disease resistance via sweet potato breeding programs. In the present study, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling of sweet potato challenged with Fob using Illumina HiSeq technology. In total, 89,944,188 clean reads were generated from 12 samples and assembled into 101,988 unigenes with an average length of 666 bp; of these unigenes, 62,605 (61.38%) were functionally annotated in the NCBI non-redundant protein database by BLASTX with a cutoff E-value of 10-5. Clusters of Orthologous Groups (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were examined to explore the unigenes' functions. We constructed four DGE libraries for the sweet potato cultivars JinShan57 (JS57, highly resistant) and XinZhongHua (XZH, highly susceptible), which were challenged with pathogenic Fob. Genes that were differentially expressed in the four libraries were identified by comparing the transcriptomes. Various genes that were differentially expressed during defense, including chitin elicitor receptor kinase 1 (CERK), mitogen-activated protein kinase (MAPK), WRKY, NAC, MYB, and ethylene-responsive transcription factor (ERF), as well as resistance genes, pathogenesis-related genes, and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling pathways, were identified. These data represent a sequence resource for genetic and genomic studies of sweet potato that will enhance the understanding of the mechanism of disease resistance.

Growth medium and incubation temperature alter the Pseudogymnoascus destructans transcriptome: implications in identifying virulence factors.

PubMed

Donaldson, Michael E; Davy, Christina M; Vanderwolf, Karen J; Willis, Craig K R; Saville, Barry J; Kyle, Christopher J

2018-02-23

Pseudogymnoascus destructans is the causal agent of bat white-nose syndrome (WNS), which is devastating some North American bat populations. Previous transcriptome studies provided insight regarding the molecular mechanisms involved in WNS; however, it is unclear how different environmental parameters could influence pathogenicity. This information could be useful in developing management strategies to mitigate the negative impacts of P. destructans on bats. We cultured three P. destructans isolates from Atlantic Canada on two growth media (potato dextrose agar and Sabouraud dextrose agar) that differ in their nitrogen source, and at two separate incubation temperatures (4 C and 15 C) that approximate the temperature range of bat hibernacula during the winter and a temperature within its optimal mycelial growth range. We conducted RNA sequencing to determine transcript levels in each sample and performed differential gene expression (DGE) analyses to test the influence of growth medium and incubation temperature on gene expression. We also compared our in vitro results with previous RNA-sequencing data sets generated from P. destructans growing on the wings of a susceptible host, Myotis lucifugus. Our findings point to a critical role for substrate and incubation temperature in influencing the P. destructans transcriptome. DGE analyses suggested that growth medium plays a larger role than temperature in determining P. destructans gene expression and that although the psychrophilic fungus responds to different nitrogen sources, it may have evolved for continued growth at a broad range of low temperatures. Further, our data suggest that down-regulation of the RNA-interference pathway and increased fatty acid metabolism are involved in the P. destructans-bat interaction. Finally, we speculate that to reduce the activation of host defense responses, P. destructans minimizes changes in the expression of genes encoding secreted proteins during bat colonization.

How to avoid glucose degradation products in peritoneal dialysis fluids.

PubMed

Erixon, Martin; Wieslander, Anders; Lindén, Torbjörn; Carlsson, Ola; Forsbäck, Gunita; Svensson, Eva; Jönsson, Jan Ake; Kjellstrand, Per

2006-01-01

The formation of glucose degradation products (GDPs) during sterilization of peritoneal dialysis fluids (PDFs) is one of the most important aspects of biocompatibility of glucose-containing PDFs. Producers of PDFs are thus trying to minimize the level of GDPs in their products. 3,4-Dideoxyglucosone-3-ene (3,4-DGE) has been identified as the most bioreactive GDP in PDFs. It exists in a temperature-dependent equilibrium with a pool of 3-deoxyglucosone (3-DG) and is a precursor in the irreversible formation of 5-hydroxymethyl furaldehyde (5-HMF). The aim of the present study was to investigate how to minimize GDPs in PDFs and how different manufacturers have succeeded in doing so. Glucose solutions at different pHs and concentrations were heat sterilized and 3-DG, 3,4-DGE, 5-HMF, formaldehyde, and acetaldehyde were analyzed. Conventional as well as biocompatible fluids from different manufacturers were analyzed in parallel for GDP concentrations. The concentrations of 3-DG and 3,4-DGE produced during heat sterilization decreased when pH was reduced to about 2. Concentration of 5-HMF decreased when pH was reduced to 2.6. After further decrease to a pH of 2.0, concentration of 5-HMF increased slightly, and below a pH of 2.0 it increased considerably, together with formaldehyde; 3-DG continued to drop and 3,4-DGE remained constant. Inhibition of cell growth was paralleled by 3,4-DGE concentration at pH 2.0 - 6.0. A high glucose concentration lowered concentrations of 3,4-DGE and 3-DG at pH 5.5 and of 5-HMF at pH 1. At pH 2.2 and 3.2, glucose concentration had a minor effect on the formation of GDPs. All conventional PDFs contained high levels of 3,4-DGE and 3-DG. Concentrations were considerably lower in the biocompatible fluids. However, the concentration of 5-H M F was slightly higher in all the biocompatible fluids. The best way to avoid reactive GDPs is to have a pH between 2.0 and 2.6 during sterilization. If pHs outside this range are used, it becomes more important to have high glucose concentration during the sterilization process. There are large variations in GDPs, both within and between biocompatible and conventionally manufactured PDFs.

Transcriptome differences in the hypopharyngeal gland between Western Honeybees (Apis mellifera) and Eastern Honeybees (Apis cerana).

PubMed

Liu, Hao; Wang, Zi-Long; Tian, Liu-Qing; Qin, Qiu-Hong; Wu, Xiao-Bo; Yan, Wei-Yu; Zeng, Zhi-Jiang

2014-08-30

Apis mellifera and Apis cerana are two sibling species of Apidae. Apis cerana is adept at collecting sporadic nectar in mountain and forest region and exhibits stiffer hardiness and acarid resistance as a result of natural selection, whereas Apis mellifera has the advantage of producing royal jelly. To identify differentially expressed genes (DEGs) that affect the development of hypopharyngeal gland (HG) and/or the secretion of royal jelly between these two honeybee species, we performed a digital gene expression (DGE) analysis of the HGs of these two species at three developmental stages (newly emerged worker, nurse and forager). Twelve DGE-tag libraries were constructed and sequenced using the total RNA extracted from the HGs of newly emerged workers, nurses, and foragers of Apis mellifera and Apis cerana. Finally, a total of 1482 genes in Apis mellifera and 1313 in Apis cerana were found to exhibit an expression difference among the three developmental stages. A total of 1417 DEGs were identified between these two species. Of these, 623, 1072, and 462 genes showed an expression difference at the newly emerged worker, nurse, and forager stages, respectively. The nurse stage exhibited the highest number of DEGs between these two species and most of these were found to be up-regulated in Apis mellifera. These results suggest that the higher yield of royal jelly in Apis mellifera may be due to the higher expression level of these DEGs. In this study, we investigated the DEGs between the HGs of two sibling honeybee species (Apis mellifera and Apis cerana). Our results indicated that the gene expression difference was associated with the difference in the royal jelly yield between these two species. These results provide an important clue for clarifying the mechanisms underlying hypopharyngeal gland development and the production of royal jelly.

Global Analysis of Transcriptome Responses and Gene Expression Profiles to Cold Stress of Jatropha curcas L.

PubMed Central

Wang, Haibo; Zou, Zhurong; Wang, Shasha; Gong, Ming

2013-01-01

Background Jatropha curcas L., also called the Physic nut, is an oil-rich shrub with multiple uses, including biodiesel production, and is currently exploited as a renewable energy resource in many countries. Nevertheless, because of its origin from the tropical MidAmerican zone, J. curcas confers an inherent but undesirable characteristic (low cold resistance) that may seriously restrict its large-scale popularization. This adaptive flaw can be genetically improved by elucidating the mechanisms underlying plant tolerance to cold temperatures. The newly developed Illumina Hiseq™ 2000 RNA-seq and Digital Gene Expression (DGE) are deep high-throughput approaches for gene expression analysis at the transcriptome level, using which we carefully investigated the gene expression profiles in response to cold stress to gain insight into the molecular mechanisms of cold response in J. curcas. Results In total, 45,251 unigenes were obtained by assembly of clean data generated by RNA-seq analysis of the J. curcas transcriptome. A total of 33,363 and 912 complete or partial coding sequences (CDSs) were determined by protein database alignments and ESTScan prediction, respectively. Among these unigenes, more than 41.52% were involved in approximately 128 known metabolic or signaling pathways, and 4,185 were possibly associated with cold resistance. DGE analysis was used to assess the changes in gene expression when exposed to cold condition (12°C) for 12, 24, and 48 h. The results showed that 3,178 genes were significantly upregulated and 1,244 were downregulated under cold stress. These genes were then functionally annotated based on the transcriptome data from RNA-seq analysis. Conclusions This study provides a global view of transcriptome response and gene expression profiling of J. curcas in response to cold stress. The results can help improve our current understanding of the mechanisms underlying plant cold resistance and favor the screening of crucial genes for genetically enhancing cold resistance in J. curcas. PMID:24349370

Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L.

PubMed

Wang, Haibo; Zou, Zhurong; Wang, Shasha; Gong, Ming

2013-01-01

Jatropha curcas L., also called the Physic nut, is an oil-rich shrub with multiple uses, including biodiesel production, and is currently exploited as a renewable energy resource in many countries. Nevertheless, because of its origin from the tropical MidAmerican zone, J. curcas confers an inherent but undesirable characteristic (low cold resistance) that may seriously restrict its large-scale popularization. This adaptive flaw can be genetically improved by elucidating the mechanisms underlying plant tolerance to cold temperatures. The newly developed Illumina Hiseq™ 2000 RNA-seq and Digital Gene Expression (DGE) are deep high-throughput approaches for gene expression analysis at the transcriptome level, using which we carefully investigated the gene expression profiles in response to cold stress to gain insight into the molecular mechanisms of cold response in J. curcas. In total, 45,251 unigenes were obtained by assembly of clean data generated by RNA-seq analysis of the J. curcas transcriptome. A total of 33,363 and 912 complete or partial coding sequences (CDSs) were determined by protein database alignments and ESTScan prediction, respectively. Among these unigenes, more than 41.52% were involved in approximately 128 known metabolic or signaling pathways, and 4,185 were possibly associated with cold resistance. DGE analysis was used to assess the changes in gene expression when exposed to cold condition (12°C) for 12, 24, and 48 h. The results showed that 3,178 genes were significantly upregulated and 1,244 were downregulated under cold stress. These genes were then functionally annotated based on the transcriptome data from RNA-seq analysis. This study provides a global view of transcriptome response and gene expression profiling of J. curcas in response to cold stress. The results can help improve our current understanding of the mechanisms underlying plant cold resistance and favor the screening of crucial genes for genetically enhancing cold resistance in J. curcas.

Assessment of tris (1, 3-dichloro-2-propyl) phosphate toxicology in PC12 cells by using digital gene expression profiling.

PubMed

Li, Li; Jiang, Shuai; Li, Kang; Lin, Bencheng; Wang, Ziyu; Zhang, Zhiqing; Fang, Yanjun

2017-09-01

Tris (1,3-dichloro-2-propyl) phosphate (TDCIPP), one of the most universally used organophosphate flame retardants (OPFRs), is an environmental pollutant. However, limited information is available regarding its toxicity and environmental health risk. In the present study, PC12 cells provided a useful model for the evaluation of the toxic effects of TDCIPP. Exposure to 7.5, 15, 30, or 60 μM TDCIPP for 72 h inhibited cell viability, and enhanced cellular apoptosis and oxidative stress. To further explore the underlying mechanisms, digital gene expression (DGE) technology was used to identify early transcriptional changes following TDCIPP exposure. Expression of the transcripts of 161 genes was significantly altered upon treatment with TDCIPP. Functional and pathway analysis of the transcriptional profile demonstrated that genes showing significant TDCIPP-associated changes in expression were involved in the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway, extracellular matrix-receptor interactions, protein digestion and absorption, and microRNAs in cancer. Using quantitative real-time PCR, we validated the differential expression of selected genes. These results showed that the expression profiles of cells exposed to 60 μM TDCIPP were consistent with the DGE data. Furthermore, western blotting showed that treatment with TDCIPP reduced the Bcl-2/Bax ratio and attenuated PI3K/Akt/Myc signaling. Taken together, these data suggest that TDCIPP exposure can reduce cell viability and induce apoptosis in PC12 cells by inhibiting activation of the PI3K/Akt/Myc signaling pathway. These observations provide valuable preliminary information regarding the mechanisms of TDCIPP-induced toxicity in PC12 cells and indicate that further study of the toxicity of other environmental OPFRs is warranted. Copyright © 2017 Elsevier Ltd. All rights reserved.

Estimation of total genetic effects for survival time in crossbred laying hens showing cannibalism, using pedigree or genomic information.

PubMed

Brinker, T; Raymond, B; Bijma, P; Vereijken, A; Ellen, E D

2017-02-01

Mortality of laying hens due to cannibalism is a major problem in the egg-laying industry. Survival depends on two genetic effects: the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its group mates (IGE). For hens housed in sire-family groups, DGE and IGE cannot be estimated using pedigree information, but the combined effect of DGE and IGE is estimated in the total breeding value (TBV). Genomic information provides information on actual genetic relationships between individuals and might be a tool to improve TBV accuracy. We investigated whether genomic information of the sire increased TBV accuracy compared with pedigree information, and we estimated genetic parameters for survival time. A sire model with pedigree information (BLUP) and a sire model with genomic information (ssGBLUP) were used. We used survival time records of 7290 crossbred offspring with intact beaks from four crosses. Cross-validation was used to compare the models. Using ssGBLUP did not improve TBV accuracy compared with BLUP which is probably due to the limited number of sires available per cross (~50). Genetic parameter estimates were similar for BLUP and ssGBLUP. For both BLUP and ssGBLUP, total heritable variance (T 2 ), expressed as a proportion of phenotypic variance, ranged from 0.03 ± 0.04 to 0.25 ± 0.09. Further research is needed on breeding value estimation for socially affected traits measured on individuals kept in single-family groups. © 2016 The Authors. Journal of Animal Breeding and Genetics Published by Blackwell Verlag GmbH.

Registration of DGE-3, a durum wheat disomic substitution line 1E(1B) involving a wheatgrass chromosome

USDA-ARS?s Scientific Manuscript database

Durum wheat (Triticum turgidum L., 2n = 4x = 28; AABB genomes) alien disomic substitution 1E(1B) line DGE-3 (PI 665473) was developed by the U.S. Department of Agriculture – Agricultural Research Service, Northern Crop Science Lab, Cereal Crops Research Unit, Fargo, ND and released in 2012. It was ...

Moving towards the New International Study Group for Pancreatic Surgery (ISGPS) definitions in pancreaticoduodenectomy: a comparison between the old and new.

PubMed

Tan, Winson Jianhong; Kow, Alfred Wei Chieh; Liau, Kui Hin

2011-08-01

The International Study Group for Pancreatic Surgery (ISGPS) has proposed several definitions for postoperative pancreatic fistula (POPF), delayed gastric emptying (DGE) and post-pancreatectomy haemorrhage (PPH). We assessed the effects of implementing these definitions on predicting outcomes. A database of 77 patients who underwent pancreaticoduodenectomy between January 2005 and December 2009 was analysed. Morbidities were defined and classified using the ISGPS definitions and recalculated based on the definitions adopted by our institution ('Old' definitions) prior to the implementation of ISGPS definitions. Data for the two groups were then compared. The morbidity rate rose to 70.1% from 27.2% when ISGPS rather than Old definitions were used to define morbidities (P < 0.001). Incidences of DGE, POPF and PPH were 20.7%, 39.0% and 10.4%, respectively. Rates of DGE and POPF were significantly higher according to ISGPS definitions than to Old definitions (20.7% vs. 5.2% [P= 0.001] and 39.0% vs. 15.6% [P= 0.004], respectively). According to the ISGPS definitions, all of the 12 additional patients with DGE and 12 of the 18 additional patients with POPF had grade A morbidities. Patients with ISGPS-defined morbidity had a longer intensive care unit (ICU) stay, longer postoperative stay and longer total stay (P= 0.030, P= 0.007 and P= 0.001, respectively). The morbidity rate more than doubled when ISGPS definitions were applied (an additional 42.9% of patients demonstrated morbidities). The majority of patients with DGE and POPF had grade A morbidities. The ISGPS definitions correlate well with ICU stay, postoperative stay and total length of stay. © 2011 International Hepato-Pancreato-Biliary Association.

Severe Delayed Gastric Emptying Induces Non-acid Reflux up to Proximal Esophagus in Neurologically Impaired Patients.

PubMed

Ishii, Shinji; Fukahori, Suguru; Asagiri, Kimio; Tanaka, Yoshiaki; Saikusa, Nobuyuki; Hashizume, Naoki; Yoshida, Motomu; Masui, Daisuke; Komatsuzaki, Naoko; Higashidate, Naruki; Sakamoto, Saki; Kurahachi, Tomohiro; Tsuruhisa, Shiori; Nakahara, Hirotomo; Yagi, Minoru

2017-10-30

The aim of this study is to investigate the degree of delayed gastric emptying (DGE) and evaluate how the severity of DGE affects gastroesophageal reflux disease (GERD) in neurologically impaired (NI) patients utilizing 24-hour multichannel intraluminal impedance pH measurements (pH/MII) and 13 C-acetate breath test ( 13 C-ABT) analyses. 13 C-ABT and pH/MII were conducted in 26 NI patients who were referred to our institution due to suspected GERD. At first, correlation analyses were performed to investigate the correlation between the 13 C-ABT parameters and the clinical or pH/MII parameters. Thereafter, all patients were divided into 2 groups (DGE and severe DGE [SDGE] group) according to each cut off half emptying time (t 1/2 , 90-170 minutes). Each pH/MII parameter was compared between the 2 groups in each set-up cutoff t 1/2 . The mean t 1/2 of all patients was 215.5 ± 237.2 minutes and the t 1/2 of 24 (92.3%) patients were > 100 minutes. Significant moderate positive correlations were observed between both t 1/2 and lag phase time and the non-acid reflux related parameters. Furthermore, the patients in the SDGE group demonstrated higher non-acid reflux related parameters than those of the DGE groups when the cutoff was t 1/2 ≥ 140 minutes. The present study demonstrated that GE with t 1/2 ≥ 140 minutes was related to an increase of non-acid exposure reaching up to the proximal esophagus in NI patients, and indicating that NI patients with SDGE might have a high risk of non-acid GERD.

De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer's properties.

PubMed

Guo, Qianqian; Ma, Xiaojun; Wei, Shugen; Qiu, Deyou; Wilson, Iain W; Wu, Peng; Tang, Qi; Liu, Lijun; Dong, Shoukun; Zu, Wei

2014-08-12

The major medicinal alkaloids isolated from Uncaria rhynchophylla (gouteng in chinese) capsules are rhynchophylline (RIN) and isorhynchophylline (IRN). Extracts containing these terpene indole alkaloids (TIAs) can inhibit the formation and destabilize preformed fibrils of amyloid β protein (a pathological marker of Alzheimer's disease), and have been shown to improve the cognitive function of mice with Alzheimer-like symptoms. The biosynthetic pathways of RIN and IRN are largely unknown. In this study, RNA-sequencing of pooled Uncaria capsules RNA samples taken at three developmental stages that accumulate different amount of RIN and IRN was performed. More than 50 million high-quality reads from a cDNA library were generated and de novo assembled. Sequences for all of the known enzymes involved in TIAs synthesis were identified. Additionally, 193 cytochrome P450 (CYP450), 280 methyltransferase and 144 isomerase genes were identified, that are potential candidates for enzymes involved in RIN and IRN synthesis. Digital gene expression profile (DGE) analysis was performed on the three capsule developmental stages, and based on genes possessing expression profiles consistent with RIN and IRN levels; four CYP450s, three methyltransferases and three isomerases were identified as the candidates most likely to be involved in the later steps of RIN and IRN biosynthesis. A combination of de novo transcriptome assembly and DGE analysis was shown to be a powerful method for identifying genes encoding enzymes potentially involved in the biosynthesis of important secondary metabolites in a non-model plant. The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the capsule extract from Uncaria, and provides information that may aid in metabolic engineering to increase yields of these important alkaloids.

Meta-analysis of antecolic versus retrocolic gastric reconstruction after a pylorus-preserving pancreatoduodenectomy.

PubMed

Bell, Richard; Pandanaboyana, Sanjay; Shah, Nehal; Bartlett, Adam; Windsor, John A; Smith, Andrew M

2015-03-01

Delayed gastric emptying (DGE) is a common complication after a pylorus-preserving pancreatoduodenectomy (PPPD) and is associated with significant morbidity. This study determines whether DGE is affected by antecolic (AC) or retrocolic (RC) reconstruction after a PPPD. An electronic search was performed of the MEDLINE, EMBASE and PubMed databases to identify all articles related to this topic. Pooled risk ratios (RR) were calculated for categorical outcomes, and mean differences (MD) for secondary continuous outcomes using the fixed-effects and random-effects models for meta-analysis. Nine studies including 878 patients met the inclusion criteria. DGE was lower with an AC reconstruction RR 0.31 [0.12, 0.78] Z = 2.47 (P = 0.010). Length of stay (LOS) MD -4 days [-7.63, -1.14] Z = 2.65 (P = 0.008) and days to commence a solid diet MD -5 days [-6.63, -3.15] Z = 5.50 (P ≤ 0.000) were also significantly in favour of the AC group. There was no difference in the incidence of pancreatic fistula, intra-abdominal collection/bile leak or mortality between the two groups. AC reconstruction after PPPD is associated with a lower incidence of DGE. Time to oral intake was significantly shorter with AC reconstruction, with a reduced hospital stay. © 2014 International Hepato-Pancreato-Biliary Association.

Effects of Titanium Dioxide Nanoparticles on the Synthesis of Fibroin in Silkworm (Bombyx mori).

PubMed

Ni, Min; Li, FanChi; Tian, JiangHai; Hu, JingSheng; Zhang, Hua; Xu, KaiZun; Wang, BinBin; Li, YangYang; Shen, WeiDe; Li, Bing

2015-08-01

Silkworm (Bombyx mori) is an economically important insect, and its silk production capacity largely depends on its ability to synthesize fibroin. While breeding of B. mori varieties has been a key strategy to improve silk production, little improvement of B. mori silk production has been achieved to date. As a result, the development of sericulture economy has not progressed well, pointing to the need of new ways for improvement of B. mori silk production. Titanium dioxide nanoparticles (TiO2 NPs), a food additive widely used for livestock, have been shown to promote animal growth and increase the protein synthesis in animals. However, no studies on effect of TiO2 NPs on fibroin synthesis in B. mori have been available. In this study, the differential expression profiles of genes and proteins in the silk gland of B. mori fed without or with TiO2 NPs (5 μg ml(-1)) were analyzed and compared using digital gene expression (DGE), reverse transcription quantitative polymerase chain reaction (RT-qPCR), semi-qPCR, and Western blot analysis. The effects of TiO2 NPs feeding on the activity of proteases in the midgut and the synthesis and transportation of amino acids in hemolymph were also investigated. DGE analyses showed that among a total of 4,741 genes detected, 306 genes were differentially expressed after the TiO2 NPs feeding, of which 137 genes were upregulated whereas 169 genes were downregulated. 106 genes were shown to be involved in fibroin synthesis, of which 97 genes, including those encoding cuticular protein glycine-rich 10, serine protease inhibitor 28, aspartate aminotransferase, lysyl-tRNA synthetase, and splicing factor arginine/serine-rich 6, and silk gland factor-1 (SGF-1), were upregulated with the maximum induction of 8.52-folds, whereas nine genes, including those encoding aspartylglucosaminidase, the cathepsin L in Tribolium castaneum, and similar to SPRY domain-containing SOCS box protein 3, were downregulated with the maximum reduction of 8.11-folds. Transcription levels of nine genes were further verified by RT-qPCR, and the results were consistent with those with DGE. Transcription and expression levels of fibroin light chain (Fib-L) gene were increased after TiO2 NPs feeding, indicating that TiO2 NPs improves fibroin synthesis. Compared with that of control, the mean protease activity was increased by 56.67% in the B. mori fed with TiO2 NPs, and the transport of four key amino acids used for fibroin synthesis in hemolymph was also increased. These findings indicated that TiO2 NPs feeding can improve the absorption and utilization of amino acids from the feed and could be a new way to increase the fibroin synthesis in B. mori.

Comparative Transcriptome Analysis of Genes Involved in Anthocyanin Biosynthesis in the Red and Yellow Fruits of Sweet Cherry (Prunus avium L.)

PubMed Central

Wei, Hairong; Chen, Xin; Zong, Xiaojuan; Shu, Huairui; Gao, Dongsheng; Liu, Qingzhong

2015-01-01

Background Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry. Methodology/Principal Findings In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3’-hydroxylase (F3’H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR). Conclusions/Significance The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop. PMID:25799516

Activated Notch signaling cascade is correlated with stem cell differentiation toward absorptive progenitors after massive small bowel resection in a rat.

PubMed

Sukhotnik, Igor; Coran, Arnold G; Pollak, Yulia; Kuhnreich, Eviatar; Berkowitz, Drora; Saxena, Amulya K

2017-09-01

Notch signaling is thought to act to drive cell versification in the lining of the small intestine. The purpose of the present study was to evaluate the role of the Notch signaling pathway in stem cell differentiation in the late stages of intestinal adaptation after massive small bowel resection in a rat. Male Sprague-Dawley rats were randomly assigned to one of two experimental groups of eight rats each: Sham rats underwent bowel transection and reanastomosis, while SBS rats underwent 75% small bowel resection. Rats were euthanized on day 14 Illumina's Digital Gene Expression (DGE) analysis was used to determine Notch signaling gene expression profiling. Notch-related gene and protein expression was determined using real-time PCR, Western blot analysis, and immunohistochemistry. From seven investigated Notch-related (by DGE analysis) genes, six genes were upregulated in SBS vs. control animals with a relative change in gene expression level of 20% or more. A significant upregulation of Notch signaling-related genes in resected animals was accompanied by a significant increase in Notch-1 protein levels (Western blot analysis) and a significant increase in the number of Notch1 and Hes1 (target gene)-positive cells (immunohistochemistry) compared with sham animals. Evaluation of cell differentiation has shown a strong increase in total number of absorptive cells (unchanged secretory cells) compared with control rats. In conclusion, 2 wk after bowel resection in rats, stimulated Notch signaling directs the crypt cell population toward absorptive progenitors. NEW & NOTEWORTHY This study provides novel insight into the mechanisms of cell proliferation following massive small bowel resection. We show that 2 wk after bowel resection in rats, enhanced stem cell activity was associated with stimulated Notch signaling pathway. We demonstrate that activated Notch signaling cascade directs the crypt cell population toward absorptive progenitors. Copyright © 2017 the American Physiological Society.

A prospective randomized comparison between pylorus- and subtotal stomach-preserving pancreatoduodenectomy on postoperative delayed gastric emptying occurrence and long-term nutritional status.

PubMed

Matsumoto, Ippei; Shinzeki, Makoto; Asari, Sadaki; Goto, Tadahiro; Shirakawa, Sachiyo; Ajiki, Tetsuo; Fukumoto, Takumi; Suzuki, Yasuyuki; Ku, Yonson

2014-06-01

Pylorus-preserving pancreatoduodenectomy (PPPD) has been associated with a high incidence of delayed gastric emptying (DGE). There are few studies comparing DGE associated with PPPD and subtotal stomach-preserving pancreatoduodenectomy (SSPPD). Moreover, differences between the procedures with respect to long-term results have not been reported. A prospective randomized study was conducted to compare perioperative complications and long-term nutritional status with PPPD and SSPPD. One hundred patients with periampullary lesions were randomized to receive either PPPD (n = 50) or SSPPD (n = 50). All patients were followed up for 3 years after surgery or to the time of recurrence to evaluate nutritional status for the study. The effects of the procedure, age, and malignancy on changes in nutritional indicators were estimated with linear mixed models. This study was registered at UMIN Clinical Trials Registry (UMIN 000012337). The incidence of DGE assessed by the International Study Group of Pancreatic Surgery was 20% with PPPD and 12% with SSPPD (P = 0.414). There were no significant differences between the two procedures on postoperative serum albumin levels, serum total cholesterol levels, and body mass index during the 3-year follow-up period. SSPPD is equally effective in DGE occurrence rate and long-term nutritional status comparing to PPPD. © 2014 Wiley Periodicals, Inc.

T1ρ-weighted Dynamic Glucose-enhanced MR Imaging in the Human Brain.

PubMed

Paech, Daniel; Schuenke, Patrick; Koehler, Christina; Windschuh, Johannes; Mundiyanapurath, Sibu; Bickelhaupt, Sebastian; Bonekamp, David; Bäumer, Philipp; Bachert, Peter; Ladd, Mark E; Bendszus, Martin; Wick, Wolfgang; Unterberg, Andreas; Schlemmer, Heinz-Peter; Zaiss, Moritz; Radbruch, Alexander

2017-12-01

Purpose To evaluate the ability to detect intracerebral regions of increased glucose concentration at T1ρ-weighted dynamic glucose-enhanced (DGE) magnetic resonance (MR) imaging at 7.0 T. Materials and Methods This prospective study was approved by the institutional review board. Nine patients with newly diagnosed glioblastoma and four healthy volunteers were included in this study from October 2015 to July 2016. Adiabatically prepared chemical exchange-sensitive spin-lock imaging was performed with a 7.0-T whole-body unit with a temporal resolution of approximately 7 seconds, yielding the time-resolved DGE contrast. T1ρ-weighted DGE MR imaging was performed with injection of 100 mL of 20% d-glucose via the cubital vein. Glucose enhancement, given by the relative signal intensity change at T1ρ-weighted MR imaging (DGEρ), was quantitatively investigated in brain gray matter versus white matter of healthy volunteers and in tumor tissue versus normal-appearing white matter of patients with glioblastoma. The median signal intensities of the assessed brain regions were compared by using the Wilcoxon rank-sum test. Results In healthy volunteers, the median signal intensity in basal ganglia gray matter (DGEρ = 4.59%) was significantly increased compared with that in white matter tissue (DGEρ = 0.65%) (P = .028). In patients, the median signal intensity in the glucose-enhanced tumor region as displayed on T1ρ-weighted DGE images (DGEρ = 2.02%) was significantly higher than that in contralateral normal-appearing white matter (DGEρ = 0.08%) (P < .0001). Conclusion T1ρ-weighted DGE MR imaging in healthy volunteers and patients with newly diagnosed, untreated glioblastoma enabled visualization of brain glucose physiology and pathophysiologically increased glucose uptake and may have the potential to provide information about glucose metabolism in tumor tissue. © RSNA, 2017 Online supplemental material is available for this article.

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

PubMed

Robinson, Mark D; McCarthy, Davis J; Smyth, Gordon K

2010-01-01

It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).

De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration.

PubMed

Gao, Bei; Zhang, Daoyuan; Li, Xiaoshuang; Yang, Honglan; Zhang, Yuanming; Wood, Andrew J

2015-05-28

The desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employed RNA-Seq and digital gene expression (DGE) technologies to study the genome-wide expression profiles of the dehydration and rehydration processes in this important desert plant. We applied a two-step approach to investigate the gene expression profile upon rehydration in the moss Bryum argenteum using Illumina HiSeq2000 sequencing platform. First, a total of 57,247 transcript assembly contigs (TACs) were obtained from 54.79 million reads by de novo assembly, with an average length of 863 bp and N50 of 1,372 bp. Among the reconstructed TACs, 36,916 (64.5%) revealed similarity with existing protein sequences in the public databases. 23,509 and 21,607 TACs were assigned GO and KEGG annotation information, respectively. Second, samples were taken from 3 hydration stages: desiccated (Dry), rehydrated 2 h (R2) and rehydrated 24 h (R24), and DEG libraries were constructed for Differentially Expressed Genes (DEGs) discovery. 4,081 and 6,709 DEGs were identified in R2 and R24, compared with Dry, respectively. Compared to the desiccated sample, up-regulated genes after two hours of hydration are primarily related to stress responses. GO function enrichment network, EKGG metabolic pathway and MapMan analysis supports the idea of the rapid recovery of photosynthesis after 24 h of rehydration. We identified 770 transcription factors (TFs) which were classified into 50 TF families. 142 TF transcripts were up-regulated upon rehydration including 23 members of the ERF family. In this study, we constructed a pioneering, high-quality reference transcriptome in B. argenteum and generated three DGE libraries to elucidate the changes of gene expression upon rehydration. Expression profiles consistent with the rapid recovery of photosynthesis (at R2) and the re-establishment of a positive carbon balance following rehydration (at R24) were observed. Our study will extend our knowledge of bryophyte transcriptomes and provide further insight into the molecular mechanisms related to rehydration and desiccation-tolerance.

Changes in the transcriptome of morula-stage bovine embryos caused by heat shock: relationship to developmental acquisition of thermotolerance

PubMed Central

2013-01-01

Background While initially sensitive to heat shock, the bovine embryo gains thermal resistance as it progresses through development so that physiological heat shock has little effect on development to the blastocyst stage by Day 5 after insemination. Here, experiments using 3’ tag digital gene expression (3’DGE) and real-time PCR were conducted to determine changes in the transcriptome of morula-stage bovine embryos in response to heat shock (40 degrees C for 8 h) that could be associated with thermotolerance. Results Using 3’DGE, expression of 173 genes were modified by heat shock, with 94 genes upregulated by heat shock and 79 genes downregulated by heat shock. A total of 38 differentially-regulated genes were associated with the ubiquitin protein, UBC. Heat shock increased expression of one heat shock protein gene, HSPB11, and one heat shock protein binding protein, HSPBP1, tended to increase expression of HSPA1A and HSPB1, but did not affect expression of 64 other genes encoding heat shock proteins, heat shock transcription factors or proteins interacting with heat shock proteins. Moreover, heat shock increased expression of five genes associated with oxidative stress (AKR7A2, CBR1, GGH, GSTA4, and MAP2K5), decreased expression of HIF3A, but did not affect expression of 42 other genes related to free radical metabolism. Heat shock also had little effect on genes involved in embryonic development. Effects of heat shock for 2, 4 and 8 h on selected heat shock protein and antioxidant genes were also evaluated by real-time PCR. Heat shock increased steady-state amounts of mRNA for HSPA1A (P<0.05) and tended to increase expression of HSP90AA1 (P<0.07) but had no effect on expression of SOD1 or CAT. Conclusions Changes in the transcriptome of the heat-shocked bovine morula indicate that the embryo is largely resistant to effects of heat shock. As a result, transcription of genes involved in thermal protection is muted and there is little disruption of gene networks involved in embryonic development. It is likely that the increased resistance of morula-stage embryos to heat shock as compared to embryos at earlier stages of development is due in part to developmental acquisition of mechanisms to prevent accumulation of denatured proteins and free radical damage. PMID:23320502

Transcriptome assembly and expression profiling of the molecular responses to cadmium toxicity in cerebral ganglia of wolf spider Pardosa pseudoannulata (Araneae: Lycosidae).

PubMed

Yang, Huilin; Peng, Yuande; Shi, Yixue; Tian, Jianxiang; Wang, Juan; Peng, Xianjin; Xie, Chunliang; Xu, Xiang; Song, Qisheng; Wang, Zhi; Lv, Zhiyue

2018-03-01

Cadmium (Cd) is a heavy metal that can cause irreversible toxicity to animals, and is an environmental pollutant in farmlands. Spiders are considered to be an excellent model for investigating the impacts of heavy metals on the environment. To date, the changes at the molecular level in the cerebral ganglia of spiders are poorly understood. Cd exposure leads to strong damage in the nervous system, such as apoptosis and necrosis of nerve cells, therefore we conducted a transcriptomic analysis of Pardosa pseudoannulata cerebral ganglia under Cd stress to profile differential gene expression (DGE). We obtained a total of 123,328 assembled unigenes, and 1441 Cd stress-associated DEGs between the Cd-treated and control groups. Expression profile analysis demonstrated that many genes involved in calcium signaling, cGMP-PKG signaling, tyrosine metabolism, phototransduction-fly, melanogenesis and isoquinoline alkaloid biosynthesis were up-regulated under Cd stress, whereas oxidative phosphorylation-related, nervous disease-associated, non-alcoholic fatty liver disease-associated, and ribosomal-associated genes were down-regulated. Here, we provide a comprehensive set of DEGs influenced by Cd stress, and heavy metal stress, and provide new information for elucidating the neurotoxic mechanisms of Cd stress in spiders.

Intermediate filament proteins and actin isoforms as markers for soft-tissue tumor differentiation and origin. III. Hemangiopericytomas and glomus tumors.

PubMed Central

Schürch, W.; Skalli, O.; Lagacé, R.; Seemayer, T. A.; Gabbiani, G.

1990-01-01

Intermediate filament proteins and actin isoforms of a series of 12 malignant hemangiopericytomas and five glomus tumors were examined by light microscopy, transmission electron microscopy, two-dimensional gel electrophoresis (2D-GE), and by immunohistochemistry, the latter using monoclonal or affinity-purified polyclonal antibodies to desmin, vimentin, cytokeratins, alpha-smooth muscle, and alpha-sarcomeric actins. By light microscopy, all hemangiopericytomas disclosed a predominant vascular pattern with scant storiform, myxoid and spindle cell areas, and with variable degrees of perivascular fibrosis. By ultrastructure, smooth muscle differentiation was observed in each hemangiopericytoma. Immunohistochemically, neoplastic cells of hemangiopericytomas expressed vimentin as the sole intermediate filament protein and lacked alpha-smooth muscle or alpha-sarcomeric actins. 2D-GE revealed only beta and gamma actins, in proportions typical for fibroblastic tissues. Glomus tumors revealed vimentin and alpha-smooth muscle actin within glomus cells by immunohistochemical techniques and disclosed ultrastructurally distinct smooth muscle differentiation. Therefore hemangiopericytomas represent a distinct soft-tissue neoplasm with uniform morphologic, immunohistochemical, and biochemical features most likely related to glomus tumors, the former representing an aggressive and potentially malignant neoplasm of vascular smooth muscle cells and the latter a well-differentiated neoplasm of vascular smooth muscle cells. Because malignant hemangiopericytomas disclose smooth muscle differentiation by ultrastructure, but do not express alpha-smooth muscle actin, as normal pericytes and glomus cells, it is suggested that these neoplasms represent highly vascularized smooth muscle neoplasms, ie, poorly differentiated leiomyosarcomas derived from vascular smooth muscle cells or their equivalent, the pericytes, which have lost alpha-smooth muscle actin as a differentiation marker that is similar to many conventional poorly differentiated leiomyosarcomas. Images Figure 6 Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:2158236

Prospective randomized clinical trial of a change in gastric emptying and nutritional status after a pylorus-preserving pancreaticoduodenectomy: comparison between an antecolic and a vertical retrocolic duodenojejunostomy.

PubMed

Imamura, Naoya; Chijiiwa, Kazuo; Ohuchida, Jiro; Hiyoshi, Masahide; Nagano, Motoaki; Otani, Kazuhiro; Kondo, Kazuhiro

2014-04-01

Although an antecolic duodenojejunostomy was reported to reduce post-operative delayed gastric emptying (DGE) compared with a retrocolic duodenojejunostomy after a pylorus-preserving pancreaticoduodenectomy (PPPD), the long-term effects of these procedures have rarely been studied. The aim of this prospective, randomized, clinical trial was to investigate the influence of the reconstruction route on post-operative gastric emptying and nutrition. Reconstruction was performed in 116 patients with an antecolic duodenojejunostomy (A group, n = 58) or a vertical retrocolic duodenojejunostomy (VR group, n = 58). Post-operative complications, including DGE, gastric emptying variables assessed by (13) C-acetate breath test and nutrition, were compared between the two groups for 1 year post-operatively. The incidence of DGE was not significantly different between the procedures (A group: 12.1%; VR group: 20.7%, P = 0.316). At post-operative month 1, gastric emptying was prolonged in the VR versus the A group but not significantly so. At post-operative month 6, gastric emptying was accelerated significantly in the A versus the VR group. Post-operative weight recovery was significantly better in the VR versus the A group at post-operative month 12 (percentage of pre-operative weight, A group: 93.8 ± 1.2%; VR group: 98.5 ± 1.3%, P = 0.015). A vertical retrocolic duodenojejunostomy was an acceptable procedure for the lower incidence of DGE and may contribute to better weight gain affected by moderate gastric emptying. © 2013 International Hepato-Pancreato-Biliary Association.

Prospective randomized clinical trial of a change in gastric emptying and nutritional status after a pylorus-preserving pancreaticoduodenectomy: comparison between an antecolic and a vertical retrocolic duodenojejunostomy

PubMed Central

Imamura, Naoya; Chijiiwa, Kazuo; Ohuchida, Jiro; Hiyoshi, Masahide; Nagano, Motoaki; Otani, Kazuhiro; Kondo, Kazuhiro

2014-01-01

Background Although an antecolic duodenojejunostomy was reported to reduce post-operative delayed gastric emptying (DGE) compared with a retrocolic duodenojejunostomy after a pylorus-preserving pancreaticoduodenectomy (PPPD), the long-term effects of these procedures have rarely been studied. The aim of this prospective, randomized, clinical trial was to investigate the influence of the reconstruction route on post-operative gastric emptying and nutrition. Methods Reconstruction was performed in 116 patients with an antecolic duodenojejunostomy (A group, n = 58) or a vertical retrocolic duodenojejunostomy (VR group, n = 58). Post-operative complications, including DGE, gastric emptying variables assessed by 13C-acetate breath test and nutrition, were compared between the two groups for 1 year post-operatively. Results The incidence of DGE was not significantly different between the procedures (A group: 12.1%; VR group: 20.7%, P = 0.316). At post-operative month 1, gastric emptying was prolonged in the VR versus the A group but not significantly so. At post-operative month 6, gastric emptying was accelerated significantly in the A versus the VR group. Post-operative weight recovery was significantly better in the VR versus the A group at post-operative month 12 (percentage of pre-operative weight, A group: 93.8 ± 1.2%; VR group: 98.5 ± 1.3%, P = 0.015). Conclusions A vertical retrocolic duodenojejunostomy was an acceptable procedure for the lower incidence of DGE and may contribute to better weight gain affected by moderate gastric emptying. PMID:23991719

Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development

PubMed Central

2013-01-01

Background Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countries. The control of flowering time is a major bottleneck in the industrialized development of C. sinense. Little is known about the mechanisms responsible for floral development in this orchid. Moreover, genome references for entire transcriptome sequences do not currently exist for C. sinense. Thus, transcriptome and expression profiling data for this species are needed as an important resource to identify genes and to better understand the biological mechanisms of floral development in C. sinense. Results In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptome analysis assembles gene-related information related to vegetative and reproductive growth of C. sinense. Illumina sequencing generated 54,248,006 high quality reads that were assembled into 83,580 unigenes with an average sequence length of 612 base pairs, including 13,315 clusters and 70,265 singletons. A total of 41,687 (49.88%) unique sequences were annotated, 23,092 of which were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Furthermore, 120 flowering-associated unigenes, 73 MADS-box unigenes and 28 CONSTANS-LIKE (COL) unigenes were identified from our collection. In addition, three digital gene expression (DGE) libraries were constructed for the vegetative phase (VP), floral differentiation phase (FDP) and reproductive phase (RP). The specific expression of many genes in the three development phases was also identified. 32 genes among three sub-libraries with high differential expression were selected as candidates connected with flower development. Conclusion RNA-seq and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral development at three development phases of C. sinense. This data could be used as an important resource for investigating the genetics of the flowering pathway and various biological mechanisms in this orchid. PMID:23617896

Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development.

PubMed

Zhang, Jianxia; Wu, Kunlin; Zeng, Songjun; Teixeira da Silva, Jaime A; Zhao, Xiaolan; Tian, Chang-En; Xia, Haoqiang; Duan, Jun

2013-04-24

Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countries. The control of flowering time is a major bottleneck in the industrialized development of C. sinense. Little is known about the mechanisms responsible for floral development in this orchid. Moreover, genome references for entire transcriptome sequences do not currently exist for C. sinense. Thus, transcriptome and expression profiling data for this species are needed as an important resource to identify genes and to better understand the biological mechanisms of floral development in C. sinense. In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptome analysis assembles gene-related information related to vegetative and reproductive growth of C. sinense. Illumina sequencing generated 54,248,006 high quality reads that were assembled into 83,580 unigenes with an average sequence length of 612 base pairs, including 13,315 clusters and 70,265 singletons. A total of 41,687 (49.88%) unique sequences were annotated, 23,092 of which were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Furthermore, 120 flowering-associated unigenes, 73 MADS-box unigenes and 28 CONSTANS-LIKE (COL) unigenes were identified from our collection. In addition, three digital gene expression (DGE) libraries were constructed for the vegetative phase (VP), floral differentiation phase (FDP) and reproductive phase (RP). The specific expression of many genes in the three development phases was also identified. 32 genes among three sub-libraries with high differential expression were selected as candidates connected with flower development. RNA-seq and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral development at three development phases of C. sinense. This data could be used as an important resource for investigating the genetics of the flowering pathway and various biological mechanisms in this orchid.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data

PubMed Central

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie

2018-01-01

Abstract Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. PMID:29106630

Effects of MicroRNA-23a on Differentiation and Gene Expression Profiles in 3T3-L1 Adipocytes

PubMed Central

Huang, Yong; Huang, Jinxiu; Qi, Renli; Wang, Qi; Wu, Yongjiang; Wang, Jing

2016-01-01

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate growth, development, and programmed death of cells. A newly-published study has shown that miRNA-23a could regulate 3T3-L1 adipocyte differentiation. Here, we identified miRNA-23a as a negative regulator of 3T3-L1 adipocyte differentiation again. Over-expression of miRNA-23a inhibited differentiation and decreased lipogenesis as well as down-regulated mRNA and protein expression of both peroxisome proliferator-activated receptor (PPAR) γ and fatty acid binding protein (FABP) 4, whereas knock down of miRNA-23a showed the opposite effects on differentiation as well as increasing the number of apoptotic cells. Additionally, digital gene expression profiling sequencing (DGE-Seq) was used to assay changes in gene expression profiles following alterations in the level of miR-23a. In total, over-expression or knock down of miRNA-23a significantly changed the expression of 313 and 425 genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these genes were mainly involved in the stress response, immune system, metabolism, cell cycle, among other pathways. Additionally, the signal transducer and activator of transcription 1 (Stat1) was shown to be a target of miRNA-23a by computational and dual-luciferase reporter assays that indicated Janus Kinase (Jak)-Stat signal pathway was implicated in regulating adipogenesis mediated by miRNA-23a in adipocytes. PMID:27783036

Role of fuel additives on reduction of NOX emission from a diesel engine powered by camphor oil biofuel.

PubMed

Subramanian, Thiyagarajan; Varuvel, Edwin Geo; Ganapathy, Saravanan; Vedharaj, S; Vallinayagam, R

2018-06-01

The present study intends to explore the effect of the addition of fuel additives with camphor oil (CMO) on the characteristics of a twin-cylinder compression ignition (CI) engine. The lower viscosity and boiling point of CMO when compared to diesel could improve the fuel atomization, evaporation, and air/fuel mixing process. However, the lower cetane index of CMO limits its use as a drop in fuel for diesel in CI engine. In general, NO X emission increases for less viscous and low cetane (LVLC) fuels due to pronounced premixed combustion phase. To improve the ignition characteristics and decrease NO X emissions, fuel additives such as diglyme (DGE)-a cetane enhancer, cumene (CU)-an antioxidant, and eugenol (EU) and acetone (A)-bio-additives, are added 10% by volume with CMO. The engine used for the experimentation is a twin-cylinder tractor engine that runs at a constant speed of 1500 rpm. The engine was operated with diesel initially to attain warm-up condition, which facilitates the operation of neat CMO. At full load condition, brake thermal efficiency (BTE) for CMO is higher (29.6%) than that of diesel (28.1%), while NO X emission is increased by 9.4%. With DGE10 (10% DGE + 90% CMO), the ignition characteristics of CMO are improved and BTE is increased to 31.7% at full load condition. With EU10 (10% EU + 90% CMO) and A10 (10% A + 90% CMO), NO X emission is decreased by 24.6 and 17.8% when compared to diesel, while BTE is comparable to diesel. While HC and CO emission decreased for DGE10 and CU10, they increased for EU10 and A10 when compared to baseline diesel and CMO.

Superiority of stapled side-to-side gastrojejunostomy over conventional hand-sewn end-to-side gastrojejunostomy for reducing the risk of primary delayed gastric emptying after subtotal stomach-preserving pancreaticoduodenectomy.

PubMed

Murata, Yasuhiro; Tanemura, Akihiro; Kato, Hiroyuki; Kuriyama, Naohisa; Azumi, Yoshinori; Kishiwada, Masashi; Mizuno, Shugo; Usui, Masanobu; Sakurai, Hiroyuki; Isaji, Shuji

2017-08-01

Delayed gastric emptying (DGE) is the most common complication following pancreaticoduodenectomy (PD). The clinical efficacy of stapled side-to-side anastomosis using a laparoscopic stapling device during alimentary reconstruction in PD is not well understood and its superiority over conventional hand-sewn end-to-side anastomosis remains controversial. The objective of this study was to evaluate the effectiveness of the stapled side-to-side anastomosis in preventing the development of DGE after PD. The subjects of this retrospective study were 137 patients who underwent pancreaticoduodenectomy, as subtotal stomach-preserving pancreaticoduodenectomy (SSPPD; n = 130), or conventional whipple procedure (n = 7) with Child reconstruction, between January 2010 and May 2014. The patients were divided into two groups according to whether they had had a stapled side-to-side anastomosis (SA group; n = 57) or a conventional hand-sewn end-to-side anastomosis (HA group; n = 80). SA reduced the operative time (SA vs. HA: 508 vs. 557 min, p = 0.028) and the incidence of delayed gastric emptying (SA vs. HA: 21.1 vs. 46.3%, p = 0.003) and was associated with shorter hospitalization (SA vs. HA: 33 vs. 39.5 days, p = 0.007). In this cohort, SA was the only significant factor contributing to a reduction in the incidence of DGE (p = 0.002). Stapled side-to-side gastrojejunostomy reduced the operative time and the incidence of DGE following PD with Child reconstruction, thereby also reducing the length of hospitalization.

High-level ab initio calculations on HGeCl and the equilibrium geometry of the A1A'' state derived from Franck-Condon analysis of the single-vibronic-level emission spectra of HGeCl and DGeCl.

PubMed

Mok, Daniel K W; Chau, Foo-Tim; Lee, Edmond P F; Dyke, John M

2010-02-01

CCSD(T) and/or CASSCF/MRCI calculations have been carried out on the X(1)A' and A(1)A'' states of HGeCl. The fully relativistic effective core potential, ECP10MDF, and associated standard valence basis sets of up to the aug-cc-pV5Z quality were employed for Ge. Contributions from core correlation and extrapolation to the complete basis set limit were included in determining the computed equilibrium geometrical parameters and relative electronic energy of these two states of HGeCl. Based on the currently, most systematic CCSD(T) calculations performed in this study, the best theoretical geometrical parameters of the X(1)A' state are r(e)(HGe) = 1.580 +/- 0.001 A, theta(e) = 93.88 +/- 0.01 degrees and r(e)(GeCl) = 2.170 +/- 0.001 A. In addition, Franck-Condon factors including allowance for anharmonicity and Duschinsky rotation between these two states of HGeCl and DGeCl were calculated employing CCSD(T) and CASSCF/MRCI potential energy functions, and were used to simulate A(1)A'' --> X(1)A' SVL emission spectra of HGeCl and DGeCl. The iterative Franck-Condon analysis (IFCA) procedure was carried out to determine the equilibrium geometrical parameters of the A(1)A'' state of HGeCl by matching the simulated, and available experimental SVL emission spectra of HGeCl and DGeCl of Tackett et al., J Chem Phys 2006, 124, 124320, using the available, estimated experimental equilibrium (r(e)(z)) structure for the X(1)A' state, while varying the equilibrium geometrical parameters of the A(1)A'' state systematically. Employing the derived IFCA geometry of r(e)(HGe) = 1.590 A, r(e)(GeCl) = 2.155 A and theta(e)(HGeCl) = 112.7 degrees for the A(1)A'' state of HGeCl in the spectral simulation, the simulated absorption and SVL emission spectra of HGeCl and DGeCl agree very well with the available experimental LIF and SVL emission spectra, respectively. Copyright 2009 Wiley Periodicals, Inc.

Identification of immunity-related genes in Plutella xylostella in response to fungal peptide destruxin A: RNA-Seq and DGE analysis.

PubMed

Shakeel, Muhammad; Xu, Xiaoxia; Xu, Jin; Zhu, Xun; Li, Shuzhong; Zhou, Xianqiang; Yu, Jialin; Xu, Xiaojing; Hu, Qiongbo; Yu, Xiaoqiang; Jin, Fengliang

2017-09-08

Plutella xylostella has become the major lepidopteran pest of Brassica owing to its strong ability of resistance development to a wide range of insecticides. Destruxin A, a mycotoxin of entomopathogenic fungus, Metarhizium anisopliae, has broad-spectrum insecticidal effects. However, the interaction mechanism of destruxin A with the immune system of P. xylostella at genomic level is still not well understood. Here, we identified 129 immunity-related genes, including pattern recognition receptors, signal modulators, few members of main immune pathways (Toll, Imd, and JAK/STAT), and immune effectors in P. xylostella in response to destruxin A at three different time courses (2 h, 4 h, and 6 h). It is worthy to mention that the immunity-related differentially expressed genes (DEGs) analysis exhibited 30, 78, and 72 up-regulated and 17, 13, and 6 down-regulated genes in P. xylostella after destruxin A injection at 2 h, 4 h, and 6 h, respectively, compared to control. Interestingly, our results revealed that the expression of antimicrobial peptides that play a vital role in insect immune system was up-regulated after the injection of destruxin A. Our findings provide a detailed information on immunity-related DEGs and reveal the potential of P. xylostella to limit the infection of fungal peptide destruxin A by increasing the activity of antimicrobial peptides.

High-temperature Y267 epdm elastomer - field and laboratory experiences, August 1981

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

Hirasuna, A.R.; Friese, G.J.; Stephens, G.A.

1982-01-01

During the period 1976 to 1979 L'Garde, Inc. developed geothermal elastomer compounds under a U.S. Department of Energy - Division of Geothermal Energy (DOE-DGE) contract. The resulting developments yielded compounds from 4 polymer systems which successfully exceeded the contract requirements. Since completion of the compound development, significant laboratory and down-hole experience occurred, primarily on the Y267 EPDM compound. This work summarizes those experiences. 11 references.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.

PubMed

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie; Zhang, Gong

2018-01-04

Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of bacterial populations in the environment using two-dimensional gel electrophoresis of genomic DNA and complementary DNA.

PubMed

Liu, Guo-Hua; Nakamura, Tatsuo; Amemiya, Takashi; Rajendran, Narasimmalu; Itoh, Kiminori

2011-01-01

Two-dimensional gel electrophoresis (2-DGE) mapping of genomic DNA and complementary DNA (cDNA) amplicons was attempted to analyze total and active bacterial populations within soil and activated sludge samples. Distinct differences in the number and species of bacterial populations and those that were metabolically active at the time of sampling were visually observed especially for the soil community. Statistical analyses and sequencing based on the 2-DGE data further revealed the relationships between total and active bacterial populations within each community. This high-resolution technique would be useful for obtaining a better understanding of bacterial population structures in the environment.

Profiling of alpha-dicarbonyl content of commercial honeys from different botanical origins: identification of 3,4-dideoxyglucoson-3-ene (3,4-DGE) and related compounds.

PubMed

Marceau, Eric; Yaylayan, Varoujan A

2009-11-25

The alpha-dicarbonyl contents of commercial honey samples from different botanical origins were analyzed as their quinoxaline derivatives using HPLC-DAD, HPLC-MS, HPLC-MS/MS, and HPLC-TOF-MS. A total of nine such compounds were detected, of which five were previously reported in honey (glucosone, 3-deoxyglucosone, glyoxal, methylglyoxal, and 2,3-butanedione) and three were reported only from sources other than honey [3-deoxypentulose, 1,4-dideoxyhexulose, and 3,4-dideoxyglucoson-3-ene (3,4-DGE)]. An unknown alpha-dicarbonyl compound was also tentatively identified as an oxidation product of 3,4-DGE and was termed 3,4-dideoxyglucosone-3,5-diene (3,4-DGD). Only glyoxal (0.3-1.3 mg/kg), methylglyoxal (0.8-33 mg/kg), and 2,3-butanedione (0-4.3 mg/kg) were quantified in all honey samples. Furthermore, analysis of the alpha-dicarbonyl profile of various honey samples indicated that certain alpha-dicarbonyl compounds are found in specific honey samples in much higher proportions relative to the average amounts. The free radical scavenging activity as measured by DPPH method has also indicated that the darker honey samples such as buckwheat, manuka, blueberry, and eucalyptus had higher antioxidant properties compared to lighter-colored samples.

Effect of Billroth II or Roux-en-Y Reconstruction for the Gastrojejunostomy After Pancreaticoduodenectomy: Meta-analysis of Randomized Controlled Trials.

PubMed

Yang, Ji; Wang, Chao; Huang, Qiang

2015-05-01

This study aimed to compare Billroth II with Roux-en-Y reconstruction after pancreaticoduodenectomy (PD). A literature search was carried out to identify all randomized controlled trials (RCTs) comparing postoperative complications of Billroth II versus Roux-en-Y reconstruction following PD published from 1 January 1990 to 31 August 2014. Pooled risk ratios (RRs) with 95 % confidence intervals (CIs) were calculated using fixed effects or random effects models In total, three RCTs with 470 patients were included. Using International Study Group of Pancreatic Surgery (ISGPS) definitions, incidences of delayed gastric emptying (DGE) [grades B and C (3.9 versus 12.9 %; RR 0.30, 95 % CI 0.11-0.79; P = 0.01), DGE grade C (0.7 versus 9.6 %; RR 0.11, 95 % CI 0.02-0.61; P = 0.01)] were significantly lower in the Billroth II group than in the Roux-en-Y group, as was the length of hospital stay (weighted mean difference -4.72, 95 % CI -8.91, -0.53; P = 0.03). Meta-analysis revealed that the incidence of DGE (grades B and C) after PD can be decreased by using Billroth II rather than Roux-en-Y reconstruction.

A hierarchy of factors influence discontinuous gas exchange in the grasshopper Paracinema tricolor (Orthoptera: Acrididae).

PubMed

Groenewald, Berlizé; Chown, Steven L; Terblanche, John S

2014-10-01

The evolutionary origin and maintenance of discontinuous gas exchange (DGE) in tracheate arthropods are poorly understood and highly controversial. We investigated prioritization of abiotic factors in the gas exchange control cascade by examining oxygen, water and haemolymph pH regulation in the grasshopper Paracinema tricolor. Using a full-factorial design, grasshoppers were acclimated to hypoxic or hyperoxic (5% O2, 40% O2) gas conditions, or dehydrated or hydrated, whereafter their CO2 release was measured under a range of O2 and relative humidity (RH) conditions (5%, 21%, 40% O2 and 5%, 60%, 90% RH). DGE was significantly less common in grasshoppers acclimated to dehydrating conditions compared with the other acclimations (hypoxia, 98%; hyperoxia, 100%; hydrated, 100%; dehydrated, 67%). Acclimation to dehydrating conditions resulted in a significant decrease in haemolymph pH from 7.0±0.3 to 6.6±0.1 (mean ± s.d., P=0.018) and also significantly increased the open (O)-phase duration under 5% O2 treatment conditions (5% O2, 44.1±29.3 min; 40% O2, 15.8±8.0 min; 5% RH, 17.8±1.3 min; 60% RH, 24.0±9.7 min; 90% RH, 20.6±8.9 min). The observed acidosis could potentially explain the extension of the O-phase under low RH conditions, when it would perhaps seem more useful to reduce the O-phase to lower respiratory water loss. The results confirm that DGE occurrence and modulation are affected by multiple abiotic factors. A hierarchical framework for abiotic factors influencing DGE is proposed in which the following stressors are prioritized in decreasing order of importance: oxygen supply, CO2 excretion and pH modulation, oxidative damage protection and water savings. © 2014. Published by The Company of Biologists Ltd.

The Entomopathogenic Fungi Isaria fumosorosea Plays a Vital Role in Suppressing the Immune System of Plutella xylostella: RNA-Seq and DGE Analysis of Immunity-Related Genes.

PubMed

Xu, Jin; Xu, Xiaoxia; Shakeel, Muhammad; Li, Shuzhong; Wang, Shuang; Zhou, Xianqiang; Yu, Jialin; Xu, Xiaojing; Yu, Xiaoqiang; Jin, Fengliang

2017-01-01

Most, if not all, entomopathogenic fungi have been used as alternative control agents to decrease the insect resistance and harmful effects of the insecticides on the environment. Among them, Isaria fumosorosea has also shown great potential to control different insect pests. In the present study, we explored the immune response of P. xylostella to the infection of I. fumosorosea at different time points by using RNA-Sequencing and differential gene expression technology at the genomic level. To gain insight into the host-pathogen interaction at the genomic level, five libraries of P. xylostella larvae at 12, 18, 24, and 36 h post-infection and a control were constructed. In total, 161 immunity-related genes were identified and grouped into four categories; immune recognition families, toll and Imd pathway, melanization, and antimicrobial peptides (AMPs). The results of differentially expressed immunity-related genes depicted that 15, 13, 53, and 14 up-regulated and 38, 51, 56, and 49 were down-regulated in P. xylostella at 12, 18, 24, and 36 h post-treatment, respectively. RNA-Seq results of immunity-related genes revealed that the expression of AMPs was reduced after treatment with I. fumosorosea . To validate RNA-Seq results by RT-qPCR, 22 immunity-related genes were randomly selected. In conclusion, our results demonstrate that I. fumosorosea has the potential to suppress the immune response of P. xylostella and can become a potential biopesticide for controlling P. xylostella .

Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome.

PubMed

Molina, Laurence; Salvetat, Nicolas; Ameur, Randa Ben; Peres, Sabine; Sommerer, Nicolas; Jarraya, Fayçal; Ayadi, Hammadi; Molina, Franck; Granier, Claude

2011-12-10

The characterization of the normal urinary proteome is steadily progressing and represents a major interest in the assessment of clinical urinary biomarkers. To estimate quantitatively the variability of the normal urinary proteome, urines of 20 healthy people were collected. We first evaluated the impact of the sample conservation temperature on urine proteome integrity. Keeping the urine sample at RT or at +4°C until storage at -80°C seems the best way for long-term storage of samples for 2D-GE analysis. The quantitative variability of the normal urinary proteome was estimated on the 20 urines mapped by 2D-GE. The occurrence of the 910 identified spots was analysed throughout the gels and represented in a virtual 2D gel. Sixteen percent of the spots were found to occur in all samples and 23% occurred in at least 90% of urines. About 13% of the protein spots were present only in 10% or less of the samples, thus representing the most variable part of the normal urinary proteome. Twenty proteins corresponding to a fraction of the fully conserved spots were identified by mass spectrometry. In conclusion, a "public" urinary proteome, common to healthy individuals, seems to coexist with a "private" urinary proteome, which is more specific to each individual. Copyright © 2011 Elsevier B.V. All rights reserved.

Azadirachtin Affects the Growth of Spodoptera litura Fabricius by Inducing Apoptosis in Larval Midgut.

PubMed

Shu, Benshui; Zhang, Jingjing; Cui, Gaofeng; Sun, Ranran; Yi, Xin; Zhong, Guohua

2018-01-01

Azadirachtin, the environmentally friendly botanical pesticide, has been used as an antifeedant and pest growth regulator in integrated pest management for decades. It has shown strong biological activity against Spodoptera litura , but the mechanism of toxicity remains unclear. The present study showed that azadirachtin inhibited the growth of S. litura larvae, which was resulted by structure destroy and size inhibition of the midgut. Digital gene expression (DGE) analysis of midgut suggested that azadirachtin regulated the transcriptional level of multiple unigenes involved in mitogen-activated protein kinase (MAPK) and calcium apoptotic signaling pathways. Simultaneously, the expression patterns of some differentially expressed unigenes were verified by quantitative real time-PCR (qRT-PCR). In addition, the enhanced terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling (TUNEL) staining, the increased expression of caspase family members and apoptosis-binding motif 1 (IBM1) on both gene and protein level and the release of cytochrome c from mitochondria to cytoplasm were induced in midgut after azadirachtin treatment. These results demonstrated that azadirachtin induced structural alteration in S. litura larval midgut by apoptosis activation. These alterations may affect the digestion and absorption of nutrients and eventually lead to the growth inhibition of larvae.

Azadirachtin Affects the Growth of Spodoptera litura Fabricius by Inducing Apoptosis in Larval Midgut

PubMed Central

Shu, Benshui; Zhang, Jingjing; Cui, Gaofeng; Sun, Ranran; Yi, Xin; Zhong, Guohua

2018-01-01

Azadirachtin, the environmentally friendly botanical pesticide, has been used as an antifeedant and pest growth regulator in integrated pest management for decades. It has shown strong biological activity against Spodoptera litura, but the mechanism of toxicity remains unclear. The present study showed that azadirachtin inhibited the growth of S. litura larvae, which was resulted by structure destroy and size inhibition of the midgut. Digital gene expression (DGE) analysis of midgut suggested that azadirachtin regulated the transcriptional level of multiple unigenes involved in mitogen-activated protein kinase (MAPK) and calcium apoptotic signaling pathways. Simultaneously, the expression patterns of some differentially expressed unigenes were verified by quantitative real time-PCR (qRT-PCR). In addition, the enhanced terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling (TUNEL) staining, the increased expression of caspase family members and apoptosis-binding motif 1 (IBM1) on both gene and protein level and the release of cytochrome c from mitochondria to cytoplasm were induced in midgut after azadirachtin treatment. These results demonstrated that azadirachtin induced structural alteration in S. litura larval midgut by apoptosis activation. These alterations may affect the digestion and absorption of nutrients and eventually lead to the growth inhibition of larvae. PMID:29535638

Identification of differentially expressed genes related to aphid resistance in cucumber (Cucumis sativus L.)

PubMed Central

Liang, Danna; Liu, Min; Hu, Qijing; He, Min; Qi, Xiaohua; Xu, Qiang; Zhou, Fucai; Chen, Xuehao

2015-01-01

Cucumber, a very important vegetable crop worldwide, is easily damaged by pests. Aphids (Aphis gossypii Glover) are among the most serious pests in cucumber production and often cause severe loss of yield and make fruit quality get worse. Identifying genes that render cucumbers resistant to aphid-induced damage and breeding aphid-resistant cucumber varieties have become the most promising control strategies. In this study, a Illumina Genome Analyzer platform was applied to monitor changes in gene expression in the whole genome of the cucumber cultivar ‘EP6392’ which is resistant to aphids. Nine DGE libraries were constructed from infected and uninfected leaves. In total, 49 differentially expressed genes related to cucumber aphid resistance were screened during the treatment period. These genes are mainly associated with signal transduction, plant-pathogen interactions, flavonoid biosynthesis, amino acid metabolism and sugar metabolism pathways. Eight of the 49 genes may be associated with aphid resistance. Finally, expression of 9 randomly selected genes was evaluated by qRT-PCR to verify the results for the tag-mapped genes. With the exception of 1-aminocyclopropane-1-carboxylate oxidase homolog 6, the expression of the chosen genes was in agreement with the results of the tag-sequencing analysis patterns. PMID:25959296

Transcriptomic response to low salinity stress in gills of the Pacific white shrimp, Litopenaeus vannamei.

PubMed

Hu, Dongxu; Pan, Luqing; Zhao, Qun; Ren, Qin

2015-12-01

The Pacific white shrimp, Litopenaeus vannamei (L. vannamei), is one of the most farmed species. Salinity is an important environmental factor that affects its growth and distribution. However, the molecular mechanism of the shrimp in response to salinity stress remains largely unclear. High-throughput sequencing is a helpful tool to analyze the molecular response to salinity challenge in shrimp. In the present study, the transcriptomic responses of the gills in L. vannamei under low salinity stress were detected by Illumina's digital gene expression system. A total of 10,725,789 and 10,827,411 reads were generated from the non-changed and low salinity changed groups, respectively. 64,590 Unigenes with an average length of 764 bp were generated. Compared with the control, 585 genes were differentially expressed under low salinity. GO functional analysis and KEGG pathway analysis indicated some vital genes in response to the challenge. Ten genes related to osmoregulation and ambient salinity adaption were selected to validate the DGE results by RT-qPCR. This work provides valuable information to study the mechanism of salinity adaption in L. vannamei. Genes and pathways from the results will be beneficial to reveal the molecular basis of osmoregulation. It also gives an insight into the response to the salinity challenge in L. vannamei. Copyright © 2015 Elsevier B.V. All rights reserved.

Numerical time evolution of ETH spin chains by means of matrix product density operators

NASA Astrophysics Data System (ADS)

White, Christopher; Zaletel, Michael; Mong, Roger; Refael, Gil

We introduce a method for approximating density operators of 1D systems that, when combined with a standard framework for time evolution (TEBD), makes possible simulation of the dynamics of strongly thermalizing systems to arbitrary times. We demonstrate that the method works on both near-equilibrium initial states (Gibbs states with spatially varying temperatures) and far-from-equilibrium initial states, including quenches across phase transitions and pure states. This work was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE \\x901144469 and by the Caltech IQIM, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore.

An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.

PubMed

Tang, Qi; Ma, Xiaojun; Mo, Changming; Wilson, Iain W; Song, Cai; Zhao, Huan; Yang, Yanfang; Fu, Wei; Qiu, Deyou

2011-07-05

Siraitia grosvenorii (Luohanguo) is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chinese medicine. The major bioactive constituents in the fruit extract are the cucurbitane-type triterpene saponins known as mogrosides. Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in S. grosvenorii, especially the late steps of the pathway. In this study, a cDNA library generated from of equal amount of RNA taken from S. grosvenorii fruit at 50 days after flowering (DAF) and 70 DAF were sequenced using Illumina/Solexa platform. More than 48,755,516 high-quality reads from a cDNA library were generated that was assembled into 43,891 unigenes. De novo assembly and gap-filling generated 43,891 unigenes with an average sequence length of 668 base pairs. A total of 26,308 (59.9%) unique sequences were annotated and 11,476 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. cDNA sequences for all of the known enzymes involved in mogrosides backbone synthesis were identified from our library. Additionally, a total of eighty-five cytochrome P450 (CYP450) and ninety UDP-glucosyltransferase (UDPG) unigenes were identified, some of which appear to encode enzymes responsible for the conversion of the mogroside backbone into the various mogrosides. Digital gene expression profile (DGE) analysis using Solexa sequencing was performed on three important stages of fruit development, and based on their expression pattern, seven CYP450s and five UDPGs were selected as the candidates most likely to be involved in mogrosides biosynthesis. A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying candidate genes encoding enzymes responsible for the biosynthesis of novel secondary metabolites in a non-model plant. Seven CYP450s and five UDPGs were selected as potential candidates involved in mogrosides biosynthesis. The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the fruit extract from S. grosvenorii.

Influence of Diet on the Proteome of Drosophila Melanogaster as Assessed by Two-Dimensional Gel Electrophoresis and Capillary Liquid Chromatography–Mass Spectrometry: The Hamburger Effect Revisited

PubMed Central

Culwell, Thomas F.; Thulin, Craig D.; Merrell, Karen J.; Graves, Steven W.

2008-01-01

Proteomic biomarker discovery has been called into question. Diamandis hypothesized that seemingly trivial factors, such as eating a hamburger, may cause sufficient proteomic change as to confound proteomic differences. This has been termed the hamburger effect. Little is known about the variability of complex proteomes in response to the environment. Two methods—two-dimensional gel electrophoresis (2DGE) and capillary liquid chromatography–electrospray ionization time-of-flight mass spectrometry (LCMS)—were used to study the hamburger effect in two cross-sections of the soluble fruit fly proteome. 2DGE measured abundant proteins, whereas LCMS measured small proteins and peptides. Proteomic differences between males and females were first evaluated to assess the discriminatory capability of the methods. Likewise, wild-type and white-eyed flies were analyzed as a further demonstration that genetically based proteomic differences could be observed above the background analytical variation. Then dietary interventions were imposed. Ethanol was added to the diet of some populations without significant proteomic effect. However, after a 24-h fast, proteomic differences were found using LCMS but not 2DGE. Even so, only three of ~1000 molecular species were altered significantly, suggesting that the influence of even an extreme diet change produced only modest proteomic variability, and that much of the fruit fly proteome remains relatively constant in response to diet. These experiments suggest that proteomics can be a viable approach to biomarker discovery. PMID:19137114

Occurrence of (Z)-3,4-Dideoxyglucoson-3-ene in Different Types of Beer and Malt Beer as a Result of 3-Deoxyhexosone Interconversion.

PubMed

Hellwig, Michael; Nobis, Arndt; Witte, Sophia; Henle, Thomas

2016-04-06

In beer, 3-deoxyglucosone (3-DG) and 3-deoxygalactosone (3-DGal) are important sugar degradation products, but little is known about the relevance of the interconversion reaction between these compounds in different types of beer. In the present study, 3-DG was quantitated at concentrations of 12.9-52.7 mg/L and 3-DGal at concentrations of 6.0-26.4 mg/L in different types of beer (pilsner, wheat, bock, dark, and alcohol-free beers). The concentrations in malt beer tended to be higher. Largely overlapping concentration ranges precluded a classification of beers by their 3-deoxyglycosone contents. 3,4-Dideoxyglucoson-3-ene (3,4-DGE) was identified as an important intermediate and quantitated in beer and malt beer for the first time. The E and Z isomers of the corresponding quinoxaline were synthesized by a new synthetic approach and isolated by semipreparative HPLC. An assay was developed for quantitation of (E)- and (Z)-3,4-DGE by HPLC-MS/MS, and the Z isomer was determined at concentrations of 0.3-1.7 mg/L in beer and 0.5-4.8 mg/L in malt beer samples. The E isomer was shown to be of little importance. Concentrations of 5-hydroxymethylfurfural (HMF) were twice as high as those of (Z)-3,4-DGE in beer samples (0.4-3.7 mg/L) but much higher in malt beer samples (1.6-336 mg/L).

Proteomic analysis reveals the enhancement of human serum apolipoprotein A-1(APO A-1) in individuals infected with multiple dengue virus serotypes.

PubMed

Manchala, Nageswar Reddy; Dungdung, Ranjeet; Pilankatta, Rajendra

2017-10-01

Human serum protein profiling of the individual infected with multiple dengue virus serotypes for identifying the potential biomarkers and to investigate the cause for the severity of dengue virus infection. Dengue virus NS1-positive serum samples were pooled into two groups (S2 and S3) based on the molecular serotyping and number of heterotypic infections. The pooled serum samples were subjected to two-dimensional gel electrophoresis (2DGE) to identify the differentially expressed proteins. The peptide masses of upregulated protein were detected by matrix-assisted laser desorption-ionisation time-of-flight MALDI-TOF mass spectrometry and analysed by MASCOT search engine. The results were compared with the control group (S1). The commonly upregulated protein was validated by quantitative ELISA and compared with control as well as single serotypic infected samples. Based on 2DGE, total thirteen proteins were differentially upregulated in S2 and S3 groups as compared to control. Some of the upregulated proteins were involved in mediating the complement activation of immune response. The apolipoprotein A-1 (APO A-1) was upregulated in S2 and S3 groups. Upon validation, APO A-1 levels were increased in line with the number of heterotypic infection of dengue viruses. Heterotypic infection of dengue viruses upregulate the serum proteins involved in the complement pathway in the early phase of infection. There was a significant increase in the level of APO A-1 in three different serotypic infections of dengue virus as compared to control. Further, the role of APO-A1 can be explored in elucidating the mechanism of dengue pathogenesis. © 2017 John Wiley & Sons Ltd.

Integrated transcriptomic and proteomic analysis of the bile stress response in probiotic Lactobacillus salivarius LI01.

PubMed

Lv, Long-Xian; Yan, Ren; Shi, Hai-Yan; Shi, Ding; Fang, Dai-Qiong; Jiang, Hui-Yong; Wu, Wen-Rui; Guo, Fei-Fei; Jiang, Xia-Wei; Gu, Si-Lan; Chen, Yun-Bo; Yao, Jian; Li, Lan-Juan

2017-01-06

Lactobacillus salivarius LI01, isolated from healthy humans, has demonstrated probiotic properties in the prevention and treatment of liver failure. Tolerance to bile stress is crucial to allow lactobacilli to survive in the gastrointestinal tract and exert their benefits. In this work, we used a Digital Gene Expression transcriptomic and iTRAQ LC-MS/MS proteomic approach to examine the characteristics of LI01 in response to bile stress. Using culture medium with or without 0.15% ox bile, 591 differentially transcribed genes and 347 differentially expressed proteins were detected in LI01. Overall, we found the bile resistance of LI01 to be based on a highly remodeled cell envelope and a reinforced bile efflux system rather than on the activity of bile salt hydrolases. Additionally, some differentially expressed genes related to regulatory systems, the general stress response and central metabolism processes, also play roles in stress sensing, bile-induced damage prevention and energy efficiency. Moreover, bile salts appear to enhance proteolysis and amino acid uptake (especially aromatic amino acids) by LI01, which may support the liver protection properties of this strain. Altogether, this study establishes a model of global response mechanism to bile stress in L. salivarius LI01. L. salivarius strain LI01 exhibits not only antibacterial and antifungal properties but also exerts a good health-promoting effect in acute liver failure. As a potential probiotic strain, the bile-tolerance trait of strain LI01 is important, though this has not yet been explored. In this study, an analysis based on DGE and iTRAQ was performed to investigate the gene expression in strain LI01 under bile stress at the mRNA and protein levels, respectively. To our knowledge, this work also represents the first combined transcriptomic and proteomic analysis of the bile stress response mechanism in L. salivarius. Copyright © 2016. Published by Elsevier B.V.

Analysis of differentially expressed genes between fluoride-sensitive and fluoride-endurable individuals in midgut of silkworm, Bombyx mori.

PubMed

Qian, Heying; Li, Gang; He, Qingling; Zhang, Huaguang; Xu, Anying

2016-08-15

Fluoride tolerance is an economically important trait of silkworm. Near-isogenic lines (NILs) of the dominant endurance to fluoride (Def) gene in Bombyx mori has been constructed before. Here, we analyzed the gene expression profiles of midgut of fluoride-sensitive and fluoride-endurable individuals of Def NILs by using high-throughput Illumina sequencing technology and bioinformatics tools, and identified differentially expressed genes between these individuals. A total of 3,612,399 and 3,567,631 clean tags for the libraries of fluoride-endurable and fluoride-sensitive individuals were obtained, which corresponded to 32,933 and 43,976 distinct clean tags, respectively. Analysis of differentially expressed genes indicates that 241 genes are differentially expressed between the two libraries. Among the 241 genes, 30 are up-regulated and 211 are down-regulated in fluoride-endurable individuals. Pathway enrichment analysis demonstrates that genes related to ribosomes, pancreatic secretion, steroid biosynthesis, glutathione metabolism, steroid biosynthesis, and glycerolipid metabolism are down-regulated in fluoride-endurable individuals. qRT-PCR was conducted to confirm the results of the DGE. The present study analyzed differential expression of related genes and tried to find out whether the crucial genes were related to fluoride detoxification which might elucidate fluoride effect and provide a new way in the fluorosis research. Copyright © 2016 Elsevier B.V. All rights reserved.

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per gasoline gallon equivalent (GGE). The liquefied natural gas (LNG) tax rate is $0.243 per diesel gallon equivalent (DGE). For taxation purposes, one GGE is equal to 5.75 pounds (lbs.) of propane and

Alternative Fuels Data Center

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the state, unless equivalent measures are established by the National Conference on Weights and Measures. According to current state law, one GGE is equal to 5.66 pounds (lbs.) of CNG. One DGE is equal

Digital gene expression analysis of corky split vein caused by boron deficiency in 'Newhall' Navel Orange (Citrus sinensis Osbeck) for selecting differentially expressed genes related to vascular hypertrophy.

PubMed

Yang, Cheng-Quan; Liu, Yong-Zhong; An, Ji-Cui; Li, Shuang; Jin, Long-Fei; Zhou, Gao-Feng; Wei, Qing-Jiang; Yan, Hui-Qing; Wang, Nan-Nan; Fu, Li-Na; Liu, Xiao; Hu, Xiao-Mei; Yan, Ting-Shuai; Peng, Shu-Ang

2013-01-01

Corky split vein caused by boron (B) deficiency in 'Newhall' Navel Orange was studied in the present research. The boron-deficient citrus exhibited a symptom of corky split vein in mature leaves. Morphologic and anatomical surveys at four representative phases of corky split veins showed that the symptom was the result of vascular hypertrophy. Digital gene expression (DGE) analysis was performed based on the Illumina HiSeq™ 2000 platform, which was applied to analyze the gene expression profilings of corky split veins at four morphologic phases. Over 5.3 million clean reads per library were successfully mapped to the reference database and more than 22897 mapped genes per library were simultaneously obtained. Analysis of the differentially expressed genes (DEGs) revealed that the expressions of genes associated with cytokinin signal transduction, cell division, vascular development, lignin biosynthesis and photosynthesis in corky split veins were all affected. The expressions of WOL and ARR12 involved in the cytokinin signal transduction pathway were up-regulated at 1(st) phase of corky split vein development. Furthermore, the expressions of some cell cycle genes, CYCs and CDKB, and vascular development genes, WOX4 and VND7, were up-regulated at the following 2(nd) and 3(rd) phases. These findings indicated that the cytokinin signal transduction pathway may play a role in initiating symptom observed in our study.

Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments

PubMed Central

Wang, Yuling; Zhang, Xinfu; Wang, Ran; Bai, Yingxin; Liu, Chenglian; Yuan, Yongbing; Yang, Yingjie; Yang, Shaolan

2017-01-01

Preharvest bagging is a simple, grower-friendly and safe physical protection technique commonly applied to many fruits, and the application of different fruit bags can have various effects. To explore the molecular mechanisms underlying the fruit quality effects of different bagging treatments, digital gene expression (DGE) profiling of bagged and unbagged ‘Chili’ (Pyrus bretschneideri Rehd.) pear pericarp during development was performed. Relative to unbagged fruit, a total of 3022 and 769 differentially expressed genes (DEGs) were detected in the polyethylene (PE)-bagged and non-woven fabric-bagged fruit, respectively. DEGs annotated as photosynthesis-antenna proteins and photosynthesis metabolism pathway were upregulated in non-woven fabric-bagged fruit but downregulated in the PE-bagged fruit. Non-woven fabric bagging inhibited lignin synthesis in ‘Chili’ pear pericarp by downregulating DEGs involved in phenylpropanoid biosynthesis; consequently, the fruit lenticels in non-woven fabric-bagged fruit were smaller than those in the other treatments. The results indicate that the non-woven fabric bagging method has a positive effect on the appearance of ‘Chili’ pear fruit but neither of the two bagging treatments is conducive to the accumulation of soluble sugar. PMID:28280542

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vehicle at 3,000 pounds (lbs.) per square inch and metered on a gasoline gallon equivalent (GGE ); liquefied natural gas (LNG) must be metered on a diesel gallon equivalent (DGE). One GGE of CNG is equal to

Involvement of Auxin and Brassinosteroid in Dwarfism of Autotetraploid Apple (Malus × domestica).

PubMed

Ma, Yue; Xue, Hao; Zhang, Lei; Zhang, Feng; Ou, Chunqing; Wang, Feng; Zhang, Zhihong

2016-05-24

The plant height is an important trait in fruit tree. However, the molecular mechanism on dwarfism is still poorly understood. We found that colchicine-induced autotetraploid apple plants (Malus × domestica) exhibited a dwarf phenotype. The vertical length of cortical parenchyma cells was shorter in autotetraploids than in diploids, by observing paraffin sections. Hormone levels of indoleacetic acid (IAA) and brassinosteroid (BR) were significantly decreased in 3- and 5-year-old autotetraploid plants. Digital gene expression (DGE) analysis showed that the differentially expressed genes were mainly involved in IAA and BR pathways. microRNA390 was significantly upregulated according to microarray analysis. Exogenous application of IAA and BR promoted stem elongation of both apple plants grown in medium. The results show that dwarfing in autotetraploid apple plants is most likely regulated by IAA and BR. The dwarf phenotype of autotetraploid apple plants could be due to accumulation of miR390 after genome doubling, leading to upregulation of apple trans-acting short-interfering RNA 3 (MdTAS3) expression, which in turn downregulates the expression of MdARF3. Overall, this leads to partial interruption of the IAA and BR signal transduction pathway. Our study provides important insights into the molecular mechanisms underlying dwarfism in autopolyploid apple plants.

Involvement of Auxin and Brassinosteroid in Dwarfism of Autotetraploid Apple (Malus × domestica)

PubMed Central

Ma, Yue; Xue, Hao; Zhang, Lei; Zhang, Feng; Ou, Chunqing; Wang, Feng; Zhang, Zhihong

2016-01-01

The plant height is an important trait in fruit tree. However, the molecular mechanism on dwarfism is still poorly understood. We found that colchicine-induced autotetraploid apple plants (Malus × domestica) exhibited a dwarf phenotype. The vertical length of cortical parenchyma cells was shorter in autotetraploids than in diploids, by observing paraffin sections. Hormone levels of indoleacetic acid (IAA) and brassinosteroid (BR) were significantly decreased in 3- and 5-year-old autotetraploid plants. Digital gene expression (DGE) analysis showed that the differentially expressed genes were mainly involved in IAA and BR pathways. microRNA390 was significantly upregulated according to microarray analysis. Exogenous application of IAA and BR promoted stem elongation of both apple plants grown in medium. The results show that dwarfing in autotetraploid apple plants is most likely regulated by IAA and BR. The dwarf phenotype of autotetraploid apple plants could be due to accumulation of miR390 after genome doubling, leading to upregulation of apple trans-acting short-interfering RNA 3 (MdTAS3) expression, which in turn downregulates the expression of MdARF3. Overall, this leads to partial interruption of the IAA and BR signal transduction pathway. Our study provides important insights into the molecular mechanisms underlying dwarfism in autopolyploid apple plants. PMID:27216878

Identification of gibberellin acid-responsive proteins in rice leaf sheath using proteomics.

PubMed

Gu, Jia-Yu; Wang, Ye; Zhang, Xu; Zhang, Shi-Hua; Gao, Yin; An, Cheng-Cai

2010-06-01

The phytohormone gibberellin acid (GA) controls many aspects of plant development. In this study, we identified proteins that are differentially expressed between the rice (Oryza sativa L.) GA-deficient cultivar, Aijiaonante, and its parental line, Nante. Proteins were extracted from rice leaf sheath and examined by 2DGE. Among more than 1200 protein spots reproducibly detected on each gel, 29 were found to be highly up-regulated by GAs in Nante, and 6 were down-regulated by GAs in Aijiaonante. These 35 proteins were identified by MALDI-TOF MS and were classified into three groups based on their putative function in metabolism, stress/defense processes and signal transduction. These data suggest that metabolic pathways are the main target of regulation by GAs during rice development. Our results provide new information about the involvement of GAs in rice development.

Communicating Low-Probability High-Consequence Risk, Uncertainty and Expert Confidence: Induced Seismicity of Deep Geothermal Energy and Shale Gas.

PubMed

Knoblauch, Theresa A K; Stauffacher, Michael; Trutnevyte, Evelina

2018-04-01

Subsurface energy activities entail the risk of induced seismicity including low-probability high-consequence (LPHC) events. For designing respective risk communication, the scientific literature lacks empirical evidence of how the public reacts to different written risk communication formats about such LPHC events and to related uncertainty or expert confidence. This study presents findings from an online experiment (N = 590) that empirically tested the public's responses to risk communication about induced seismicity and to different technology frames, namely deep geothermal energy (DGE) and shale gas (between-subject design). Three incrementally different formats of written risk communication were tested: (i) qualitative, (ii) qualitative and quantitative, and (iii) qualitative and quantitative with risk comparison. Respondents found the latter two the easiest to understand, the most exact, and liked them the most. Adding uncertainty and expert confidence statements made the risk communication less clear, less easy to understand and increased concern. Above all, the technology for which risks are communicated and its acceptance mattered strongly: respondents in the shale gas condition found the identical risk communication less trustworthy and more concerning than in the DGE conditions. They also liked the risk communication overall less. For practitioners in DGE or shale gas projects, the study shows that the public would appreciate efforts in describing LPHC risks with numbers and optionally risk comparisons. However, there seems to be a trade-off between aiming for transparency by disclosing uncertainty and limited expert confidence, and thereby decreasing clarity and increasing concern in the view of the public. © 2017 Society for Risk Analysis.

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motor fuel tax of $0.05 per gasoline gallon equivalent (GGE) until January 1, 2020. Beginning January 1 also subject to a state motor fuel tax rate of $0.05 per diesel gallon equivalent (DGE) until January 1

An analysis of indirect genetic effects on adult body weight of the Pacific white shrimp Litopenaeus vannamei at low rearing density.

PubMed

Luan, Sheng; Luo, Kun; Chai, Zhan; Cao, Baoxiang; Meng, Xianhong; Lu, Xia; Liu, Ning; Xu, Shengyu; Kong, Jie

2015-12-14

Our aim was to estimate the genetic parameters for the direct genetic effect (DGE) and indirect genetic effects (IGE) on adult body weight in the Pacific white shrimp. IGE is the heritable effect of an individual on the trait values of its group mates. To examine IGE on body weight, 4725 shrimp from 105 tagged families were tested in multiple small test groups (MSTG). Each family was separated into three groups (15 shrimp per group) that were randomly assigned to 105 concrete tanks with shrimp from two other families. To estimate breeding values, one large test group (OLTG) in a 300 m(2) circular concrete tank was used for the communal rearing of 8398 individuals from 105 families. Body weight was measured after a growth-test period of more than 200 days. Variance components for body weight in the MSTG programs were estimated using an animal model excluding or including IGE whereas variance components in the OLTG programs were estimated using a conventional animal model that included only DGE. The correlation of DGE between MSTG and OLTG programs was estimated by a two-trait animal model that included or excluded IGE. Heritability estimates for body weight from the conventional animal model in MSTG and OLTG programs were 0.26 ± 0.13 and 0.40 ± 0.06, respectively. The log likelihood ratio test revealed significant IGE on body weight. Total heritable variance was the sum of direct genetic variance (43.5%), direct-indirect genetic covariance (2.1%), and indirect genetic variance (54.4%). It represented 73% of the phenotypic variance and was more than two-fold greater than that (32%) obtained by using a classical heritability model for body weight. Correlations of DGE on body weight between MSTG and OLTG programs were intermediate regardless of whether IGE were included or not in the model. Our results suggest that social interactions contributed to a large part of the heritable variation in body weight. Small and non-significant direct-indirect genetic correlations implied that neutral or slightly cooperative heritable interactions, rather than competition, were dominant in this population but this may be due to the low rearing density.

Comparative Proteomic and Nutritional Composition Analysis of Independent Transgenic Pigeon Pea Seeds Harboring cry1AcF and cry2Aa Genes and Their Nontransgenic Counterparts.

PubMed

Mishra, Pragya; Singh, Shweta; Rathinam, Maniraj; Nandiganti, Muralimohan; Ram Kumar, Nikhil; Thangaraj, Arulprakash; Thimmegowda, Vinutha; Krishnan, Veda; Mishra, Vagish; Jain, Neha; Rai, Vandna; Pattanayak, Debasis; Sreevathsa, Rohini

2017-02-22

Safety assessment of genetically modified plants is an important aspect prior to deregulation. Demonstration of substantial equivalence of the transgenics compared to their nontransgenic counterparts can be performed using different techniques at various molecular levels. The present study is a first-ever comprehensive evaluation of pigeon pea transgenics harboring two independent cry genes, cry2Aa and cry1AcF. The absence of unintended effects in the transgenic seed components was demonstrated by proteome and nutritional composition profiling. Analysis revealed that no significant differences were found in the various nutritional compositional analyses performed. Additionally, 2-DGE-based proteome analysis of the transgenic and nontransgenic seed protein revealed that there were no major changes in the protein profile, although a minor fold change in the expression of a few proteins was observed. Furthermore, the study also demonstrated that neither the integration of T-DNA nor the expression of the cry genes resulted in the production of unintended effects in the form of new toxins or allergens.

Application of industrial scale genomics to discovery of therapeutic targets in heart failure.

PubMed

Mehraban, F; Tomlinson, J E

2001-12-01

In recent years intense activity in both academic and industrial sectors has provided a wealth of information on the human genome with an associated impressive increase in the number of novel gene sequences deposited in sequence data repositories and patent applications. This genomic industrial revolution has transformed the way in which drug target discovery is now approached. In this article we discuss how various differential gene expression (DGE) technologies are being utilized for cardiovascular disease (CVD) drug target discovery. Other approaches such as sequencing cDNA from cardiovascular derived tissues and cells coupled with bioinformatic sequence analysis are used with the aim of identifying novel gene sequences that may be exploited towards target discovery. Additional leverage from gene sequence information is obtained through identification of polymorphisms that may confer disease susceptibility and/or affect drug responsiveness. Pharmacogenomic studies are described wherein gene expression-based techniques are used to evaluate drug response and/or efficacy. Industrial-scale genomics supports and addresses not only novel target gene discovery but also the burgeoning issues in pharmaceutical and clinical cardiovascular medicine relative to polymorphic gene responses.

Proteomic analysis of early phase of conidia germination in Aspergillus nidulans.

PubMed

Oh, Young Taek; Ahn, Chun-Seob; Kim, Jeong Geun; Ro, Hyeon-Su; Lee, Chang-Won; Kim, Jae Won

2010-03-01

In order to investigate proteins involved in early phase of conidia germination, proteomic analysis was performed using two-dimensional gel electrophoresis (2D-GE) in conjunction with MALDI-TOF mass spectrometry (MS). The expression levels of 241 proteins varied quantitatively with statistical significance (P<0.05) at the early phase of the germination stage. Out of these 57 were identified by MALDI-TOF MS. Through classification of physiological functions from Conserved Domain Database analysis, among the identified proteins, 21, 13, and 6 proteins were associated with energy metabolism, protein synthesis, and protein folding process, respectively. Interestingly, eight proteins, which are involved in detoxification of reactive oxygen species (ROS) including catalase A, thioredoxin reductase, and mitochondrial peroxiredoxin, were also identified. The expression levels of the genes were further confirmed using Northern blot and reverse transcriptase (RT)-PCR analyses. This study represents the first proteomic analysis of early phase of conidia germination and will contribute to a better understanding of the molecular events involved in conidia germination process. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Alternative Fuels Data Center: Smithtown Selects CNG to Cut Refuse

Science.gov Websites

additional revenue to the state of $0.05 per gasoline gallon equivalent. Clean Energy expanded the Hauppauge started at $2.33 per diesel gallon equivalent (DGE) through 2008 and increase each year to conclude at

An Efficient Means of Determining the Newtonian Potential for Highly Flattened Mass Distributions

NASA Astrophysics Data System (ADS)

Cohl, H.

1999-05-01

In this dissertation talk we present a mathematical result that, to the best of our knowledge, has been previously undiscovered. That is, the Green's function in a variety of orthogonal coordinate systems may be expressed in terms of a single sum over the azimuthal quantum number, m, of terms involving Toroidal Harmonics. We show how this new addition theorem can be effectively applied to a variety of potential problems in gravitation, electrostatics and magnetostatics and, in particular, demonstrate how it may be used to analyze the properties of general nonaxisymmetric disk systems with and without vertical extent. Finally, we describe our numerical implementation of the addition theorem in order to determine the Newtonian potential extremely close to highly flattened mass distributions. This yields an extremely efficient technique for computing the boundary values in a general algorithm that is designed to solve the 3D Poisson equation on a cylindrical coordinate lattice. We acknowledge support from the U.S. National Science Foundation through grant AST-9528424 and DGE-9355007, the latter of which has been issued through the NSF's Graduate Traineeships Program. This work also has been supported, in part, by grants of high-performance-computing time on NPACI facilities at SDSC and UT, Austin, and through the PET program of NAVOCEANO DoD Major Shared Resource Center in Stennis, MS.

Braiding light quanta

NASA Astrophysics Data System (ADS)

Iadecola, Thomas; Schuster, Thomas; Chamon, Claudio

The possibility that anyons -- quantum particles other than fermions or bosons -- can emerge in condensed matter systems has motivated generations of physicists. In addition to being of fundamental scientific importance, so-called non-Abelian anyons are particularly sought-after for potential applications to quantum computing. However, experimental evidence of anyons in electronic systems remains inconclusive. We propose to demonstrate non-Abelian braiding by injecting coherent states of light into ``topological guided modes'' in specially-fabricated photonic waveguide arrays. These modes are photonic analogues of topological zero modes in electronic systems. Light traveling inside spatially well-separated topological guided modes can be braided, leading to the accumulation of non-Abelian phases. We propose an optical interference experiment to probe this non-Abelian braiding directly. T.I. is supported by a National Science Foundation Graduate Research Fellowship under Grant No. DGE-1247312.

Differentially expressed genes in the ovary of the sixth day of pupal "Ming" lethal egg mutant of silkworm, Bombyx mori.

PubMed

Gao, Peng; Chen, An-Li; Zhao, Qiao-Ling; Shen, Xing-Jia; Qiu, Zhi-Yong; Xia, Ding-Guo; Tang, Shun-Ming; Zhang, Guo-Zheng

2013-09-15

The "Ming" lethal egg mutant (l-em) is a vitelline membrane mutant in silkworm, Bombyx mori. The eggs laid by the l-em mutant lose water, ultimately causing death within an hour. Previous studies have shown that the deletion of BmEP80 is responsible for the l-em mutation in silkworm, B. mori. In the current study, digital gene expression (DGE) was performed to investigate the difference of gene expression in ovaries between wild type and l-em mutant on the sixth day of the pupal stage to obtain a global view of gene expression profiles using the ovaries of three l-em mutants and three wild types. The results showed a total of 3,463,495 and 3,607,936 clean tags in the wild type and the l-em mutant libraries, respectively. Compared with those of wild type, 239 differentially expressed genes were detected in the l-em mutant, wherein 181 genes are up-regulated and 58 genes are down-regulated in the mutant strain. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis results showed that no pathway was significantly enriched and three pathways are tightly related to protein synthesis among the five leading pathways. Moreover, the expression profiles of eight important differentially expressed genes related to oogenesis changed. These results provide a comprehensive gene expression analysis of oogenesis and vitellogenesis in B. mori which facilitates understanding of both the specific molecular mechanism of the 1-em mutant and Lepidopteran oogenesis in general. Copyright © 2013 Elsevier B.V. All rights reserved.

Alternative Fuels Data Center

Science.gov Websites

), propane, electricity, and renewable diesel. For taxation purposes, one GGE of CNG is equal to 5.66 pounds (lbs.), one DGE of LNG is equal to 6.06 lbs., one GGE of propane is equal to 1.35 gallons, and one GGE

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in Portunus trituberculatus

PubMed Central

Zhang, Longtao; Liu, Ping; Li, Jian

2017-01-01

Background Molting is an essential biological process throughout the life history of crustaceans, which is regulated by many neuropeptide hormones expressed in the eyestalk. To better understand the molting mechanism in Portunus trituberculatus, we used digital gene expression (DGE) to analyze single eyestalk samples during the molting cycle by high-throughput sequencing. Results We obtained 14,387,942, 12,631,508 and 13,060,062 clean sequence reads from inter-molt (InM), pre-molt (PrM) and post-molt (PoM) cDNA libraries, respectively. A total of 1,394 molt-related differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analysis identified some important processes and pathways with key roles in molting regulation, such as chitin metabolism, peptidase inhibitor activity, and the ribosome. We first observed a pattern associated with the neuromodulator-related pathways during the molting cycle, which were up-regulated in PrM and down-regulated in PoM. Four categories of important molting-related transcripts were clustered and most of them had similar expression patterns, which suggests that there is a connection between these genes throughout the molt cycle. Conclusion Our work is the first molt-related investigation of P. trituberculatus focusing on the eyestalk at the whole transcriptome level. Together, our results, including DEGs, identification of molting-related biological processes and pathways, and observed expression patterns of important genes, provide a novel insight into the function of the eyestalk in molting regulation. PMID:28394948

Comprehensive transcriptome-based characterization of differentially expressed genes involved in microsporogenesis of radish CMS line and its maintainer.

PubMed

Xie, Yang; Zhang, Wei; Wang, Yan; Xu, Liang; Zhu, Xianwen; Muleke, Everlyne M; Liu, Liwang

2016-09-01

Microsporogenesis is an indispensable period for investigating microspore development and cytoplasmic male sterility (CMS) occurrence. Radish CMS line plays a critical role in elite F1 hybrid seed production and heterosis utilization. However, the molecular mechanisms of microspore development and CMS occurrence have not been thoroughly uncovered in radish. In this study, a comparative analysis of radish floral buds from a CMS line (NAU-WA) and its maintainer (NAU-WB) was conducted using next generation sequencing (NGS) technology. Digital gene expression (DGE) profiling revealed that 3504 genes were significantly differentially expressed between NAU-WA and NAU-WB library, among which 1910 were upregulated and 1594 were downregulated. Gene ontology (GO) analysis showed that these differentially expressed genes (DEGs) were mainly enriched in extracellular region, catalytic activity, and response to stimulus. KEGG enrichment analysis revealed that the DEGs were predominantly associated with flavonoid biosynthesis, glycolysis, and biosynthesis of secondary metabolites. Real-time quantitative PCR analysis showed that the expression profiles of 13 randomly selected DEGs were in high agreement with results from Illumina sequencing. Several candidate genes encoding ATP synthase, auxin response factor (ARF), transcription factors (TFs), chalcone synthase (CHS), and male sterility (MS) were responsible for microsporogenesis. Furthermore, a schematic diagram for functional interaction of DEGs from NAU-WA vs. NAU-WB library in radish plants was proposed. These results could provide new information on the dissection of the molecular mechanisms underlying microspore development and CMS occurrence in radish.

The ghrelin agonist RM-131 accelerates gastric emptying of solids and reduces symptoms in patients with type 1 diabetes mellitus.

PubMed

Shin, Andrea; Camilleri, Michael; Busciglio, Irene; Burton, Duane; Smith, Steven A; Vella, Adrian; Ryks, Michael; Rhoten, Deborah; Zinsmeister, Alan R

2013-11-01

RM-131, a synthetic ghrelin agonist, greatly accelerates gastric emptying of solids in patients with type 2 diabetes and delayed gastric emptying (DGE). We investigated the safety and effects of a single dose of RM-131 on gastric emptying and upper gastrointestinal (GI) symptoms in patients with type 1 diabetes and previously documented DGE. In a double-blind cross-over study, 10 patients with type 1 diabetes (age, 45.7 ± 4.4 y; body mass index, 24.1 ± 1.1 kg/m(2)) and previously documented DGE were assigned in random order to receive a single dose of RM-131 (100 μg, subcutaneously) or placebo. Thirty minutes later, they ate a radiolabeled solid-liquid meal containing EggBeaters (ConAgra Foods, Omaha, NE), and then underwent 4 hours of gastric emptying and 6 hours of colonic filling analyses by scintigraphy. Upper GI symptoms were assessed using a daily diary, gastroparesis cardinal symptom index (total GCSI-DD) and a combination of nausea, vomiting, fullness, and pain (NVFP) scores (each rated on a 0-5 scale). At screening, participants' mean level of hemoglobin A1c was 9.1% ± 0.5%; their total GCSI-DD score was 1.66 ± 0.38 (median, 1.71), and their total NVFP score was 1.73 ± 0.39 (median, 1.9). The t1/2 of solid gastric emptying was 84.9 ± 31.6 minutes when subjects were given RM-131 and 118.7 ± 26.7 when they were given a placebo. The median difference (Δ)was 33.9 minutes (interquartile range [IQR] -12, -49), or -54.7% (IQR, -21%,-110%). RM-131 decreased gastric retention of solids at 1 hour (P = .005) and 2 hours (P = .019). Numeric differences in t1/2 for gastric emptying of liquids, solid gastric emptying lag time, and colonic filling at 6 hours were not significant. Total GCSI-DD scores were 0.79 on placebo (IQR, 0.75, 2.08) and 0.17 on RM-131 (IQR, 0.00, 0.67; P = .026); NVFP scores were lower on RM-131 (P = .041). There were no significant adverse effects. RM-131 significantly accelerates gastric emptying of solids and reduces upper GI symptoms in patients with type 1 diabetes and documented DGE. Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.

Simultaneous acquisition of perfusion and permeability from corrected relaxation rates with dynamic susceptibility contrast dual gradient echo.

PubMed

Kim, Eun-Ju; Kim, Dae-Hong; Lee, Sang Hoon; Huh, Yong-Min; Song, Ho-Taek; Suh, Jin-Suck

2004-04-01

This study compared two methods, corrected (separation of T(1) and T(2)* effects) and uncorrected, in order to determine the suitability of the perfusion and permeability measures through Delta R(2)* and Delta R(1) analyses. A dynamic susceptibility contrast dual gradient echo (DSC-DGE) was used to image the fixed phantoms and flow phantoms (Sephadex perfusion phantoms and dialyzer phantom for the permeability measurements). The results confirmed that the corrected relaxation rate was linearly proportional to gadolinium-diethyltriamine pentaacetic acid (Gd-DTPA) concentration, whereas the uncorrected relaxation rate did not in the fixed phantom and simulation experiments. For the perfusion measurements, it was found that the correction process was necessary not only for the Delta R(1) time curve but also for the Delta R(2)* time curve analyses. Perfusion could not be measured without correcting the Delta R(2)* time curve. The water volume, which was expressed as the perfusion amount, was found to be closer to the theoretical value when using the corrected Delta R(1) curve in the calculations. However, this may occur in the low concentration of Gd-DTPA in tissue used in this study. For the permeability measurements based on the two-compartment model, the permeability factor (k(ev); e = extravascular, v = vascular) from the outside to the inside of the hollow fibers was greater in the corrected Delta R(1) method than in the uncorrected Delta R(1) method. The differences between the corrected and the uncorrected Delta R(1) values were confirmed by the simulation experiments. In conclusion, this study proposes that the correction for the relaxation rates, Delta R(2)* and Delta R(1), is indispensable in making accurate perfusion and permeability measurements, and that DSC-DGE is a useful method for obtaining information on perfusion and permeability, simultaneously.

Digital gene expression analysis in mice lung with coinfection of influenza and streptococcus pneumoniae.

PubMed

Luo, Jun; Zhou, Linlin; Wang, Hongren; Qin, Zhen; Xiang, Li; Zhu, Jie; Huang, Xiaojun; Yang, Yuan; Li, Wanyi; Wang, Baoning; Li, Mingyuan

2017-12-22

Influenza A virus (IAV) and Streptococcus pneumoniae (SP) are two major upper respiratory tract pathogens that can also cause infection in polarized bronchial epithelial cells to exacerbate disease in coinfected individuals which may result in significant morbidity. However, the underlying molecular mechanism is poorly understood. Here, we employed BALB/c ByJ mice inflected with SP, IAV, IAV followed by SP (IAV+SP) and PBS (Control) as models to survey the global gene expression using digital gene expression (DGE) profiling. We attempt to gain insights into the underlying genetic basis of this synergy at the expression level. Gene expression profiles were obtain using the Illimina/Hisseq sequencing technique, and further analyzed by enrichment analysis of Gene Ontology (GO) and Pathway function. The hematoxylin-eosin (HE) staining revealed different tissue changes in groups during which IAV+SP group showed the most severe cell apoptosis. Compared with Control, a total of 2731, 3221 and 3946 differentially expressed genes (DEGs) were detected in SP, IAV and IAV+SP respectively. Besides, sixty-two GO terms were identified by Gene Ontology functional enrichment analysis, such as cell killing, biological regulation, response to stimulus, signaling, biological adhesion, enzyme regulator activity, receptor regulator activity and translation regulator activity. Pathway significant enrichment analysis indicated the dysregulation of multiple pathways, including apoptosis pathway. Among these, five selected genes were further verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). This study shows that infection with SP, IAV or IAV+SP induces apoptosis with different degrees which might provide insights into the molecular mechanisms to facilitate further research.

Bovine mammary gene expression profiling during the onset of lactation.

PubMed

Gao, Yuanyuan; Lin, Xueyan; Shi, Kerong; Yan, Zhengui; Wang, Zhonghua

2013-01-01

Lactogenesis includes two stages. Stage I begins a few weeks before parturition. Stage II is initiated around the time of parturition and extends for several days afterwards. To better understand the molecular events underlying these changes, genome-wide gene expression profiling was conducted using digital gene expression (DGE) on bovine mammary tissue at three time points (on approximately day 35 before parturition (-35 d), day 7 before parturition (-7 d) and day 3 after parturition (+3 d)). Approximately 6.2 million (M), 5.8 million (M) and 6.1 million (M) 21-nt cDNA tags were sequenced in the three cDNA libraries (-35 d, -7 d and +3 d), respectively. After aligning to the reference sequences, the three cDNA libraries included 8,662, 8,363 and 8,359 genes, respectively. With a fold change cutoff criteria of ≥ 2 or ≤-2 and a false discovery rate (FDR) of ≤ 0.001, a total of 812 genes were significantly differentially expressed at -7 d compared with -35 d (stage I). Gene ontology analysis showed that those significantly differentially expressed genes were mainly associated with cell cycle, lipid metabolism, immune response and biological adhesion. A total of 1,189 genes were significantly differentially expressed at +3 d compared with -7 d (stage II), and these genes were mainly associated with the immune response and cell cycle. Moreover, there were 1,672 genes significantly differentially expressed at +3 d compared with -35 d. Gene ontology analysis showed that the main differentially expressed genes were those associated with metabolic processes. The results suggest that the mammary gland begins to lactate not only by a gain of function but also by a broad suppression of function to effectively push most of the cell's resources towards lactation.

Physiological and Transcriptomic Responses of Chinese Cabbage (Brassica rapa L. ssp. Pekinensis) to Salt Stress

PubMed Central

Gao, Jianwei

2017-01-01

Salt stress is one of the major abiotic stresses that severely impact plant growth and development. In this study, we investigated the physiological and transcriptomic responses of Chinese cabbage “Qingmaye” to salt stress, a main variety in North China. Our results showed that the growth and photosynthesis of Chinese cabbage were significantly inhibited by salt treatment. However, as a glycophyte, Chinese cabbage could cope with high salinity; it could complete an entire life cycle at 100 mM NaCl. The high salt tolerance of Chinese cabbage was achieved by accumulating osmoprotectants and by maintaining higher activity of antioxidant enzymes. Transcriptomic responses were analyzed using the digital gene expression profiling (DGE) technique after 12 h of treatment by 200 mM NaCl. A total of 1235 differentially expressed genes (DEGs) including 740 up- and 495 down-regulated genes were identified. Functional annotation analyses showed that the DEGs were related to signal transduction, osmolyte synthesis, transcription factors, and antioxidant proteins. Taken together, this study contributes to our understanding of the mechanism of salt tolerance in Chinese cabbage and provides valuable information for further improvement of salt tolerance in Chinese cabbage breeding programs. PMID:28895882

Teachers Modify Geometry Problems: From Proof to Investigation

ERIC Educational Resources Information Center

Leikin, Roza; Grossman, Dorith

2013-01-01

We explored transformations that teachers made to modify geometry proof problems into investigation problems and analyzed how these transformations differ in teachers who use a dynamic geometry environment (DGE) in their classes and those who do not. We devised a framework for the analysis of problem transformations and types of teacher-generated…

Durum wheat genetic stocks involving chromosome 1E of diploid wheatgrass: Resistance to Fusarium head blight

USDA-ARS?s Scientific Manuscript database

Durum wheat (Triticum turgidum L., 2n = 4x = 28; AABB genomes) is the preferred wheat for preparing pasta products. Current durum cultivars have little resistance to a ravaging fungal disease, Fusarium head blight (FHB), or scab. In our Durum Germplasm Enhancement (DGE) project, we previously show...

Exposures of Sus scrofa to a TASER(®) conducted electrical weapon: no effects on 2-dimensional gel electrophoresis patterns of plasma proteins.

PubMed

Jauchem, James R; Cerna, Cesario Z; Lim, Tiffany Y; Seaman, Ronald L

2014-12-01

In an earlier study, we found significant changes in red-blood-cell, leukocyte, and platelet counts, and in red-blood-cell membrane proteins, following exposures of anesthetized pigs to a conducted electrical weapon. In the current study, we examined potential changes in plasma proteins [analyzed via two-dimensional gel electrophoresis (2-DGE)] following two 30 s exposures of anesthetized pigs (Sus scrofa) to a TASER (®) C2 conducted electrical weapon. Patterns of proteins, separated by 2-DGE, were consistent and reproducible between animals and between times of sampling. We determined that the blood plasma collection, handling, storage, and processing techniques we used are suitable for swine blood. There were no statistically significant changes in plasma proteins following the conducted-electrical-weapon exposures. Overall gel patterns of fibrinogen were similar to results of other studies of both pigs and humans (in control settings, not exposed to conducted electrical weapons). The lack of significant changes in plasma proteins may be added to the body of evidence regarding relative safety of TASER C2 device exposures.

Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops

PubMed Central

Sun, Xiujun; Liu, Zhihong; Zhou, Liqing; Wu, Biao; Dong, Yinghui; Yang, Aiguo

2016-01-01

The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture. PMID:27563719

Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study.

PubMed

Soman, Kizhake V; Stafford, Susan J; Pazdrak, Konrad; Wu, Zheng; Luo, Xuemei; White, Wendy I; Wiktorowicz, John E; Calhoun, William J; Kurosky, Alexander

2017-08-04

Activated eosinophils contribute to airway dysfunction and tissue remodeling in asthma and thus are considered to be important factors in asthma pathology. We report here comparative proteomic and phosphoproteomic changes upon activation of eosinophils using eight cytokines individually and in selected cytokine combinations in time-course reactions. Differential protein and phosphoprotein expressions were determined by mass spectrometry after 2-dimensional gel electrophoresis (2DGE) and by LC-MS/MS. We found that each cytokine-stimulation produced significantly different changes in the eosinophil proteome and phosphoproteome, with phosphoproteomic changes being more pronounced and having an earlier onset. Furthermore, we observed that IL-5, GM-CSF, and IL-3 showed the greatest change in protein expression and phosphorylation, and this expression differed markedly from those of the other five cytokines evaluated. Comprehensive univariate and multivariate statistical analyses were employed to evaluate the comparative results. We also monitored eosinophil activation using flow cytometry (FC) analysis of CD69. In agreement with our proteomic studies, FC indicated that IL-5, GM-CSF, and IL-3 were more effective than the other five cytokines studied in stimulating a cell surface CD69 increase indicative of eosinophil activation. Moreover, selected combinations of cytokines revealed proteomic patterns with many proteins in common with single cytokine expression patterns but also showed a greater effect of the two cytokines employed, indicating a more complex signaling pathway that was reflective of a more typical inflammatory pathology.

Variation in Hsp70-1A expression contributes to skin color diversity

PubMed Central

Murase, Daiki; Hachiya, Akira; Fullenkamp, Rachel; Beck, Anita; Moriwaki, Shigeru; Hase, Tadashi; Takema, Yoshinori; Manga, Prashiela

2017-01-01

The wide range in human skin color results from varying levels of the pigment melanin. Genetic mechanisms underlying coloration differences have been explored, but identified genes do not account for all variation seen in the skin color spectrum. Post-transcriptional and post-translational regulation of factors that determine skin color, including melanin synthesis in epidermal melanocytes, melanosome transfer to keratinocytes and melanosome degradation, is also critical for pigmentation. We therefore investigated proteins that are differentially expressed in melanocytes derived from either White or African American (AA) skin. Two dimensional gel electrophoresis (2-DGE) and mass spectrometry demonstrated that Heat Shock Protein 70-1A (Hsp70-1A) protein levels were significantly higher in AA melanocytes compared to White melanocytes. Hsp70-1A expression significantly correlated with levels of tyrosinase, the rate-limiting melanogenic enzyme, consistent with a proposed role for Hsp70-family members in tyrosinase post-translational modification. Additionally, pharmacologic inhibition and siRNA-mediated down-regulation of Hsp70-1A correlated with pigmentation changes in cultured melanocytes, modified human skin substitutes and ex vivo skin. Furthermore, Hsp70-1A inhibition led to increased autophagy-mediated melanosome degradation in keratinocytes. Our data thus reveal that epidermal Hsp70-1A contributes to the diversity of skin color by regulating the amount of melanin synthesized in melanocytes and modulating autophagic melanosome degradation in keratinocytes. PMID:27094592

Transcriptome and Differential Expression Profiling Analysis of the Mechanism of Ca2+ Regulation in Peanut (Arachis hypogaea) Pod Development

PubMed Central

Yang, Sha; Li, Lin; Zhang, Jialei; Geng, Yun; Guo, Feng; Wang, Jianguo; Meng, Jingjing; Sui, Na; Wan, Shubo; Li, Xinguo

2017-01-01

Calcium not only serves as a necessary nutrient for plant growth but also acts as a ubiquitous central hub in a large number of signaling pathways. Free Ca2+ deficiency in the soil may cause early embryo abortion, which eventually led to abnormal development of peanut pod during the harvest season. To understand the mechanisms of Ca2+ regulation in pod development, transcriptome analysis of peanut gynophores and pods was performed by comparing the treatments between free Ca2+ sufficiency and free Ca2+ deficiency using Illumina HiSeq™ 2000. 9,903,082,800 nt bases are generated totally. After assembly, the average length of 102,819 unigenes is 999 nt, N50 is 1,782 nt. RNA-seq based gene expression profilings showed a large number of genes at the transcriptional level changed significantly between the aerial pegs and underground swelling pods under free Ca2+ sufficienct or deficiency treatments, respectively. Genes encoding key members of Ca2+ signaling transduction pathway, enzymes for hormone metabolism, cell division and growth, transcriptional factor as well as embryo development were highlighted. This information provides useful information for our further study. The results of digital gene expression (DGE) indicated that exogenous calcium might contribute to the development of peanut pod through its signal transduction pathway, meanwhile, promote the normal transition of the gynophores to the reproductive development. PMID:29033956

Using combined bio-omics methods to evaluate the complicated toxic effects of mixed chemical wastewater and its treated effluent.

PubMed

Zhang, Yan; Deng, Yongfeng; Zhao, Yanping; Ren, Hongqiang

2014-05-15

Mixed chemical wastewaters (MCWW) from industrial park contain complex mixtures of trace contaminants, which cannot be effectively removed by wastewater treatment plants (WWTP) and have become an unignored threat to ambient environment. However, limited information is available to evaluate the complicated toxic effects of MCWW and its effluent from wastewater treatment plant (WTPE) from the perspective of bio-omics. In this study, mice were exposed to the MCWW and WTPE for 90 days and distinct differences in the hepatic transcriptome and serum metabolome were analyzed by digital gene expression (DGE) and proton nuclear magnetic resonance ((1)H-NMR) spectra, respectively. Our results indicated that disruption of lipid metabolism in liver and hepatotoxicity were induced by both MCWW and WTPE exposure. WTPE is still a health risk to the environment, which is in need of more attention. Furthermore, we demonstrated the potential ability of bio-omics approaches for evaluating toxic effects of MCWW and WTPE. Copyright © 2014 Elsevier B.V. All rights reserved.

Geothermal Energy Resources of Navy/Marine Corps Installations on the Atlantic and Gulf Coastal Plain.

DTIC Science & Technology

1980-03-01

Geological Survey ( AAPG -USGS) thermal gradient map of North America, at a scale of 1:5,000,000, gives the hypothesized average depth (by contours) in...file reports; USGS topographic and geologic maps; AAPG -USGS special geologic maps; APL/JHU reports; VPI-SU progress re- ports to DOE/DGE; technical

Synthesis and application of a novel environmental C26 diglycidyl ester plasticizer based on castor oil for poly(vinyl chloride)

USDA-ARS?s Scientific Manuscript database

In this work, for the first time, a castor oil derived diglycidyl ester plasticizer (C26-DGE) was prepared and incorporated into poly(vinyl chloride) (PVC). The chemical structure of the product was characterized by Fourier transform infrared spectroscopy (FT-IR), proton nuclear magnetic resonance (...

Investigating the Problem Solving Competency of Pre Service Teachers in Dynamic Geometry Environment

ERIC Educational Resources Information Center

Haja, Shajahan

2005-01-01

This study investigated the problem-solving competency of four secondary pre service teachers (PSTs) of University of London as they explored geometry problems in dynamic geometry environment (DGE) in 2004. A constructivist experiment was designed in which dynamic software Cabri-Geometre II (hereafter Cabri) was used as an interactive medium.…

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.

PubMed

Siebert, Stefan; Robinson, Mark D; Tintori, Sophia C; Goetz, Freya; Helm, Rebecca R; Smith, Stephen A; Shaner, Nathan; Haddock, Steven H D; Dunn, Casey W

2011-01-01

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing.

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

PubMed Central

Siebert, Stefan; Robinson, Mark D.; Tintori, Sophia C.; Goetz, Freya; Helm, Rebecca R.; Smith, Stephen A.; Shaner, Nathan; Haddock, Steven H. D.; Dunn, Casey W.

2011-01-01

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing. PMID:21829563

Nitroproteins in Human Astrocytomas Discovered by Gel Electrophoresis and Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Peng, Fang; Li, Jianglin; Guo, Tianyao; Yang, Haiyan; Li, Maoyu; Sang, Shushan; Li, Xuejun; Desiderio, Dominic M.; Zhan, Xianquan

2015-12-01

Protein tyrosine nitration is involved in the pathogenesis of highly fatal astrocytomas, a type of brain cancer. To understand the molecular mechanisms of astrocytomas and to discover new biomarkers/therapeutic targets, we sought to identify nitroproteins in human astrocytoma tissue. Anti-nitrotyrosine immunoreaction-positive proteins from a high-grade astrocytoma tissue were detected with two-dimensional gel electrophoresis (2DGE)-based nitrotyrosine immunoblots, and identified with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Fifty-seven nitrotyrosine immunopositive protein spots were detected. A total of 870 proteins (nitrated and non-nitrated) in nitrotyrosine-immunopositive 2D gel spots were identified, and 18 nitroproteins and their 20 nitrotyrosine sites were identified with MS/MS analysis. These nitroproteins participate in multiple processes, including drug-resistance, signal transduction, cytoskeleton, transcription and translation, cell proliferation and apoptosis, immune response, phenotypic dedifferentiation, cell migration, and metastasis. Among those nitroproteins that might play a role in astrocytomas was nitro-sorcin, which is involved in drug resistance and metastasis and might play a role in the spread and treatment of an astrocytoma. Semiquantitative immune-based measurements of different sorcin expressions were found among different grades of astrocytomas relative to controls, and a semiquantitative increased nitration level in high-grade astrocytoma relative to control. Nitro-β-tubulin functions in cytoskeleton and cell migration. Semiquantitative immunoreactivity of β-tubulin showed increased expression among different grades of astrocytomas relative to controls and semiquantitatively increased nitration level in high-grade astrocytoma relative to control. Each nitroprotein was rationalized and related to the corresponding functional system to provide new insights into tyrosine nitration and its potential role in the pathogenesis of astrocytoma formation.

High-throughput transcriptome analysis of barley (Hordeum vulgare) exposed to excessive boron.

PubMed

Tombuloglu, Guzin; Tombuloglu, Huseyin; Sakcali, M Serdal; Unver, Turgay

2015-02-15

Boron (B) is an essential micronutrient for optimum plant growth. However, above certain threshold B is toxic and causes yield loss in agricultural lands. While a number of studies were conducted to understand B tolerance mechanism, a transcriptome-wide approach for B tolerant barley is performed here for the first time. A high-throughput RNA-Seq (cDNA) sequencing technology (Illumina) was used with barley (Hordeum vulgare), yielding 208 million clean reads. In total, 256,874 unigenes were generated and assigned to known peptide databases: Gene Ontology (GO) (99,043), Swiss-Prot (38,266), Clusters of Orthologous Groups (COG) (26,250), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) (36,860), as determined by BLASTx search. According to the digital gene expression (DGE) analyses, 16% and 17% of the transcripts were found to be differentially regulated in root and leaf tissues, respectively. Most of them were involved in cell wall, stress response, membrane, protein kinase and transporter mechanisms. Some of the genes detected as highly expressed in root tissue are phospholipases, predicted divalent heavy-metal cation transporters, formin-like proteins and calmodulin/Ca(2+)-binding proteins. In addition, chitin-binding lectin precursor, ubiquitin carboxyl-terminal hydrolase, and serine/threonine-protein kinase AFC2 genes were indicated to be highly regulated in leaf tissue upon excess B treatment. Some pathways, such as the Ca(2+)-calmodulin system, are activated in response to B toxicity. The differential regulation of 10 transcripts was confirmed by qRT-PCR, revealing the tissue-specific responses against B toxicity and their putative function in B-tolerance mechanisms. Copyright © 2014. Published by Elsevier B.V.

Kinetics of motility-induced phase separation and swim pressure

NASA Astrophysics Data System (ADS)

Patch, Adam; Yllanes, David; Marchetti, M. Cristina

Active Brownian particles (ABPs) represent a minimal model of active matter consisting of self-propelled spheres with purely repulsive interactions and rotational noise. We correlate the time evolution of the mean pressure towards its steady state value with the kinetics of motility-induced phase separation. For parameter values corresponding to phase separated steady states, we identify two dynamical regimes. The pressure grows monotonically in time during the initial regime of rapid cluster formation, overshooting its steady state value and then quickly relaxing to it, and remains constant during the subsequent slower period of cluster coalescence and coarsening. The overshoot is a distinctive feature of active systems. NSF-DMR-1305184, NSF-DGE-1068780, ACI-1341006, FIS2015-65078-C02, BIFI-ZCAM.

Comparative Digital Gene Expression Analysis of Tissue-Cultured Plantlets of Highly Resistant and Susceptible Banana Cultivars in Response to Fusarium oxysporum

PubMed Central

Niu, Yuqing; Hu, Bei; Li, Xiaoquan; Chen, Houbin; Šamaj, Jozef; Xu, Chunxiang

2018-01-01

Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive soil-borne diseases. In this study, young tissue-cultured plantlets of banana (Musa spp. AAA) cultivars differing in Foc susceptibility were used to reveal their differential responses to this pathogen using digital gene expression (DGE). Data were evaluated by various bioinformatic tools (Venn diagrams, gene ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses) and immunofluorescence labelling method to support the identification of gene candidates determining the resistance of banana against Foc. Interestingly, we have identified MaWRKY50 as an important gene involved in both constitutive and induced resistance. We also identified new genes involved in the resistance of banana to Foc, including several other transcription factors (TFs), pathogenesis-related (PR) genes and some genes related to the plant cell wall biosynthesis or degradation (e.g., pectinesterases, β-glucosidases, xyloglucan endotransglucosylase/hydrolase and endoglucanase). The resistant banana cultivar shows activation of PR-3 and PR-4 genes as well as formation of different constitutive cell barriers to restrict spreading of the pathogen. These data suggest new mechanisms of banana resistance to Foc. PMID:29364855

Standardization and streamlining of a pancreas surgery practice improves outcomes and resource utilization: A single institution's 20-year experience.

PubMed

Stauffer, John A; Onkendi, Edwin O; Wallace, Michael B; Raimondo, Massimo; Woodward, Timothy A; Lukens, Frank J; Asbun, Horacio J

2017-09-01

In the past two decades, pancreas surgery (PS) has undergone significant advances in operative techniques and with a focus on multidisciplinary high-volume practices. A review of patients undergoing PS from 3/1995-2/2015 was conducted; dividing patients into group A (1995-2005) and group B (2005-2015) for a detailed comparison. Effect of surgeon volume in group B was determined. A total of 1001 patients underwent PS (group A: 259; group B: 742). The mean age was 62.7 years and 52.8% were female. Group B patients were associated with a higher rate of pylorus preservation and minimally invasive resection and a lower rate of morbidity, pancreas fistula (PF), and delayed gastric emptying (DGE) than group A. High-volume surgeons (HVS) had lower operative blood loss (300 mL vs 600 mL), transfusion requirements, PF (14% vs 20%), DGE, surgical site infections, reoperations, and major morbidity rate (15.5 vs 39%) than low-volume surgeons. This study demonstrates improved patient outcomes and hospital resource utilization over the past 20 years. Concentration of PS to HVS results in superior results. Copyright © 2017 Elsevier Inc. All rights reserved.

Free α-dicarbonyl compounds in coffee, barley coffee and soy sauce and effects of in vitro digestion.

PubMed

Papetti, Adele; Mascherpa, Dora; Gazzani, Gabriella

2014-12-01

α-Dicarbonyl (α-DC) compounds were characterised in roasted (coffee, barley coffee) and in fermented (soy sauce) food matrices. Glyoxal (GO), methylglyoxal (MGO), diacetyl (DA) and 3-deoxyglucosone (3-DG) were found in all samples, and hydroxypyruvaldehyde and 5-hydroxypentane-2,3-dione in barley and soy. Cis and trans 3,4-dideoxyglucosone-3-ene (3,4-DGE) isomers and 4-glucosyl-5,6-dihydroxy-2-oxohexanal (4-G,3-DG) were found only in barley, and 3,4-DGE only in soy sauce with molasses. GO, MGO, and DA were quantified. Findings indicate that i) α-DC profiles depend on the food matrix and any technological treatments applied; ii) α-DC quantitation by HPLC requires matrix-specific, validated methods; iii) GO and MGO were the most abundant α-DCs; and iv) barley coffee was the matrix richest in α-DCs both qualitatively and quantitatively. In vitro simulated digestion reduced (coffee) or strongly increased (barley, soy sauce) free α-DC content. These findings suggest that α-DC bioavailability could actually depend not on food content but rather on reactions occurring during digestion. Copyright © 2014 Elsevier Ltd. All rights reserved.

Utility of feeding jejunostomy tubes in pancreaticoduodenectomy.

PubMed

Waliye, Hussein E; Wright, G Paul; McCarthy, Caitlin; Johnson, Jared; Scales, Alex; Wolf, Andrea; Chung, Mathew

2017-03-01

Routine placement of jejunostomy tubes (JT) during pancreaticoduodenectomy (PD) is controversial. A retrospective chart review of patients undergoing PD from 1/1/08 through 12/31/14 was performed. The patients were divided into groups by placement of JT. Outcome measures were 90-day morbidity, 90-day mortality, length of stay, rate of delayed gastric emptying (DGE), and JT-specific complications. 256 patients were included. There were no significant differences in 90-day morbidity (39.9% vs. 37.9%, p = 0.747), 90-day mortality (3.9% vs. 1.0%, p = 0.247) or TPN use (24.8 vs. 25.2%, p = 0.941) between those with and without JT, respectively. Patients with a JT had a higher rate of DGE (p < 0.001), longer hospital stay (14.3 vs. 11.6, p < 0.001), and longer time to solid intake (9.4 vs. 7.3, p < 0.001). Eleven patients (7.2%) with JT had tube-related morbidity. Routine placement of JT at the time of PD should be abandoned with efforts focused on preoperative nutrition optimization and early oral diet trials. Copyright © 2016 Elsevier Inc. All rights reserved.

Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways.

PubMed

Zhao, Ying; Liang, Haiying; Li, Lan; Tang, Sha; Han, Xiao; Wang, Congpeng; Xia, Xinli; Yin, Weilun

2015-01-01

Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Samples from hormone-treated cone reproductive shoots and naturally occurring non-cone setting shoots were analyzed using 24 digital gene expression (DGE) tag profiles using Illumina, generating a total of 69,520 putative transcripts. Next, 32 differentially and specifically expressed transcripts were determined using quantitative real-time polymerase chain reaction, including the upregulation of MADS-box transcription factors involved in male bud transition and flowering time control proteins involved in female bud transition. These differentially expressed transcripts were associated with 243 KEGG pathways. Among the significantly changed pathways, sugar pathways were mediated by hormone signals during the vegetative-to-reproductive phase transition, including glycolysis/gluconeogenesis and sucrose and starch metabolism pathways. Key enzymes were identified in these pathways, including alcohol dehydrogenase (NAD) and glutathione dehydrogenase for the glycolysis/gluconeogenesis pathway, and glucanphosphorylase for sucrose and starch metabolism pathways. Our results increase our understanding of the reproductive bud transition in gymnosperms. In addition, these studies on hormone-mediated sugar pathways increase our understanding of the relationship between sugar and hormone signaling during female and male bud initiation in Metasequoia.

Characterization of transcriptome in the Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) and gene expression analysis during developmental stages.

PubMed

Tang, Pei-An; Wu, Hai-Jing; Xue, Hao; Ju, Xing-Rong; Song, Wei; Zhang, Qi-Lin; Yuan, Ming-Long

2017-07-30

The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P. interpunctella (egg, third-instar larvae, pupae and adult). We obtained approximate 9gigabyte (GB) of clean data and recovered 84,938 unigenes, including 37,602 clusters and 47,336 singletons. These unigenes were annotated using BLAST against the non-redundant protein databases and then functionally classified based on Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes databases (KEGG). A large number of differentially expressed genes were identified by pairwise comparisons among different developmental stages. Gene expression profiles dramatically changed between developmental stage transitions. Some of these differentially expressed genes were related to digestion and cuticularization. Quantitative real-time PCR results of six randomly selected genes conformed the findings in the DGEs. Furthermore, we identified over 8000 microsatellite markers and 97,648 single nucleotide polymorphisms which will be useful for population genetics studies of P. interpunctella. This transcriptomic information provided insight into the developmental basis of P. interpunctella and will be helpful for establishing integrated management strategies and developing new targets of insecticides for this serious pest. Copyright © 2017 Elsevier B.V. All rights reserved.

Phenotypic plasticity of gas exchange pattern and water loss in Scarabaeus spretus (Coleoptera: Scarabaeidae): deconstructing the basis for metabolic rate variation.

PubMed

Terblanche, John S; Clusella-Trullas, Susana; Chown, Steven L

2010-09-01

Investigation of gas exchange patterns and modulation of metabolism provide insight into metabolic control systems and evolution in diverse terrestrial environments. Variation in metabolic rate in response to environmental conditions has been explained largely in the context of two contrasting hypotheses, namely metabolic depression in response to stressful or resource-(e.g. water) limited conditions, or elevation of metabolism at low temperatures to sustain life in extreme conditions. To deconstruct the basis for metabolic rate changes in response to temperature variation, here we undertake a full factorial study investigating the longer- and short-term effects of temperature exposure on gas exchange patterns. We examined responses of traits of gas exchange [standard metabolic rate (SMR); discontinuous gas exchange (DGE) cycle frequency; cuticular, respiratory and total water loss rate (WLR)] to elucidate the magnitude and form of plastic responses in the dung beetle, Scarabaeus spretus. Results showed that short- and longer-term temperature variation generally have significant effects on SMR and WLR. Overall, acclimation to increased temperature led to a decline in SMR (from 0.071+/-0.004 ml CO(2) h(-1) in 15 degrees C-acclimated beetles to 0.039+/-0.004 ml CO(2) h(-1) in 25 degrees C-acclimated beetles measured at 20 degrees C) modulated by reduced DGE frequency (15 degrees C acclimation: 0.554+/-0.027 mHz, 20 degrees C acclimation: 0.257+/-0.030 mHz, 25 degrees C acclimation: 0.208+/-0.027 mHz recorded at 20 degrees C), reduced cuticular WLRs (from 1.058+/-0.537 mg h(-1) in 15 degrees C-acclimated beetles to 0.900+/-0.400 mg h(-1) in 25 degrees C-acclimated beetles measured at 20 degrees C) and reduced total WLR (from 4.2+/-0.5 mg h(-1) in 15 degrees C-acclimated beetles to 3.1+/-0.5 mg h(-1) in 25 degrees C-acclimated beetles measured at 25 degrees C). Respiratory WLR was reduced from 2.25+/-0.40 mg h(-1) in 15 degrees C-acclimated beetles to 1.60+/-0.40 mg h(-1) in 25 degrees C-acclimated beetles measured at 25 degrees C, suggesting conservation of water during DGE bursts. Overall, this suggests water conservation is a priority for S. spretus exposed to longer-term temperature variation, rather than elevation of SMR in response to low temperature acclimation, as might be expected from a beetle living in a relatively warm, low rainfall summer region. These results are significant for understanding the evolution of gas exchange patterns and trade-offs between metabolic rate and water balance in insects and other terrestrial arthropods.

The Effect of Inquiry-Based Explorations in a Dynamic Geometry Environment on Sixth Grade Students' Achievements in Polygons

ERIC Educational Resources Information Center

Erbas, Ayhan Kursat; Yenmez, Arzu Aydogan

2011-01-01

The purpose of this study was to investigate the effects of using a dynamic geometry environment (DGE) together with inquiry-based explorations on the sixth grade students' achievements in polygons and congruency and similarity of polygons. Two groups of sixth grade students were selected for this study: an experimental group composed of 66…

Finite-size effects in simulations of electrolyte solutions under periodic boundary conditions

NASA Astrophysics Data System (ADS)

Thompson, Jeffrey; Sanchez, Isaac

The equilibrium properties of charged systems with periodic boundary conditions may exhibit pronounced system-size dependence due to the long range of the Coulomb force. As shown by others, the leading-order finite-size correction to the Coulomb energy of a charged fluid confined to a periodic box of volume V may be derived from sum rules satisfied by the charge-charge correlations in the thermodynamic limit V -> ∞ . In classical systems, the relevant sum rule is the Stillinger-Lovett second-moment (or perfect screening) condition. This constraint implies that for large V, periodicity induces a negative bias of -kB T(2 V) - 1 in the total Coulomb energy density of a homogeneous classical charged fluid of given density and temperature. We present a careful study of the impact of such finite-size effects on the calculation of solute chemical potentials from explicit-solvent molecular simulations of aqueous electrolyte solutions. National Science Foundation Graduate Research Fellowship Program, Grant No. DGE-1610403.

Phase Transition of a Dynamical System with a Bi-Directional, Instantaneous Coupling to a Virtual System

NASA Astrophysics Data System (ADS)

Gintautas, Vadas; Hubler, Alfred

2006-03-01

As worldwide computer resources increase in power and decrease in cost, real-time simulations of physical systems are becoming increasingly prevalent, from laboratory models to stock market projections and entire ``virtual worlds'' in computer games. Often, these systems are meticulously designed to match real-world systems as closely as possible. We study the limiting behavior of a virtual horizontally driven pendulum coupled to its real-world counterpart, where the interaction occurs on a time scale that is much shorter than the time scale of the dynamical system. We find that if the physical parameters of the virtual system match those of the real system within a certain tolerance, there is a qualitative change in the behavior of the two-pendulum system as the strength of the coupling is increased. Applications include a new method to measure the physical parameters of a real system and the use of resonance spectroscopy to refine a computer model. As virtual systems better approximate real ones, even very weak interactions may produce unexpected and dramatic behavior. The research is supported by the National Science Foundation Grant No. NSF PHY 01-40179, NSF DMS 03-25939 ITR, and NSF DGE 03-38215.

Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas

PubMed Central

Tao, Xiang; Lai, Xian-Jun; Zhang, Yi-Zheng; Tan, Xue-Mei; Wang, Haiyan

2014-01-01

Background Transposable elements (TEs) are the most abundant genomic components in eukaryotes and affect the genome by their replications and movements to generate genetic plasticity. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization. Complete identification of TEs is essential for the study of genome evolution. However, the TEs of sweet potato are still poorly understood because of its complex hexaploid genome and difficulty in genome sequencing. The recent availability of the sweet potato transcriptome databases provides an opportunity for discovering and characterizing the expressed TEs. Methodology/Principal Findings We first established the integrated-transcriptome database by de novo assembling four published sweet potato transcriptome databases from three cultivars in China. Using sequence-similarity search and analysis, a total of 1,405 TEs including 883 retrotransposons and 522 DNA transposons were predicted and categorized. Depending on mapping sets of RNA-Seq raw short reads to the predicted TEs, we compared the quantities, classifications and expression activities of TEs inter- and intra-cultivars. Moreover, the differential expressions of TEs in seven tissues of Xushu 18 cultivar were analyzed by using Illumina digital gene expression (DGE) tag profiling. It was found that 417 TEs were expressed in one or more tissues and 107 in all seven tissues. Furthermore, the copy number of 11 transposase genes was determined to be 1–3 copies in the genome of sweet potato by Real-time PCR-based absolute quantification. Conclusions/Significance Our result provides a new method for TE searching on species with transcriptome sequences while lacking genome information. The searching, identification and expression analysis of TEs will provide useful TE information in sweet potato, which are valuable for the further studies of TE-mediated gene mutation and optimization in asexual reproduction. It contributes to elucidating the roles of TEs in genome evolution. PMID:24608103

Protein-transitions in and out of the dough matrix in wheat flour mixing.

PubMed

Wang, Xiaolong; Appels, Rudi; Zhang, Xiaoke; Bekes, Ferenc; Torok, Kitti; Tomoskozi, Sandor; Diepeveen, Dean; Ma, Wujun; Islam, Shahidul

2017-02-15

Sequential protein behavior in the wheat dough matrix under continuous mixing and heating treatment has been studied using Mixolab-dough samples from two Australian wheat cultivars, Westonia and Wyalkatchem. Size exclusion high performance liquid chromatography (SE-HPLC) and two-dimensional gel electrophoresis (2-DGE) analysis indicated that 32min (80°C) was a critical time point in forming large protein complexes and loosing extractability of several protein groups like y-type high molecular weight glutenin subunits (HMW-GSs), gamma-gliadins, beta-amylases, serpins, and metabolic proteins with higher mass. Up to 32min (80°C) Westonia showed higher protein extractability compared to Wyalkatchem although it was in the opposite direction thereafter. Twenty differentially expressed proteins could be assigned to chromosomes 1D, 3A, 4A, 4B, 4D, 6A, 6B, 7A and 7B. The results expanded the range of proteins associated with changes in the gluten-complex during processing and provided targets for selecting new genetic variants associated with altered quality attributes of the flour. Copyright © 2016 Elsevier Ltd. All rights reserved.

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

PubMed

Townsley, Brad T; Covington, Michael F; Ichihashi, Yasunori; Zumstein, Kristina; Sinha, Neelima R

2015-01-01

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

Program review: resource evaluation, reservoir confirmation, and exploration technology

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

Ward, S.H.

1978-05-01

The details of the program review are reported. A summary of the recommendations, means for their implementation, and a six year program of expenditures which would accomplish the objectives of the recommendations are presented. Included in appendices are the following: DOE/DGE consortia participants; program managers contacted for opinion; communications received from program managers; participants, program review panel; and program strategy for resource evaluation and reservoir confirmation. (MHR)

Comparative study of gastric emptying and nutritional status after pylorus-preserving vs. subtotal stomach-preserving pancreaticoduodenectomy.

PubMed

Hiyoshi, Masahide; Chijiiwa, Kazuo; Ohuchida, Jiro; Imamura, Naoya; Nagano, Motoaki

2012-06-01

Delayed gastric emptying (DGE) is a specific, worrisome complication after pancreaticoduodenectomy (PPPD), whereas subtotal stomach-preserving pancreaticoduodenectomy (SSPPD) that excises the pylorus ring seems to be effective in reducing DGE. This study compared gastric emptying and nutritional status between PPPD and SSPPD over 1 year. From June 2003 to December 2007, 41 patients (PPPD: 33, SSPPD: 8) were enrolled in this study to evaluate differences in gastric emptying and nutritional status at 1, 3, 6, 9 and 12 months after pancreaticoduodenectomy. Gastric emptying was evaluated by 13C-acetate breath test. Nutritional status (body weight, serum levels of total protein, albumin and total cholesterol) was similarly assessed. At 1 month, gastric emptying evaluated at T1/2 (half-emptying time) was significantly prolonged in the PPPD but not in the SSPPD compared to the preoperative level. Thereafter, T1/2 was decreased and showed function significantly better preserved at 3, 6 and 12 months after PPPD than after SSPPD. Body weight recovery was significantly better at 6 and 12 months after PPPD than after SSPPD. Other nutritional parameters were better preserved in the PPPD during 1-year follow-up. PPPD seems to be a more suitable surgical procedure than SSPPD in regard to gastric emptying and nutritional status.

Transcriptome and Proteome Exploration to Provide a Resource for the Study of Agrocybe aegerita

PubMed Central

Jiang, Shuai; Chen, Yijie; Yin, Yalin; Pan, Yongfu; Yu, Guojun; Li, Yamu; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

2013-01-01

Background Agrocybe aegerita, the black poplar mushroom, has been highly valued as a functional food for its medicinal and nutritional benefits. Several bioactive extracts from A. aegerita have been found to exhibit antitumor and antioxidant activities. However, limited genetic resources for A. aegerita have hindered exploration of this species. Methodology/Principal Findings To facilitate the research on A. aegerita, we established a deep survey of the transcriptome and proteome of this mushroom. We applied high-throughput sequencing technology (Illumina) to sequence A. aegerita transcriptomes from mycelium and fruiting body. The raw clean reads were de novo assembled into a total of 36,134 expressed sequences tags (ESTs) with an average length of 663 bp. These ESTs were annotated and classified according to Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Gene expression profile analysis showed that 18,474 ESTs were differentially expressed, with 10,131 up-regulated in mycelium and 8,343 up-regulated in fruiting body. Putative genes involved in polysaccharide and steroid biosynthesis were identified from A. aegerita transcriptome, and these genes were differentially expressed at the two stages of A. aegerita. Based on one-dimensional gel electrophoresis (1-DGE) coupled with electrospray ionization liquid chromatography tandem MS (LC-ESI-MS/MS), we identified a total of 309 non-redundant proteins. And many metabolic enzymes involved in glycolysis were identified in the protein database. Conclusions/Significance This is the first study on transcriptome and proteome analyses of A. aegerita. The data in this study serve as a resource of A. aegerita transcripts and proteins, and offer clues to the applications of this mushroom in nutrition, pharmacy and industry. PMID:23418592

Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways

PubMed Central

Zhao, Ying; Liang, Haiying; Li, Lan; Tang, Sha; Han, Xiao; Wang, Congpeng; Xia, Xinli; Yin, Weilun

2015-01-01

Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Samples from hormone-treated cone reproductive shoots and naturally occurring non-cone setting shoots were analyzed using 24 digital gene expression (DGE) tag profiles using Illumina, generating a total of 69,520 putative transcripts. Next, 32 differentially and specifically expressed transcripts were determined using quantitative real-time polymerase chain reaction, including the upregulation of MADS-box transcription factors involved in male bud transition and flowering time control proteins involved in female bud transition. These differentially expressed transcripts were associated with 243 KEGG pathways. Among the significantly changed pathways, sugar pathways were mediated by hormone signals during the vegetative-to-reproductive phase transition, including glycolysis/gluconeogenesis and sucrose and starch metabolism pathways. Key enzymes were identified in these pathways, including alcohol dehydrogenase (NAD) and glutathione dehydrogenase for the glycolysis/gluconeogenesis pathway, and glucanphosphorylase for sucrose and starch metabolism pathways. Our results increase our understanding of the reproductive bud transition in gymnosperms. In addition, these studies on hormone-mediated sugar pathways increase our understanding of the relationship between sugar and hormone signaling during female and male bud initiation in Metasequoia. PMID:26157452

Transcriptome and proteome exploration to provide a resource for the study of Agrocybe aegerita.

PubMed

Wang, Man; Gu, Bianli; Huang, Jie; Jiang, Shuai; Chen, Yijie; Yin, Yalin; Pan, Yongfu; Yu, Guojun; Li, Yamu; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

2013-01-01

Agrocybe aegerita, the black poplar mushroom, has been highly valued as a functional food for its medicinal and nutritional benefits. Several bioactive extracts from A. aegerita have been found to exhibit antitumor and antioxidant activities. However, limited genetic resources for A. aegerita have hindered exploration of this species. To facilitate the research on A. aegerita, we established a deep survey of the transcriptome and proteome of this mushroom. We applied high-throughput sequencing technology (Illumina) to sequence A. aegerita transcriptomes from mycelium and fruiting body. The raw clean reads were de novo assembled into a total of 36,134 expressed sequences tags (ESTs) with an average length of 663 bp. These ESTs were annotated and classified according to Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Gene expression profile analysis showed that 18,474 ESTs were differentially expressed, with 10,131 up-regulated in mycelium and 8,343 up-regulated in fruiting body. Putative genes involved in polysaccharide and steroid biosynthesis were identified from A. aegerita transcriptome, and these genes were differentially expressed at the two stages of A. aegerita. Based on one-dimensional gel electrophoresis (1-DGE) coupled with electrospray ionization liquid chromatography tandem MS (LC-ESI-MS/MS), we identified a total of 309 non-redundant proteins. And many metabolic enzymes involved in glycolysis were identified in the protein database. This is the first study on transcriptome and proteome analyses of A. aegerita. The data in this study serve as a resource of A. aegerita transcripts and proteins, and offer clues to the applications of this mushroom in nutrition, pharmacy and industry.

De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers.

PubMed

Xanthopoulou, Aliki; Ganopoulos, Ioannis; Psomopoulos, Fotis; Manioudaki, Maria; Moysiadis, Theodoros; Kapazoglou, Aliki; Osathanunkul, Maslin; Michailidou, Sofia; Kalivas, Apostolos; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

2017-07-30

The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits. Copyright © 2017. Published by Elsevier B.V.

Proteomic identification of processes and pathways characteristic of osmoregulatory tissues in spiny dogfish shark (Squalus acanthias).

PubMed

Lee, Jinoo; Valkova, Nelly; White, Mark P; Kültz, Dietmar

2006-09-01

We used dogfish shark (Squalus acanthias) as a model for proteome analysis of six different tissues to evaluate tissue-specific protein expression on a global scale and to deduce specific functions and the relatedness of multiple tissues from their proteomes. Proteomes of heart, brain, kidney, intestine, gill, and rectal gland were separated by two-dimensional gel electrophoresis (2DGE), gel images were matched using Delta 2D software and then evaluated for tissue-specific proteins. Sixty-one proteins (4%) were found to be in only a single type of tissue and 535 proteins (36%) were equally abundant in all six tissues. Relatedness between tissues was assessed based on tissue-specific expression patterns of all 1465 consistently resolved protein spots. This analysis revealed that tissues with osmoregulatory function (kidney, intestine, gill, rectal gland) were more similar in their overall proteomes than non-osmoregulatory tissues (heart, brain). Sixty-one proteins were identified by MALDI-TOF/TOF mass spectrometry and biological functions characteristic of osmoregulatory tissues were derived from gene ontology and molecular pathway analysis. Our data demonstrate that the molecular machinery for energy and urea metabolism and the Rho-GTPase/cytoskeleton pathway are enriched in osmoregulatory tissues of sharks. Our work provides a strong rationale for further study of the contribution of these mechanisms to the osmoregulation of marine sharks.

Digital Gene Expression Analysis Provides Insight into the Transcript Profile of the Genes Involved in Aporphine Alkaloid Biosynthesis in Lotus (Nelumbo nucifera)

PubMed Central

Yang, Mei; Zhu, Lingping; Li, Ling; Li, Juanjuan; Xu, Liming; Feng, Ji; Liu, Yanling

2017-01-01

The predominant alkaloids in lotus leaves are aporphine alkaloids. These are the most important active components and have many pharmacological properties, but little is known about their biosynthesis. We used digital gene expression (DGE) technology to identify differentially-expressed genes (DEGs) between two lotus cultivars with different alkaloid contents at four leaf development stages. We also predicted potential genes involved in aporphine alkaloid biosynthesis by weighted gene co-expression network analysis (WGCNA). Approximately 335 billion nucleotides were generated; and 94% of which were aligned against the reference genome. Of 22 thousand expressed genes, 19,000 were differentially expressed between the two cultivars at the four stages. Gene Ontology (GO) enrichment analysis revealed that catalytic activity and oxidoreductase activity were enriched significantly in most pairwise comparisons. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, dozens of DEGs were assigned to the categories of biosynthesis of secondary metabolites, isoquinoline alkaloid biosynthesis, and flavonoid biosynthesis. The genes encoding norcoclaurine synthase (NCS), norcoclaurine 6-O-methyltransferase (6OMT), coclaurine N-methyltransferase (CNMT), N-methylcoclaurine 3′-hydroxylase (NMCH), and 3′-hydroxy-N-methylcoclaurine 4′-O-methyltransferase (4′OMT) in the common pathways of benzylisoquinoline alkaloid biosynthesis and the ones encoding corytuberine synthase (CTS) in aporphine alkaloid biosynthetic pathway, which have been characterized in other plants, were identified in lotus. These genes had positive effects on alkaloid content, albeit with phenotypic lag. The WGCNA of DEGs revealed that one network module was associated with the dynamic change of alkaloid content. Eleven genes encoding proteins with methyltransferase, oxidoreductase and CYP450 activities were identified. These were surmised to be genes involved in aporphine alkaloid biosynthesis. This transcriptomic database provides new directions for future studies on clarifying the aporphine alkaloid pathway. PMID:28197160

How different is the proteome of the extended spectrum β-lactamase producing Escherichia coli strains from seagulls of the Berlengas natural reserve of Portugal?

PubMed

Monteiro, R; Hébraud, M; Chafsey, I; Poeta, P; Igrejas, G

2016-08-11

β-Lactam antibiotics like cefotaxime are the most commonly used antibacterial agents. Escherichia coli strains 5A, 10A, 12A and 23B isolated from Seagulls feces, are cefotaxime-resistant strains that produces extended-spectrum beta-lactamases. Bacterial resistance to these antibiotics occurs predominantly through structural modification on the penicillin-binding proteins and enzymatic inactivation by extended-spectrum β-lactamases. Using classical proteomic techniques (2D-GE) coupled to mass spectrometry and bioinformatics extended analysis, in this study, we report several significant differences in cytoplasmic proteins expression when the strains were submitted to antibiotic stress and when the resistant strains were compared with a non-resistant strain. A total of 79 differentially expressed spots were collected for protein identification. Significant level of expression was found in antibiotic resistant proteins like β-lactamase CTX-M-1 and TEM and also in proteins related with oxidative stress. This approach might help us understand which pathways form barriers for antibiotics, another possible new pathways involved in antibiotic resistance to devise appropriate strategies for their control already recognized by the World Health Organization and the European Commission. This study highlights the protein differences when a resistant strain is under antibiotic pressure and how different can be a sensible and resistant strain at the protein level. This survey might help us to understand the specifics barriers for antibiotics and which pathways are involved in its resistance crosswise the wildlife. Copyright © 2016 Elsevier B.V. All rights reserved.

Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing.

PubMed

Zhang, Yuhong; Wu, Hongsheng; Xie, Jiaqin; Jiang, Ruixin; Deng, Congshuang; Pang, Hong

2015-11-19

Changed temperature not only threaten agricultural production, but they also affect individual biological behavior, population and community of many insects, and consequently reduce the stability of our ecosystem. Insect's ability to respond to temperature stress evolved through a complex adaptive process, thus resulting in varied temperature tolerance among different insects. Both high and low extreme temperatures are detrimental to insect development since they constitute an important abiotic stress capable of inducing abnormal biological responses. Many studies on heat or cold tolerance of ladybirds have focused on measurements of physiological and biochemical indexes such as supercooling point, higher/lower lethal temperatures, survival rate, dry body weight, water content, and developmental duration. And studies of the molecular mechanisms of ladybird responses to heat or cold stress have focused on single genes, such as those encoding heat shock proteins, but has not been analyzed by transcriptome profiling. In this study, we report the use of Digital Gene Expression (DGE) tag profiling to gain insight into transcriptional events associated with heat- and cold-stress in C. montrouzieri. About 6 million tags (49 bp in length) were sequenced in a heat stress group, a cold stress group and a negative control group. We obtained 687 and 573 genes that showed significantly altered expression levels following heat and cold shock treatments, respectively. Analysis of the global gene expression pattern suggested that 42 enzyme-encoding genes mapped to many Gene Ontology terms are associated with insect's response to heat- and cold-stress. These results provide a global assessment of genes and molecular mechanisms involved in heat and cold tolerance.

Canonical Sectors and Evolution of Firms in the US Stock Markets

NASA Astrophysics Data System (ADS)

Hayden, Lorien; Chachra, Ricky; Alemi, Alexander; Ginsparg, Paul; Sethna, James

2015-03-01

In this work, we show how unsupervised machine learning can provide a more objective and comprehensive broad-level sector decomposition of stocks. Classification of companies into sectors of the economy is important for macroeconomic analysis, and for investments into the sector-specific financial indices and exchange traded funds (ETFs). Historically, these major industrial classification systems and financial indices have been based on expert opinion and developed manually. Our method, in contrast, produces an emergent low-dimensional structure in the space of historical stock price returns. This emergent structure automatically identifies ``canonical sectors'' in the market, and assigns every stock a participation weight into these sectors. Furthermore, by analyzing data from different periods, we show how these weights for listed firms have evolved over time. This work was partially supported by NSF Grants DMR 1312160, OCI 0926550 and DGE-1144153 (LXH).

Observation of two-dimensional Fermi surface and Dirac dispersion in the new material YbMnSb2

NASA Astrophysics Data System (ADS)

Kealhofer, Robert; Jang, Sooyoung; Griffin, Sinead; John, Caolan; Doyle, Spencer; Neaton, Jeffrey; Analytis, James G.; Denlinger, J. D.; Benavides, Katherine; Chan, Julia

We present the synthesis, crystal structure, electronic structure, and transport properties of the new material YbMnSb2. Our measurements reveal that this system is a low-carrier-density semimetal with a 2D Fermi surface arising from a 3D Dirac dispersion. This Fermi surface is consistent with the predictions of antiferromagnetic density functional theory calculations and the Fermi surface observed via angle-resolved photoemission spectroscopy. The quantitative agreement between these measurements and calculations indicates that YbMnSb2 may be a new topological semimetal in the presence of magnetic order. R. K. is supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1106400. C. J., J. G. A., and much of this work received support from the Gordon and Betty Moore Foundation Grant No. GBMF4374.

Drydocking Facilities Characteristics. Design Manual 29.3.

DTIC Science & Technology

1981-11-01

BEAM -7’ I07 PRECAST COLUMN j! ’~ FULLY RELIEVED ’ 6 EeDGE OF...SUBMARINE LONGITUDINAL SECTION (VIEW LOOKING WEST) 715𔄀" TO INNER FACE OF CAISSON INOUE SA CRANE TRACKS- PLAN VIEW COPING EL +20.0- 3’ 42’ BEAM ..f... connections west side. Chilled water ..... 6" supply and return mains, 600 gpm at 65 psi, one 6" supply and one 6" return connections west side. Low

Quantum Quench of the Sachdev-Ye-Kitaev Model

NASA Astrophysics Data System (ADS)

Steinberg, Julia; Eberlein, Andreas; Sachdev, Subir

The Sachdev-Ye-Kitaev model is a single site model containing N flavors of fermions with random infinite range interactions. It is exactly solvable in the large N limit and has an emergent reparameterization symmetry in time at low temperatures and strong coupling. This leads to many interesting properties such as locally critical behavior in correlation functions and the saturation of the chaos bound proposed .We start with the generalized Sachdev-Ye-Kitaev with quadratic and quartic interactions. This Hamiltonian has the form of a 0+1d Fermi liquid and contains long-lived quasiparticles at all values of the quadratic coupling. We quench the system into a locally critical state without quasiparticles by turning off the quadratic coupling at some initial time. We numerically study the spectral function at intermediate and long times and determine the timescale in which the system loses memory of the quasiparticles. J.S. is supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE1144152.

Restricted Euler dynamics along trajectories of small inertial particles in turbulence

NASA Astrophysics Data System (ADS)

Johnson, Perry; Meneveau, Charles

2016-11-01

The fate of small particles in turbulent flows depends strongly on the surrounding fluid's velocity gradient properties such as rotation and strain-rates. For non-inertial (fluid) particles, the Restricted Euler model provides a simple, low-dimensional dynamical system representation of Lagrangian evolution of velocity gradients in fluid turbulence, at least for short times. Here we derive a new restricted Euler dynamical system for the velocity gradient evolution of inertial particles such as solid particles in a gas or droplets and bubbles in turbulent liquid flows. The model is derived in the limit of small (sub Kolmogorov scale) particles and low Stokes number. The system exhibits interesting fixed points, stability and invariant properties. Comparisons with data from Direct Numerical Simulations show that the model predicts realistic trends such as the tendency of increased straining over rotation along heavy particle trajectories and, for light particles such as bubbles, the tendency of severely reduced self-stretching of strain-rate. Supported by a National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1232825 and by a Grant from The Gulf of Mexico Research Initiative.

Entropically Stabilized Colloidal Crystals Hold Entropy in Collective Modes

NASA Astrophysics Data System (ADS)

Antonaglia, James; van Anders, Greg; Glotzer, Sharon

Ordered structures can be stabilized by entropy if the system has more ordered microstates available than disordered ones. However, ``locating'' the entropy in an ordered system is challenging because entropic ordering is necessarily a collective effort emerging from the interactions of large numbers of particles. Yet, we can characterize these crystals using simple traditional tools, because entropically stabilized crystals exhibit collective motion and effective stiffness. For a two-dimensional system of hard hexagons, we calculate the dispersion relations of both vibrational and librational collective modes. We find the librational mode is gapped, and the gap provides an emergent, macroscopic, and density-dependent length scale. We quantify the entropic contribution of each collective mode and find that below this length scale, the dominant entropic contributions are librational, and above this length scale, vibrations dominate. This length scale diverges in the high-density limit, so entropy is found predominantly in libration near dense packing. National Science Foundation Graduate Research Fellowship Program Grant No. DGE 1256260, Advanced Research Computing at the University of Michigan, Ann Arbor, and the Simons Foundation.

Vertical Interaction in Open Software Engineering Communities

DTIC Science & Technology

2009-03-01

Program in CASOS (NSF,DGE-9972762), the Office of Naval Research under Dynamic Network Analysis program (N00014-02-1-0973, the Air Force Office of...W91WAW07C0063) for research in the area of dynamic network analysis. Additional support was provided by CASOS - the center for Computational Analysis of Social...methods across the domain. For a given project, de - velopers can choose from dozens of models, tools, platforms, and languages for specification, design

The Effect of Ambient Temperatures of Two Threatened Caribbean Coral Species: a Proteomic Study

NASA Astrophysics Data System (ADS)

Ricaurte, M.; Schizas, N. V.; Weil, E.; Ciborowski, P.; Boukli, N. M.

2016-02-01

Coral reefs are among the most valuable ecosystems on the earth. Increasing water temperatures as a consequence of global warming have been identified, as an overriding cause of coral decline (e.g. increased incidence of diseases, bleaching), and one of the regions that has been identified vulnerable to climatic changes, is the Caribbean. Laboratory experiments have shown negative effects of different temperatures in coral growth, larval and adult survival, and gene expression. In order to understand the molecular and cellular basis in the protein regulation during changes in temperature in the field, a comparative proteomic analysis associated with thermal fluctuations was made from wet and dry season of 2014. In the study, we investigated alterations in proteins of Acropora palmata and Orbicella faveolata by two-dimensional gel electrophoresis (2D-GE) followed by liquid chromatography-tandem mass spectrometry, protein identification, and confirmation at the gene expression level by qRT-PCR.Proteomes of related samples demonstrated 195 differentially expressed proteins (DEP) in A. palmata during dry season and 108 (DEP) during wet season of 2014. O. faveolata overexpressed 62 (DEP) in dry season and 190 (DEP) during wet season of 2014. All proteins had a two-fold or greater change in expression due to temperature, altering several components of the cellular stress response that include chaperones, stress proteins, antioxidant enzymes, proteases, cytoskeletal and apoptosis regulating proteins. Our results suggest that A. palmata and O. faveolata display a distinct response by expressing these key protein signatures in dry and wet season. This proteomic approach may open new avenues of research to detect potential early biomarkers involved in response to these stressors, during seasonal changes in water temperatures. The results provide insight into targets and mechanistic strategies to detect potential markers involved in response to temperature change for A. palmata and O. faveolata during seasonal changes in water temperatures.

Yin Yang-1 suppresses invasion and metastasis of pancreatic ductal adenocarcinoma by downregulating MMP10 in a MUC4/ErbB2/p38/MEF2C-dependent mechanism.

PubMed

Zhang, Jing-Jing; Zhu, Yi; Xie, Kun-Ling; Peng, Yun-Peng; Tao, Jin-Qiu; Tang, Jie; Li, Zheng; Xu, Ze-Kuan; Dai, Cun-Cai; Qian, Zhu-Yin; Jiang, Kui-Rong; Wu, Jun-Li; Gao, Wen-Tao; Du, Qing; Miao, Yi

2014-05-29

Increasing evidence indicates an important role of transcription factor Yin Yang-1 (YY1) in human tumorigenesis. However, its function in cancer remains controversial and the relevance of YY1 to pancreatic ductal adenocarcinoma (PDAC) remains to be clarified. In this study, we detected YY1 expression in clinical PDAC tissue samples and cell lines using quantitative RT-PCR, immunohistochemistry and western blotting. We also detected MUC4 and MMP10 mRNA levels in 108 PDAC samples using qRT-PCR and analyzed the correlations between YY1 and MUC4 or MMP10 expression. The role of YY1 in the proliferation, invasion and metastatic abilities of PDAC cells in vitro was studied by CCK-8 assay, cell migration and invasion assays. In vivo pancreatic tumor growth and metastasis was studied by a xenogenous subcutaneously implant model and a tail vein metastasis model. The potential mechanisms underlying YY1 mediated tumor progression in PDAC were explored by digital gene expression (DGE) sequencing, signal transduction pathways blockage experiments and luciferase assays. Statistical analysis was performed using the SPSS 15.0 software. We found that the expression of YY1 in PDACs was higher compared with their adjacent non-tumorous tissues and normal pancreas tissues. However, PDAC patients with high level overexpression of YY1 had better outcome than those with low level overexpression. YY1 expression levels were statistically negatively correlated with MMP10 expression levels, but not correlated with MUC4 expression levels. YY1 overexpression suppressed, whereas YY1 knockdown enhanced, the proliferation, invasion and metastatic properties of BXPC-3 cells, both in vitro and in vivo. YY1 suppresses invasion and metastasis of pancreatic cancer cells by downregulating MMP10 in a MUC4/ErbB2/p38/MEF2C-dependent mechanism. The present study suggested that YY1 plays a negative role, i.e. is a tumor suppressor, in PDAC, and may become a valuable diagnostic and prognostic marker of PDAC.

Essence of Excellence - Lessons from Naval Executives About Superior Performing Tactical and Readiness Staffs.

DTIC Science & Technology

1985-06-01

the organization. 21 7L III. CONSISTENCY -THE INSTRUMENT OF PERFORMANCE "Knowle -dge of our duties is the most essential part of the philosophy of life ...to accomplish them. This means remaining flex- ible under the operation of everyday crisis situ- ations. It requires focusing on what is important...as a way of life . All actions are dominated by a common vision or goal shared throughout the staff. These staffs are innovators, 15 - . t. excellent

Non-Abelian Bosonization and Fractional Quantum Hall Transitions

NASA Astrophysics Data System (ADS)

Hui, Aaron; Mulligan, Michael; Kim, Eun-Ah

A fully satisfying theoretical description for the quantum phase transition between fractional quantum Hall plateaus remains an outstanding problem. Experiments indicate scaling exponents that are not readily obtained in conventional theories. Using insights from duality, we describe a class of quantum critical effective theories that produce qualitatively realistic scaling exponents for the transition. We discuss the implications of our results for the physically-relevant interactions controlling this broad class of quantum critical behavior. Supported by National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1650441.

Sales Training for Army Recruiter Success: Sales Strategies and Skills Used by Excellent U. S. Army Recruiters

DTIC Science & Technology

1987-11-01

Army recruiters. Neurolinguistic programming (NLP) was used as the protocol for modeling performance and acquiring information on the communication...kills -Linguistic pattern~ Sales cycle, Communica tion s trategies Mode-H.R-g. Sales skills, {:( ~Expert kn0\\vlc dge1 ’ Neurolinguist ic~ Sales...describe s a program of r esearch on the communicat ion st rate - gies a nd skills use d by excellen t Army r ecrui t e rs. Information to be used to

The role of intermediate filaments in maintaining integrity and function of intestinal epithelial cells after massive bowel resection in a rat.

PubMed

Sukhotnik, I; Shahar, Y Ben; Pollak, Y; Dorfman, T; Shefer, H Kreizman; Assi, Z E; Mor-Vaknin, N; Coran, A G

2018-02-01

Intermediate filaments (IFs) are a part of the cytoskeleton that extend throughout the cytoplasm of all cells and function in the maintenance of cell-shape by bearing tension and serving as structural components of the nuclear lamina. In normal intestine, IFs provide a tissue-specific three-dimensional scaffolding with unique context-dependent organizational features. The purpose of this study was to evaluate the role of IFs during intestinal adaptation in a rat model of short bowel syndrome (SBS). Male rats were divided into two groups: Sham rats underwent bowel transection and SBS rats underwent a 75% bowel resection. Parameters of intestinal adaptation, enterocyte proliferation and apoptosis were determined 2 weeks after operation. Illumina's Digital Gene Expression (DGE) analysis was used to determine the cytoskeleton-related gene expression profiling. IF-related genes and protein expression were determined using real-time PCR, Western blotting and immunohistochemistry. Massive small bowel resection resulted in a significant increase in enterocyte proliferation and concomitant increase in cell apoptosis. From the total number of 20,000 probes, 16 cytoskeleton-related genes were investigated. Between these genes, only myosin and tubulin levels were upregulated in SBS compared to sham animals. Between IF-related genes, desmin, vimentin and lamin levels were down-regulated and keratin and neurofilament remain unchanged. The levels of TGF-β, vimentin and desmin gene and protein were down-regulated in resected rats (vs sham animals). Two weeks following massive bowel resection in rats, the accelerated cell turnover was accompanied by a stimulated microfilaments and microtubules, and by inhibited intermediate filaments. Resistance to cell compression rather that maintenance of cell-shape by bearing tension are responsible for contraction, motility and postmitotic cell separation in a late stage of intestinal adaptation.

PpYUC11, a strong candidate gene for the stony hard phenotype in peach (Prunus persica L. Batsch), participates in IAA biosynthesis during fruit ripening

PubMed Central

Pan, Lei; Zeng, Wenfang; Niu, Liang; Lu, Zhenhua; Liu, Hui; Cui, Guochao; Zhu, Yunqin; Chu, Jinfang; Li, Weiping; Fang, Weichao; Cai, Zuguo; Li, Guohuai; Wang, Zhiqiang

2015-01-01

High concentrations of indole-3-acetic acid (IAA) are required for climacteric ethylene biosynthesis to cause fruit softening in melting flesh peaches at the late ripening stage. By contrast, the fruits of stony hard peach cultivars do not soften and produce little ethylene due to the low IAA concentrations. To investigate the regulation of IAA accumulation during peach ripening [the transition from stage S3 to stage S4 III (climacteric)], a digital gene expression (DGE) analysis was performed. The expression patterns of auxin-homeostasis-related genes were compared in fruits of the melting flesh peach ‘Goldhoney 3’ and the stony hard flesh peach ‘Yumyeong’ during the ripening stage. It is revealed here that a YUCCA flavin mono-oxygenase gene (PpYUC11, ppa008176m), a key gene in auxin biosynthesis, displayed an identical differential expression profile to the profiles of IAA accumulation and PpACS1 transcription: the mRNA transcripts increased at the late ripening stage in melting flesh peaches but were below the limit of detection in mature fruits of stony hard peaches. In addition, the strong association between intron TC microsatellite genotypes of PpYUC11 and the flesh texture (normal or stony hard) is described in 43 peach varieties, indicating that this locus may be responsible for the stony hard phenotype in peach. These findings support the hypothesis that PpYUC11 may play an essential role in auxin biosynthesis during peach fruit ripening and is a candidate gene for the control of the stony hard phenotype in peach. PMID:26307136

Abundance of Plasma Antioxidant Proteins Confers Tolerance to Acute Hypobaric Hypoxia Exposure

PubMed Central

Padhy, Gayatri; Sethy, Niroj Kumar; Ganju, Lilly

2013-01-01

Abstract Padhy, Gayatri, Niroj Kumar Sethy, Lilly Ganju, and Kalpana Bhargava. Abundance of plasma antioxidant proteins confers tolerance to acute hypobaric hypoxia exposure. High Alt Med Biol 14:289–297, 2013—Systematic identification of molecular signatures for hypobaric hypoxia can aid in better understanding of human adaptation to high altitude. In an attempt to identify proteins promoting hypoxia tolerance during acute exposure to high altitude, we screened and identified hypoxia tolerant and susceptible rats based on hyperventilation time to a simulated altitude of 32,000 ft (9754 m). The hypoxia tolerance was further validated by estimating 8-isoprotane levels and protein carbonyls, which revealed that hypoxia tolerant rats possessed significant lower plasma levels as compared to susceptible rats. We used a comparative plasma proteome profiling approach using 2-dimensional gel electrophoresis (2-DGE) combined with MALDI TOF/TOF for both groups, along with an hypoxic control group. This resulted in the identification of 19 differentially expressed proteins. Seven proteins (TTR, GPx-3, PON1, Rab-3D, CLC11, CRP, and Hp) were upregulated in hypoxia tolerant rats, while apolipoprotein A-I (APOA1) was upregulated in hypoxia susceptible rats. We further confirmed the consistent higher expression levels of three antioxidant proteins (PON1, TTR, and GPx-3) in hypoxia-tolerant animals using ELISA and immunoblotting. Collectively, these proteomics-based results highlight the role of antioxidant enzymes in conferring hypoxia tolerance during acute hypobaric hypoxia. The expression of these antioxidant enzymes could be used as putative biomarkers for screening altitude adaptation as well as aiding in better management of altered oxygen pathophysiologies. PMID:24067188

Anomalous B-field Dependence of Spin-flip Time in High Purity InP

NASA Astrophysics Data System (ADS)

Linpeng, Xiayu; Karin, Todd; Barbour, Russell; Glazov, Mikhail; Fu, Kai-Mei

2015-03-01

We observe an anomalous B-field dependence of the spin-flip time (T1) of electrons bound to shallow donors which cannot be explained by current spin-relaxation theories. We conduct resonant pump-probe measurements in high-purity InP from the low to high magnetic field regimes, with a maximum T1 (400 μs) observed near the turning point gμB B ~=kB T . At low B, the T1 dependence on B is consistent with an electron correlation time (τc) in the tens of nanoseconds. The physical mechanism for the short τc in this high-purity sample (n ~= 2 ×1014 cm-3) is unclear, but a strong temperature (T) dependence indicates T1 can be further increased by lowering T below the 1.5 K experimental temperature. At high B, a B-3 dependence is observed, in contrast to the expected B-5 predicted by single-phonon spin-orbit mediated interactions. An understanding of the anomalous B-field dependence is expected to elucidate the effect of electron transport (low-field) and phonons (high-field) on T1 for shallow donors, which is of interest for both ensemble and single-spin quantum information applications. This material is based upon work supported by the National Science Foundation under Grant No. 1150647, DGE-0718124 and DGE-1256082. InP samples were graciously provided by Simon Watkins at Simon Fraser University.

Early oral feeding after pancreatoduodenectomy enhances recovery without increasing morbidity

PubMed Central

Gerritsen, Arja; Wennink, Roos A W; Besselink, Marc G H; van Santvoort, Hjalmar C; Tseng, Dorine S J; Steenhagen, Elles; Borel Rinkes, Inne H M; Molenaar, I Quintus

2014-01-01

Objective The aim of this study was to evaluate whether a change in the routine feeding strategy applied after pancreatoduodenectomy (PD) from nasojejunal tube (NJT) feeding to early oral feeding improved clinical outcomes. Methods An observational cohort study was performed in 102 consecutive patients undergoing PD. In period 1 (n = 51, historical controls), the routine postoperative feeding strategy was NJT feeding. This was changed to a protocol of early oral feeding with on-demand NJT feeding in period 2 (n = 51, consecutive prospective cohort). The primary outcome was time to resumption of adequate oral intake. Results The baseline characteristics of study subjects in both periods were comparable. In period 1, 98% (n = 50) of patients received NJT feeding, whereas in period 2, 53% (n = 27) of patients did so [for delayed gastric empting (DGE) (n = 20) or preoperative malnutrition (n = 7)]. The time to resumption of adequate oral intake significantly decreased from 12 days in period 1 to 9 days in period 2 (P = 0.015), and the length of hospital stay shortened from 18 days in period 1 to 13 days in period 2 (P = 0.015). Overall, there were no differences in the incidences of complications of Clavien–Dindo Grade III or higher, DGE, pancreatic fistula, postoperative haemorrhage and mortality between the two periods. Conclusions The introduction of an early oral feeding strategy after PD reduced the time to resumption of adequate oral intake and length of hospital stay without negatively impacting postoperative morbidity. PMID:24308458

An effective placental cotyledons proteins extraction method for 2D gel electrophoresis.

PubMed

Tan, Niu J; Daim, Leona D J; Jamil, Amilia A M; Mohtarrudin, Norhafizah; Thilakavathy, Karuppiah

2017-03-01

Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Does Stereotype Threat Affect Post-Course Scores on the Astronomy Diagnostic Test?

NASA Astrophysics Data System (ADS)

Deming, G. L.; Hufnagel, B.; Landato, J. M.; Hodari, A. K.

2003-12-01

During the 1990s, Claude Steele and others demonstrated that women mathematics students under-performed while men over-performed on selected GRE questions when told that the exam could differentiate by gender. Stereotype threat is triggered for these women when they fear someone else may negatively stereotype them, and therefore, their performance is affected. In a limited study involving 229 students, we investigated the effect of stereotype threat on performance on the Astronomy Diagnostic Test (ADT). The ADT was administered as a pre-test in four introductory astronomy classes intended for non-science majors. The same professors taught pairs of classes at the University of Maryland, a large research institution, and W. R. Harper College, a small liberal arts school. The classes were treated the same until the final day before the post-course ADT was given. One "threatened" class at each campus was told that gender mattered so they should be sure to include it on the ADT. The "control" classes were told that gender does not matter. The results show no stereotype threat effect on the women in these introductory classes. The university men did slightly over-perform at low statistical significance. As Steele suggested, students must identify with a subject in order to strongly invoke a stereotype threat. This research was supported in part by the National Science Foundation through grants REC-0089239 to GLD, DGE-97014489 to BH, and DGE-9714452 for AKH.

Meeting the nutritional requirements of hospitalized patients: an interdisciplinary approach to hospital catering.

PubMed

Iff, S; Leuenberger, M; Rösch, S; Knecht, G; Tanner, B; Stanga, Z

2008-12-01

The study served to assure the quality of our catering, to locate problems, and to define further optimization measures at the Bern University Hospital. The main objective was to investigate whether the macronutrient and energy content of the hospital food complies with the nutritional value calculated from recipes as well as with the recommendations issued by the German Nutrition Society (DGE). Prospective, randomized, single-center quality study. Complete standard meals were analyzed over seven consecutive days for each seasonal menu plan in one year. The quantitative and qualitative chemical content of a randomly chosen menu was determined by an external laboratory. Sixty meals were analyzed. The amount of food served and the ratio of macronutrients contained in the food satisfactorily reflected all recipes. Not surprisingly, the energy and carbohydrate content of our meals was lower than in the German recommendations, because the report of the DGE is based on the sum of meals, snacks and beverages consumed over the whole day and not only on the main meals, as we analyzed. Periodic quality control is essential in order to meet recommendations and patients' expectations in hospital catering. Members of the catering service should undergo regularly repeated skills training, and continuous efforts should be made to ensure portion size for all delivered meals. Food provision in the hospital setting needs to be tailored to meet the demands of the different patient groups, to optimize nutritional support, and to minimize food waste.

Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus

PubMed Central

2013-01-01

Background The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants. Results In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data. Conclusions A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic traits in NR1 line. Further study of the unknown tags which were specifically expressed in Fer will help to explore desirable agronomic traits from wild species. PMID:23324545

Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus.

PubMed

Yan, Xiaohong; Dong, Caihua; Yu, Jingyin; Liu, Wanghui; Jiang, Chenghong; Liu, Jia; Hu, Qiong; Fang, Xiaoping; Wei, Wenhui

2013-01-16

The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants. In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data. A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic traits in NR1 line. Further study of the unknown tags which were specifically expressed in Fer will help to explore desirable agronomic traits from wild species.

Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq.

PubMed

Shen, Yan Hong; Lu, Bing Guo; Feng, Li; Yang, Fei Ying; Geng, Jiao Jiao; Ming, Ray; Chen, Xiao Jing

2017-08-31

Since papaya is a typical climacteric fruit, exogenous ethylene (ETH) applications can induce premature and quicker ripening, while 1-methylcyclopropene (1-MCP) slows down the ripening processes. Differential gene expression in ETH or 1-MCP-treated papaya fruits accounts for the ripening processes. To isolate the key ripening-related genes and better understand fruit ripening mechanisms, transcriptomes of ETH or 1-MCP-treated, and non-treated (Control Group, CG) papaya fruits were sequenced using Illumina Hiseq2500. A total of 18,648 (1-MCP), 19,093 (CG), and 15,321 (ETH) genes were detected, with the genes detected in the ETH-treatment being the least. This suggests that ETH may inhibit the expression of some genes. Based on the differential gene expression (DGE) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, 53 fruit ripening-related genes were selected: 20 cell wall-related genes, 18 chlorophyll and carotenoid metabolism-related genes, four proteinases and their inhibitors, six plant hormone signal transduction pathway genes, four transcription factors, and one senescence-associated gene. Reverse transcription quantitative PCR (RT-qPCR) analyses confirmed the results of RNA-seq and verified that the expression pattern of six genes is consistent with the fruit senescence process. Based on the expression profiling of genes in carbohydrate metabolic process, chlorophyll metabolism pathway, and carotenoid metabolism pathway, the mechanism of pulp softening and coloration of papaya was deduced and discussed. We illustrate that papaya fruit softening is a complex process with significant cell wall hydrolases, such as pectinases, cellulases, and hemicellulases involved in the process. Exogenous ethylene accelerates the coloration of papaya changing from green to yellow. This is likely due to the inhibition of chlorophyll biosynthesis and the α-branch of carotenoid metabolism. Chy-b may play an important role in the yellow color of papaya fruit. Comparing the differential gene expression in ETH/1-MCP-treated papaya using RNA-seq is a sound approach to isolate ripening-related genes. The results of this study can improve our understanding of papaya fruit ripening molecular mechanism and reveal candidate fruit ripening-related genes for further research.

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba).

PubMed

Rahi, Md Lifat; Amin, Shorash; Mather, Peter B; Hurwood, David A

2017-01-01

The endemic Australian freshwater prawn, Macrobrachium koombooloomba , provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200-18,050 bp) with an N50 value of 1597. In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba . Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobrachium prawns and other crustaceans more broadly.

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba)

PubMed Central

Amin, Shorash; Mather, Peter B.; Hurwood, David A.

2017-01-01

Background The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. Methods The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597. Results In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. Discussion The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobrachium prawns and other crustaceans more broadly. PMID:28194319

Transcriptome profiling of the floral buds and discovery of genes related to sex-differentiation in the dioecious cucurbit Coccinia grandis (L.) Voigt.

PubMed

Mohanty, Jatindra Nath; Nayak, Sanghamitra; Jha, Sumita; Joshi, Raj Kumar

2017-08-30

Dioecious species offer an inclusive structure to study the molecular basis of sexual dimorphism in angiosperms. Despite having a small genome and heteromorphic sex chromosomes, Coccinia grandis is a highly neglected dioecious species with little information available on its physical state, genetic orientation and key sex-defining elements. In the present study, we performed RNA-Seq and DGE analysis of male (MB) and female (FB) buds in C. grandis to gain insights into the molecular basis of sex determination in this plant. De novo assembly of 75 million clean reads resulted in 72,479 unigenes for male library and 63,308 unigenes for female library with a mean length of 736bp. 61,458 (85.57%) unigenes displayed significant similarity with protein sequences from publicly available databases. Comparative transcriptome analyses revealed 1410 unigenes as differentially expressed (DEGs) between MB and FB samples. A consistent correlation between the expression levels of DEGs was observed for the RNA-Seq pattern and qRT-PCR validation. Functional annotation showed high enrichment of DEGs involved in phytohormone biosynthesis, hormone signaling and transduction, transcriptional regulation and methyltransferase activity. High induction of hormone responsive genes such as ARF6, ACC synthase1, SNRK2 and BRI1-associated receptor kinase 1 (BAK1) suggest that multiple phytohormones and their signaling crosstalk play crucial role in sex determination in this species. Beside, the transcription factors such as zinc fingers, homeodomain leucine zippers and MYBs were identified as major determinants of male specific expression. Moreover, the detection of multiple DEGs as the miRNA target site implies that a small RNA mediated gene silencing cascade may also be regulating gender differentiation in C. grandis. Overall, the present transcriptome resources provide us a large number of DEGs involved in sex expression and could form the groundwork for unravelling the molecular mechanism of sex determination in C. grandis. Copyright © 2017 Elsevier B.V. All rights reserved.

Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis)

PubMed Central

Zheng, Chao; Zhao, Lei; Wang, Yu; Shen, Jiazhi; Zhang, Yinfei; Jia, Sisi; Li, Yusheng; Ding, Zhaotang

2015-01-01

Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology. PMID:25901577

Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).

PubMed

Zheng, Chao; Zhao, Lei; Wang, Yu; Shen, Jiazhi; Zhang, Yinfei; Jia, Sisi; Li, Yusheng; Ding, Zhaotang

2015-01-01

Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants' growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., 'Photosynthesis'), GO terms (e.g., 'response to karrikin') and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology.

Simultaneous, multi-wavelength flare observations of nearby low-mass stars

NASA Astrophysics Data System (ADS)

Thackeray, Beverly; Barclay, Thomas; Quintana, Elisa; Villadsen, Jacqueline; Wofford, Alia; Schlieder, Joshua; Boyd, Patricia

2018-01-01

Low-mass stars are the most common stars in the Galaxy and have been targeted in the tens-of-thousands by K2, the re-purposed Kepler mission, as they are prime targets to search for and characterize small, Earth-like planets. Understanding how these fully convective stars drive magnetic activity that manifests as stochastic, short-term brightenings, or flares, provides insight into the prospects of planetary habitability. High energy radiation and energetic particle emission associated with these stars can erode atmospheres, and impact habitability. An innovative campaign to study low mass stars through simultaneous multi-wavelength observations is currently underway with observations ongoing in the X-ray, UV, optical, and radio. I will present early results of our pilot study of the nearby M-Dwarf star Wolf 359 (CN Leo) using K2, SWIFT, and ground based radio observatories, forming a comprehensive picture of flare activity from an M-Dwarf, and discuss the potential impact of these results on exoplanets. "This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE1322106. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation."

Observations of Macroscopic Shocks in the Laboratory

NASA Astrophysics Data System (ADS)

Endrizzi, Douglass; Laufman-Wollitzer, Lauren; Clark, Mike; Olson, Joseph; Myers, Rachel; Forest, Cary; Gota, Hiroshi; WiPAL Team; Tri Alpha Energy Team

2016-10-01

A magnetized coaxial plasma gun (MCPG) built by Tri Alpha Energy has been installed on the Wisconsin Plasma Astrophysics Lab (WiPAL) vacuum vessel. The MCPG fires a dense (1018m-3) and warm (10-30 eV) compact toroid (CT) at speeds of order 100 km/s. The CT is characterized using B magnetic diagnostics, multi-tip temperature probes, Ion saturation density probes, and a fast Phantom camera. The CT is injected into vacuum field, neutral gas, and plasmas of various beta. Results and evidence for propagating shocks will be presented. This work supported the NSF GRFP under Grant No. DGE-1256259.

Final Environmental Assessment for Republic of Singapore Air Force F-15SG Beddown at Mountain Home AFB

DTIC Science & Technology

2007-03-01

aide from the government for each child of a US military family that attends school off base. In 2005, MHSD received $3,893 in impact aid for each...Oltl bas~ l>cfl>re. ~ porn .W.:V miCtar,, lodlng-dge doarlne,- tmlt\\ II’OCUrct!!Ct’l CleOs!cm 1\\a.o made -.n 1n OOI .. ult’a bravado concerning...included in the ADA (Average Daily Attendance) and reimbursed by the State ofldaho. Ifthe "Educating Today’s Students for Tomorrow’s World" child is not in

Electrochemical CO2 Reduction via Gas-Phase Catholyte

NASA Astrophysics Data System (ADS)

Carter, Brittany E.; Nesbitt, Nathan T.; D'Imperio, Luke A.; Naughton, Jeffrey R.; Courtney, Dave T.; Shepard, Steve; Burns, Michael J.; Vermaas, David A.; Smith, Wilson A.; Naughton, Michael J.

Reducing CO2 to CO through electrolysis, for the eventual conversion to hydrocarbons, provides a path towards utility-scale seasonal storage of renewable energy. Electrochemical reduction of CO2 has previously been achieved using a two chamber system. The chambers are typically separated by a semipermeable Nafion membrane, with an oxygen evolution catalyst anode on one side, a gold cathode on the other, and a solution containing CO2 on both sides. If instead, CO2 gas was in the second chamber, the reaction should yield more CO formed from CO2 at a given overpotential; this would result from the increased concentration of CO2 at the cathode surface and more facile mass transport of the CO and CO2. With liquid in one chamber and gas in the other, electrolysis is performed by integrating the cathode onto the semipermeable Nafion membrane. This membrane electrode assembly is fabricated via nanoimprint lithography (NIL), simultaneously achieving high active surface area and permeability. Challenges to the Nafion NIL process, and the performance of the system in CO2 reduction, will be presented. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. (DGE-1258923).

Confinement of active systems: trapping, swim pressure, and explosions

NASA Astrophysics Data System (ADS)

Takatori, Sho; de Dier, Raf; Vermant, Jan; Brady, John

2015-11-01

We analyze the run-and-tumble dynamics and motion of living bacteria and self-propelled Janus motors confined in an acoustic trap. Since standard optical tweezers are far too weak, we developed an acoustic trap strong enough to confine swimmers over distances large compared to the swimmers' size and run length. The external trap behaves as an ``osmotic barrier'' that confines the swimmers inside the trapping region, analogous to semipermeable membranes that confine passive Brownian particles inside a boundary. From the swimmers' restricted motion inside the trap, we calculate the unique swim pressure generated by active systems originating from the force required to confine them by boundaries. We apply a strong trap to collect the swimmers into a close-packed active crystal and then turn off the trap which causes the crystal to ``explode'' due to an imbalance of the active pressure. We corroborate all experimental results with Brownian dynamics simulations and analytical theory. ST is supported by a Gates Millennium Scholars fellowship and a NSF Fellowship No. DGE-1144469. RDD is supported by a doctoral fellowship of the fund for scientific research (FWO-Vlaanderen). This work is also supported by NSF Grant CBET 1437570.

Comparative transcriptome profiling of Pyropia yezoensis (Ueda) M.S. Hwang & H.G. Choi in response to temperature stresses.

PubMed

Sun, Peipei; Mao, Yunxiang; Li, Guiyang; Cao, Min; Kong, Fanna; Wang, Li; Bi, Guiqi

2015-06-17

Pyropia yezoensis is a model organism often used to investigate the mechanisms underlying stress tolerance in intertidal zones. The digital gene expression (DGE) approach was used to characterize a genome-wide comparative analysis of differentially expressed genes (DEGs) that influence the physiological, developmental or biochemical processes in samples subjected to 4 treatments: high-temperature stress (HT), chilling stress (CS), freezing stress (FS) and normal temperature (NT). Equal amounts of total RNAs collected from 8 samples (two biological replicates per treatment) were sequenced using the Illumina/Solexa platform. Compared with NT, a total of 2202, 1334 and 592 differentially expressed unigenes were detected in HT, CS and FS respectively. Clustering analysis suggested P. yezoensis acclimates to low and high-temperature stress condition using different mechanisms: In heat stress, the unigenes related to replication and repair of DNA and protein processing in endoplasmic reticulum were active; however at low temperature stresses, unigenes related to carbohydrate metabolism and energy metabolism were active. Analysis of gene differential expression showed that four categories of DEGs functioning as temperature sensors were found, including heat shock proteins, H2A, histone deacetylase complex and transcription factors. Heat stress caused chloroplast genes down-regulated and unigenes encoding metacaspases up-regulated, which is an important regulator of PCD. Cold stress caused an increase in the expression of FAD to improve the proportion of polyunsaturated fatty acids. An up-regulated unigene encoding farnesyl pyrophosphate synthase was found in cold stress, indicating that the plant hormone ABA also played an important role in responding to temperature stress in P. yezoensis. The variation of amount of unigenes and different gene expression pattern under different temperature stresses indicated the complicated and diverse regulation mechanism in response to temperature stress in P. yezoensis. Several common metabolism pathways were found both in P. yezoensis and in higher plants, such as FAD in low-temperature stress and HSP in heat stress. Meanwhile, many chloroplast genes and unigene related to the synthesis of abscisic acid were detected, revealing its unique temperature-regulation mechanism in this intertidal species. This sequencing dataset and analysis may serve as a valuable resource to study the mechanisms involved in abiotic stress tolerance in intertidal seaweeds.

Perioperative Hydrocortisone Reduces Major Complications After Pancreaticoduodenectomy: A Randomized Controlled Trial.

PubMed

Laaninen, Matias; Sand, Juhani; Nordback, Isto; Vasama, Kaija; Laukkarinen, Johanna

2016-11-01

The aim of this study was to study whether post-pancreaticoduodenectomy complications (PPDC) in high-risk patients can be reduced with hydrocortisone. Soft pancreas is a well-known risk factor for PPDC. Previously, we have shown that patients with >40% acini in the pancreatic transection line are most prone to PPDC. Recent studies have demonstrated that surgical trauma leads to inflammation of the pancreatic remnant, which precedes PPDC. On the basis of power analysis, randomized controlled trial (RCT) (Clinicaltrials.gov NCT01460615), 155 patients (February 2011-May 2015) scheduled for pancreaticoduodenectomy were randomized to intravenous (i.v.) treatment with hydrocortisone 100 mg or placebo. All patients received the first dose at the induction of anesthesia. During the operation, the percentage of acini was calculated from pancreatic transection line frozen samples by a pathologist. As planned, only the high-risk patients with >40% acini (n = 62) continued in the study to receive in total 8 doses of randomization-based hydrocortisone/placebo every 8 hours. Primary endpoints were urine trypsinogen positive days and overall complications (Clavien-Dindo III-IV). Postoperative pancreatic fistulas (POPFs), postpancreatectomy hemorrhage (PPH), and delayed gastric emptying (DGE) were also graded. Hydrocortisone treatment did not alter trypsinogen release (2 or more positive days 46% vs 50%), but it significantly reduced overall complications compared with placebo in the high-risk patients (18% vs 41%; P < 0.05; Clavien-Dindo III-IV). Also, clinically significant POPF (11% vs 27%), PPH (14% vs 24%), and DGE (29% vs 44%) tended to be lower in the hydrocortisone group. Ninety-day mortality was zero. This RCT shows that in high-risk patients, overall PPDC can be significantly reduced with hydrocortisone treatment. Inflammation may be an important mediator of PPDC.

The spectrum of isotropic diffuse gamma-ray emission between 100 MeV and 820 GeV

DOE PAGES

Ackermann, M.; Ajello, M.; Albert, A.; ...

2015-01-19

We present that the γ-ray sky can be decomposed into individually detected sources, diffuse emission attributed to the interactions of Galactic cosmic rays with gas and radiation fields, and a residual all-sky emission component commonly called the isotropic diffuse γ-ray background (IGRB). The IGRB comprises all extragalactic emissions too faint or too diffuse to be resolved in a given survey, as well as any residual Galactic foregrounds that are approximately isotropic. The first IGRB measurement with the Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope (Fermi) used 10 months of sky-survey data and considered an energy rangemore » between 200 MeV and 100 GeV. Improvements in event selection and characterization of cosmic-ray backgrounds, better understanding of the diffuse Galactic emission (DGE), and a longer data accumulation of 50 months allow for a refinement and extension of the IGRB measurement with the LAT, now covering the energy range from 100 MeV to 820 GeV. The IGRB spectrum shows a significant high-energy cutoff feature and can be well described over nearly four decades in energy by a power law with exponential cutoff having a spectral index of 2.32 ± 0.02 and a break energy of (279 ± 52) GeV using our baseline DGE model. In conclusion, the total intensity attributed to the IGRB is (7.2 ± 0.6) × 10 –6 cm –2 s –1 sr –1 above 100 MeV, with an additional +15%/–30% systematic uncertainty due to the Galactic diffuse foregrounds.« less

Natronobiforma cellulositropha gen. nov., sp. nov., a novel haloalkaliphilic member of the family Natrialbaceae (class Halobacteria) from hypersaline alkaline lakes.

PubMed

Sorokin, Dimitry Y; Khijniak, Tatiana V; Kostrikina, Nadezhda A; Elcheninov, Alexander G; Toshchakov, Stepan V; Bale, Nicole J; Damsté, Jaap S Sinninghe; Kublanov, Ilya V

2018-04-27

Six strains of extremely halophilic and alkaliphilic euryarchaea were enriched and isolated in pure culture from surface brines and sediments of hypersaline alkaline lakes in various geographical locations with various forms of insoluble cellulose as growth substrate. The cells are mostly flat motile rods with a thin monolayer cell wall while growing on cellobiose. In contrast, the cells growing with cellulose are mostly nonmotile cocci covered with a thick external EPS layer. The isolates, designated AArcel, are obligate aerobic heterotrophs with a narrow substrate spectrum. All strains can use insoluble celluloses, cellobiose, a few soluble glucans and xylan as their carbon and energy source. They are extreme halophiles, growing within the range from 2.5 to 4.8M total Na + (optimum at 4M) and obligate alkaliphiles, with the pH range for growth from 7.5 to 9.9 (optimum at 8.5-9). The core archaeal lipids of strain AArcel5 T were dominated by C 20 -C 20 dialkyl glycerol ether (DGE) (i.e. archaeol) and C 20 -C 25 DGE in nearly equal proportion. The 16S rRNA gene analysis indicated that all six isolates belong to a single genomic species mostly related to the genera Saliphagus-Natribaculum-Halovarius. Taking together a substantial phenotypic difference of the new isolates from the closest relatives and the phylogenetic distance, it is concluded that the AArcel group represents a novel genus-level branch within the family Natrialbaceae for which the name Natronobiforma cellulositropha gen. nov., sp. nov. is proposed with AArcel5 T as the type strain (JCM 31939 T =UNIQEM U972 T ). Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.

Tips and tricks of the surgical technique for borderline resectable pancreatic cancer: mesenteric approach and modified distal pancreatectomy with en-bloc celiac axis resection.

PubMed

Hirono, Seiko; Yamaue, Hiroki

2015-02-01

Borderline resectable (BR) pancreatic cancer involves the portal vein and/or superior mesenteric vein (PV/SMV), major arteries including the superior mesenteric artery (SMA) or common hepatic artery (CHA), and sometimes includes the involvement of the celiac axis. We herein describe tips and tricks for a surgical technique with video assistance, which may increase the R0 rates and decrease the mortality and morbidity for BR pancreatic cancer patients. First, we describe the techniques used for the "artery-first" approach for BR pancreatic cancer with involvement of the PV/SMV and/or SMA. Next, we describe the techniques used for distal pancreatectomy with en-bloc celiac axis resection (DP-CAR) and tips for decreasing the delayed gastric emptying (DGE) rates for advanced pancreatic body cancer. The mesenteric approach, followed by the dissection of posterior tissues of the SMV and SMA, is a feasible procedure to obtain R0 rates and decrease the mortality and morbidity, and the combination of this aggressive procedure and adjuvant chemo(radiation) therapy may improve the survival of BR pancreatic cancer patients. The DP-CAR procedure may increase the R0 rates for pancreatic cancer patients with involvement within 10 mm from the root of the splenic artery, as well as the CHA or celiac axis, and preserving the left gastric artery may lead to a decrease in the DGE rates in cases where there is more than 10 mm between the tumor edge and the root of the left gastric artery. The development of safer surgical procedures is necessary to improve the survival of BR pancreatic cancer patients. © 2014 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

THE SPECTRUM OF ISOTROPIC DIFFUSE GAMMA-RAY EMISSION BETWEEN 100 MeV AND 820 GeV

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

Ackermann, M.; Buehler, R.; Ajello, M.

2015-01-20

The γ-ray sky can be decomposed into individually detected sources, diffuse emission attributed to the interactions of Galactic cosmic rays with gas and radiation fields, and a residual all-sky emission component commonly called the isotropic diffuse γ-ray background (IGRB). The IGRB comprises all extragalactic emissions too faint or too diffuse to be resolved in a given survey, as well as any residual Galactic foregrounds that are approximately isotropic. The first IGRB measurement with the Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope (Fermi) used 10 months of sky-survey data and considered an energy range between 200 MeV and 100 GeV. Improvementsmore » in event selection and characterization of cosmic-ray backgrounds, better understanding of the diffuse Galactic emission (DGE), and a longer data accumulation of 50 months allow for a refinement and extension of the IGRB measurement with the LAT, now covering the energy range from 100 MeV to 820 GeV. The IGRB spectrum shows a significant high-energy cutoff feature and can be well described over nearly four decades in energy by a power law with exponential cutoff having a spectral index of 2.32 ± 0.02 and a break energy of (279 ± 52) GeV using our baseline DGE model. The total intensity attributed to the IGRB is (7.2 ± 0.6) × 10{sup –6} cm{sup –2} s{sup –1} sr{sup –1} above 100 MeV, with an additional +15%/–30% systematic uncertainty due to the Galactic diffuse foregrounds.« less

A proteomics strategy to discover beta-glucosidases from Aspergillus fumigatus with two-dimensional page in-gel activity assay and tandem mass spectrometry.

PubMed

Kim, Kee-Hong; Brown, Kimberly M; Harris, Paul V; Langston, James A; Cherry, Joel R

2007-12-01

Economically competitive production of ethanol from lignocellulosic biomass by enzymatic hydrolysis and fermentation is currently limited, in part, by the relatively high cost and low efficiency of the enzymes required to hydrolyze cellulose to fermentable sugars. Discovery of novel cellulases with greater activity could be a critical step in overcoming this cost barrier. beta-Glucosidase catalyzes the final step in conversion of glucose polymers to glucose. Despite the importance, only a few beta-glucosidases are commercially available, and more efficient ones are clearly needed. We developed a proteomics strategy aiming to discover beta-glucosidases present in the secreted proteome of the cellulose-degrading fungus Aspergillus fumigatus. With the use of partial or complete protein denaturing conditions, the secretory proteome was fractionated in a 2DGE format and beta-glucosidase activity was detected in the gel after infusion with a substrate analogue that fluoresces upon hydrolysis. Fluorescing spots were subjected to tryptic-digestion, and identification as beta-glucosidases was confirmed by tandem mass spectrometry. Two novel beta-glucosidases of A. fumigatus were identified by this in situ activity staining method, and the gene coding for a novel beta-glucosidase ( EAL88289 ) was cloned and heterologously expressed. The expressed beta-glucosidase showed far superior heat stability to the previously characterized beta-glucosidases of Aspergillus niger and Aspergillus oryzae. Improved heat stability is important for development of the next generation of saccharifying enzymes capable of performing fast cellulose hydrolysis reactions at elevated temperatures, thereby lowering the cost of bioethanol production. The in situ activity staining approach described here would be a useful tool for cataloguing and assessing the efficiency of beta-glucosidases in a high throughput fashion.

Sequencing and de novo analysis of the hemocytes transcriptome in Litopenaeus vannamei response to white spot syndrome virus infection.

PubMed

Xue, Shuxia; Liu, Yichen; Zhang, Yichen; Sun, Yan; Geng, Xuyun; Sun, Jinsheng

2013-01-01

White spot syndrome virus (WSSV) is a causative pathogen found in most shrimp farming areas of the world and causes large economic losses to the shrimp aquaculture. The mechanism underlying the molecular pathogenesis of the highly virulent WSSV remains unknown. To better understand the virus-host interactions at the molecular level, the transcriptome profiles in hemocytes of unchallenged and WSSV-challenged shrimp (Litopenaeus vannamei) were compared using a short-read deep sequencing method (Illumina). RNA-seq analysis generated more than 25.81 million clean pair end (PE) reads, which were assembled into 52,073 unigenes (mean size = 520 bp). Based on sequence similarity searches, 23,568 (45.3%) genes were identified, among which 6,562 and 7,822 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 14,941 (63.4%) unigenes to 240 KEGG pathways. Among all the annotated unigenes, 1,179 were associated with immune-related genes. Digital gene expression (DGE) analysis revealed that the host transcriptome profile was slightly changed in the early infection (5 hours post injection) of the virus, while large transcriptional differences were identified in the late infection (48 hpi) of WSSV. The differentially expressed genes mainly involved in pattern recognition genes and some immune response factors. The results indicated that antiviral immune mechanisms were probably involved in the recognition of pathogen-associated molecular patterns. This study provided a global survey of host gene activities against virus infection in a non-model organism, pacific white shrimp. Results can contribute to the in-depth study of candidate genes in white shrimp, and help to improve the current understanding of host-pathogen interactions.

One dimensional magneto-optical compression of a cold CaF molecular beam

NASA Astrophysics Data System (ADS)

Chae, Eunmi; Anderegg, Loic; Augenbraun, Benjamin; Ravi, Aakash; Hemmerling, Boerge; Hutzler, Nicholas; Collopy, Alejandra; Ye, Jun; Ketterle, Wolfgang; Doyle, John

2017-04-01

We demonstrate one dimensional, transverse magneto-optical compression of a cold beam of calcium monofluoride (CaF). By continually alternating the magnetic field direction and laser polarizations of the magneto-optical force (RF-MOT), a photon scattering rate of 2 π x 0.4 MHz is achieved. A 3D model for this RF-MOT, validated by agreement with data, predicts a 3D RF-MOT capture velocity for CaF of 5 m/s. This work was supported by the ARO, the CUA, and the NSF. BLA is supported by the National Science Foundation Graduate Research Fellowship under NSF Grant No. DGE1144152.

Guide to the Construction of a Simple 1500 C Test Furnace. Revision

DTIC Science & Technology

1983-01-01

A.v e ~1 ue , ’..J -3- ~h i n~,;tor , [)( 20a:p. .. ·HTr~ : 0. Grove $ :~ . r~ . ~.p ;~ir;gs ~l o . of Copies. To ~~Liond l Scrence Foundat ioo...a~-. r~. !.indley ArRese<n·ch Manuf acturi ng Company , AiRe~earOr Cas t ing Company, ?s;~, Wr st ! 90th <,treet, Torrance, CA 90S05 .~TTN : Mr...Tec hnol ogy, De par t men t of i"P to 1 I.Jrgy and Mater i a ls Science , Cambri dge, MA 02139 ATTN : Prof . R. L. Cob l e Prof. H. K. Bowen

Comparative transcriptomics and proteomics analysis of citrus fruit, to improve understanding of the effect of low temperature on maintaining fruit quality during lengthy post-harvest storage

PubMed Central

Yun, Ze; Jin, Shuai; Ding, Yuduan; Wang, Zhuang; Gao, Huijun; Pan, Zhiyong; Xu, Juan; Cheng, Yunjiang; Deng, Xiuxin

2012-01-01

Fruit quality is a very complex trait that is affected by both genetic and non-genetic factors. Generally, low temperature (LT) is used to delay fruit senescence and maintain fruit quality during post-harvest storage but the molecular mechanisms involved are poorly understood. Hirado Buntan Pummelo (HBP; Citrus grandis × C. paradis) fruit were chosen to explore the mechanisms that maintain citrus fruit quality during lengthy LT storage using transcriptome and proteome studies based on digital gene expression (DGE) profiling and two-dimensional gel electrophoresis (2-DE), respectively. Results showed that LT up-regulated stress-responsive genes, arrested signal transduction, and inhibited primary metabolism, secondary metabolism and the transportation of metabolites. Calcineurin B-like protein (CBL)–CBL-interacting protein kinase complexes might be involved in the signal transduction of LT stress, and fruit quality is likely to be regulated by sugar-mediated auxin and abscisic acid (ABA) signalling. Furthermore, ABA was specific to the regulation of citrus fruit senescence and was not involved in the LT stress response. In addition, the accumulation of limonin, nomilin, methanol, and aldehyde, together with the up-regulated heat shock proteins, COR15, and cold response-related genes, provided a comprehensive proteomics and transcriptomics view on the coordination of fruit LT stress responses. PMID:22323274

Protein interactions during flour mixing using wheat flour with altered starch.

PubMed

Wang, Xiaolong; Appels, Rudi; Zhang, Xiaoke; Diepeveen, Dean; Torok, Kitti; Tomoskozi, Sandor; Bekes, Ferenc; Ma, Wujun; Sharp, Peter; Islam, Shahidul

2017-09-15

Wheat grain proteins responses to mixing and thermal treatment were investigated using Mixolab-dough analysis systems with flour from two cultivars, Ventura-26 (normal amylose content) and Ventura-19 (reduced amylose content). Size exclusion high performance liquid chromatography (SE-HPLC) and two-dimensional gel electrophoresis (2-DGE) analysis revealed that, stress associated and metabolic proteins largely interacted with dough matrix of Ventura-26 after 26min (56°C); gliadins, avenin-like b proteins, LMW-GSs, and partial globulins showed stronger interactions within the dough matrix of Ventura-26 at 32min/C3 (80°C), thereafter, however, stronger protein interactions were observed within the dough matrix of Ventura-19 at 38min/C4 (85°C) and 43min (80°C). Thirty-seven proteins associated with changes in dough matrix due to reduced amylose content were identified by mass spectrometry and mainly annotated to the chromosome group 1, 4, and 6. The findings provide new entry points for modifying final product attributes. Copyright © 2017 Elsevier Ltd. All rights reserved.

X-ray Reflectivity Study of a Highly Rough Surface: Si Nanowires Grown by Ag Nanoparticle Etching

NASA Astrophysics Data System (ADS)

Kremenak, Jesse; Arendse, Christopher; Cummings, Franscious; Chen, Yiyao; Miceli, Paul

Vertically oriented Si nanowires (SiNWs) formed by Ag-assisted wet chemical etching of a Si(100) substrate was studied by X-ray reflectivity (XRR) in combination with electron microscopy. Si(100) wafers coated with Ag nanoparticles, which serve as a catalyst, were etched for different durations in a HF/H2O2/DI-H2O solution. Because of the extreme roughness of these surfaces, there are challenges for using XRR methods in such systems. Therefore, significant attention is given to the analysis method of the XRR measurements. This sample-average information presents a valuable complement to electron microscopy studies, which focus on small sections of the sample. The present work shows-for the first time-the amount and distribution of Ag during the formation of SiNWs fabricated by Ag-assisted wet chemical etching, which is vital information for understanding the etching mechanisms. Support is gratefully acknowledged from the National Science Foundation (USA) - DGE1069091, the National Research Foundation (RSA) - TTK14052167658, 76568, 92520, and 93212; and the University of Missouri/University of Western Cape Linkage Program.

Modeling the Mitral Valve

NASA Astrophysics Data System (ADS)

Kaiser, Alexander

2016-11-01

The mitral valve is one of four valves in the human heart. The valve opens to allow oxygenated blood from the lungs to fill the left ventricle, and closes when the ventricle contracts to prevent backflow. The valve is composed of two fibrous leaflets which hang from a ring. These leaflets are supported like a parachute by a system of strings called chordae tendineae. In this talk, I will describe a new computational model of the mitral valve. To generate geometry, general information comes from classical anatomy texts and the author's dissection of porcine hearts. An MRI image of a human heart is used to locate the tips of the papillary muscles, which anchor the chordae tendineae, in relation to the mitral ring. The initial configurations of the valve leaflets and chordae tendineae are found by solving solving an equilibrium elasticity problem. The valve is then simulated in fluid (blood) using the immersed boundary method over multiple heart cycles in a model valve tester. We aim to identify features and mechanisms that influence or control valve function. Support from National Science Foundation, Graduate Research Fellowship Program, Grant DGE 1342536.

Salt stress-induced changes in antioxidative defense system and proteome profiles of salt-tolerant and sensitive Frankia strains.

PubMed

Srivastava, Amrita; Singh, Anumeha; Singh, Satya S; Mishra, Arun K

2017-04-16

An appreciation of comparative microbial survival is most easily done while evaluating their adaptive strategies during stress. In the present experiment, antioxidative and whole cell proteome variations based on spectrophotometric analysis and SDS-PAGE and 2-dimensional gel electrophoresis have been analysed among salt-tolerant and salt-sensitive Frankia strains. This is the first report of proteomic basis underlying salt tolerance in these newly isolated Frankia strains from Hippophae salicifolia D. Don. Salt-tolerant strain HsIi10 shows higher increment in the contents of superoxide dismutase, catalase and ascorbate peroxidase as compared to salt-sensitive strain HsIi8. Differential 2-DGE profile has revealed differential profiles for salt-tolerant and salt-sensitive strains. Proteomic confirmation of salt tolerance in the strains with inbuilt efficiency of thriving in nitrogen-deficient locales is a definite advantage for these microbes. This would be equally beneficial for improvement of soil nitrogen status. Efficient protein regulation in HsIi10 suggests further exploration for its potential use as biofertilizer in saline soils.

INSPIRE: Initiating New Science Partnerships in Rural Education

NASA Astrophysics Data System (ADS)

Pierce, Donna M.; McNeal, K. S.; Bruce, L. M.; Harpole, S. H.; Schmitz, D. W.

2010-10-01

INSPIRE, Initiating New Science Partnerships in Rural Education, is a partnership between Mississippi State University and three school districts in Mississippi's Golden Triangle (Starkville, Columbus, West Point). This program recruits ten graduate fellows each year from geosciences, physics, astronomy, and engineering and pairs them with a participating middle school or high school teacher. The graduate fellows provide technology-supported inquiry-based learning in the earth and space sciences by incorporating their research into classroom instruction and using multiple resources such as Google Earth, geographic information systems (GIS), Celestia, and others. In addition to strengthening the communication skills of the graduate fellows, INSPIRE will increase the content knowledge of participating teachers, provide high-quality instruction using multiple technologies, promote higher education to area high-school students, and provide fellows and teachers with international research experience through our partners in Australia, The Bahamas, England, and Poland. INSPIRE is funded by the Graduate STEM Fellows in K-12 Education Program (GK-12; Award No. DGE-0947419), which is part of the Division for Graduate Education of the National Science Foundation.

Polymerization and processing of polymers in magnetic fields

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

Benicewicz, B.C.; Smith, M.E.; Douglas, E.P.

1997-04-01

Liquid crystalline thermosets (LCT`s) have become recognized over the past few years as an important class of materials. Numerous reports from the authors laboratory and others have described their synthesis and phase behavior. In particular, the authors have described important effects due to the orientation of the rodlike molecules in a liquid crystalline phase. They have found that curing rates are enhanced compared to reaction in an isotropic phase, and that the glass transition of the fully cured material can be significantly higher than the final cure temperature. For structural applications, orientation of LCT`s will allow maximum improvement in mechanicalmore » properties. A few studies have described use of magnetic fields to orient LCT`s. However, no measurements were made of the tensile properties of materials processed in magnetic fields. The authors have conducted experiments which describe the tensile modulus dependence of an LCT over the complete range of magnetic field strengths from 0 to 18 Tesla. Their work has focused on the system composed of the diglycidyl ether of dihydroxy-{alpha}-methylstilbene (DGE-DHAMS) cured with sulfanilamide (SAA).« less

Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions

PubMed Central

2013-01-01

Background Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacted by drought stress. In the face of limited water resources, drought-responsive genes are therefore of interest. Identification and analysis of dehydration- and rehydration-inducible differentially expressed genes (DEGs) would not only aid elucidation of molecular mechanisms of stress response, but also enable improvement of crop stress tolerance via gene transfer. Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes. Results Two soybean genotypes—drought-tolerant Jindou21 and drought-sensitive Zhongdou33—were subjected to dehydration and rehydration conditions. For analysis of DEGs under dehydration conditions, 20 cDNA libraries were generated from roots and leaves at two different time points under well-watered and dehydration conditions. We also generated eight libraries for analysis under rehydration conditions. Sequencing of the 28 libraries produced 25,000–33,000 unambiguous tags, which were mapped to reference sequences for annotation of expressed genes. Many genes exhibited significant expression differences among the libraries. DEGs in the drought-tolerant genotype were identified by comparison of DEGs among treatments and genotypes. In Jindou21, 518 and 614 genes were differentially expressed under dehydration in leaves and roots, respectively, with 24 identified both in leaves and roots. The main functional categories enriched in these DEGs were metabolic process, response to stresses, plant hormone signal transduction, protein processing, and plant-pathogen interaction pathway; the associated genes primarily encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significantly expressed (|log2 ratio| ≥ 8) genes— Glyma15g03920, Glyma05g02470, Glyma15g15010, Glyma05g09070, Glyma06g35630, Glyma08g12590, and Glyma11g16000—are more likely to determine drought stress tolerance. The expression patterns of eight randomly-selected genes were confirmed by quantitative RT-PCR; the results of QRT-PCR analysis agreed with transcriptional profile data for 96 out of 128 (75%) data points. Conclusions Many soybean genes were differentially expressed between drought-tolerant and drought-sensitive genotypes. Based on GO functional annotation and pathway enrichment analysis, some of these genes encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significant DEGs are candidates for improving soybean drought tolerance. These findings will be helpful for analysis and elucidation of molecular mechanisms of drought tolerance; they also provide a basis for cultivating new varieties of drought-tolerant soybean. PMID:24093224

Controlled finite momentum pairing and spatially varying order parameter in proximitized HgTe quantum wells

NASA Astrophysics Data System (ADS)

Hart, Sean; Ren, Hechen; Kosowsky, Michael; Ben-Shach, Gilad; Leubner, Philipp; Bruene, Christoph; Buhmann, Hartmut; Molenkamp, Laurens; Halperin, Bertrand; Yacoby, Amir

Conventional s-wave superconductivity arises from singlet pairing of electrons with opposite Fermi momenta, forming Cooper pairs with zero net momentum. Recent studies have focused on coupling s-wave superconductors to systems with an unusual configuration of electronic spin and momentum at the Fermi surface, where the nature of the paired state can be modified and the system may even undergo a topological phase transition. Here we present measurements on Josephson junctions based on HgTe quantum wells coupled to aluminum or niobium superconductors, and subject to a magnetic field in the plane of the quantum well. We observe that the in-plane magnetic field modulates the Fraunhofer interference pattern, and that this modulation depends both on electron density and on the direction of the in-plane field with respect to the junction. However, the orientation of the junction with respect to the underlying crystal lattice does not impact the measurements. These findings suggest that spin-orbit coupling plays a role in the observed behavior, and that measurements of Josephson junctions in the presence of an in-plane field can elucidate the Fermi surface properties of the weak link material. NSF DMR-1206016; STC Center for Integrated Quantum Materials under NSF Grant No. DMR-1231319; NSF GRFP under Grant DGE1144152, Microsoft Corporation Project Q.

Spatially and time resolved kinetics of indirect magnetoexcitons

NASA Astrophysics Data System (ADS)

Hasling, Matthew; Dorow, Chelsey; Calman, Erica; Butov, Leonid; Wilkes, Joe; Campman, Kenneth; Gossard, Arthur

The small exciton mass and binding energy give the opportunity to realize the high magnetic field regime for excitons in magnetic fields of few Tesla achievable in lab Long lifetimes of indirect exciton give the opportunity to study kinetics of magnetoexciton transport by time-resolved optical imaging of exciton emission. We present spatially and time resolved measurements showing the effect of increased magnetic field on transport of magnetoexcitons. We observe that increased magnetic field leads to slowing down of magnetoexciton transport. Supported by NSF Grant No. 1407277. J.W. was supported by the EPSRC (Grant EP/L022990/1). C.J.D. was supported by the NSF Graduate Research Fellowship Program under Grant No. DGE-1144086.

Swimming of the Honey Bees

NASA Astrophysics Data System (ADS)

Roh, Chris; Gharib, Morteza

2016-11-01

When the weather gets hot, nursing honey bees nudge foragers to collect water for thermoregulation of their hive. While on their mission to collect water, foragers sometimes get trapped on the water surface, forced to interact with a different fluid environment. In this study, we present the survival strategy of the honey bees at the air-water interface. A high-speed videography and shadowgraph were used to record the honey bees swimming. A unique thrust mechanism through rapid vibration of their wings at 60 to 150 Hz was observed. This material is based upon work supported by the National Science Foundation under Grant No. CBET-1511414; additional support by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1144469.

Population Dynamics of Viral Inactivation

NASA Astrophysics Data System (ADS)

Freeman, Krista; Li, Dong; Behrens, Manja; Streletzky, Kiril; Olsson, Ulf; Evilevitch, Alex

We have investigated the population dynamics of viral inactivation in vitrousing time-resolved cryo electron microscopy combined with light and X-ray scattering techniques. Using bacteriophage λ as a model system for pressurized double-stranded DNA viruses, we found that virions incubated with their cell receptor eject their genome in a stochastic triggering process. The triggering of DNA ejection occurs in a non synchronized manner after the receptor addition, resulting in an exponential decay of the number of genome-filled viruses with time. We have explored the characteristic time constant of this triggering process at different temperatures, salt conditions, and packaged genome lengths. Furthermore, using the temperature dependence we determined an activation energy for DNA ejections. The dependences of the time constant and activation energy on internal DNA pressure, affected by salt conditions and encapsidated genome length, suggest that the triggering process is directly dependent on the conformational state of the encapsidated DNA. The results of this work provide insight into how the in vivo kinetics of the spread of viral infection are influenced by intra- and extra cellular environmental conditions. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1252522.

Particle sedimentation in a sheared viscoelastic fluid

NASA Astrophysics Data System (ADS)

Murch, William L.; Krishnan, Sreenath; Shaqfeh, Eric S. G.; Iaccarino, Gianluca

2017-11-01

Particle suspensions are ubiquitous in engineered processes, biological systems, and natural settings. For an engineering application - whether the intent is to suspend and transport particles (e.g., in hydraulic fracturing fluids) or allow particles to sediment (e.g., in industrial separations processes) - understanding and prediction of the particle mobility is critical. This task is often made challenging by the complex nature of the fluid phase, for example, due to fluid viscoelasticity. In this talk, we focus on a fully 3D flow problem in a viscoelastic fluid: a settling particle with a shear flow applied in the plane perpendicular to gravity (referred to as orthogonal shear). Previously, it has been shown that an orthogonal shear flow can reduce the settling rate of particles in viscoelastic fluids. Using experiments and numerical simulations across a wide range of sedimentation and shear Weissenberg number, this talk will address the underlying physical mechanism responsible for the additional drag experienced by a rigid sphere settling in a confined viscoelastic fluid with orthogonal shear. We will then explore multiple particle effects, and discuss the implications and extensions of this work for particle suspensions. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-114747 (WLM).

Investigating the Formation and Sub-Structure of Unmagnetized Collisionless Shocks

NASA Astrophysics Data System (ADS)

Endrizzi, Douglass; Egedal, J.; Forest, C.; Greess, S.; Millet-Ayala, A.; Olson, J.; Ready, A.; Waleffe, R.; Gota, H.

2017-10-01

Collisionless shocks, where the shock thickness is much smaller than the collisional mean free path, are ubiquitous astrophysical phenomena. In all shocks, the Rankine-Hugoniot jump conditions are satisfied through entropy generation at the interface; the shock propagation angle with respect to the magnetic field affects the mechanism by which this entropy is generated. Two experiments on the Big Red Ball (BRB) at UW-Madison explored the formation mechanisms of parallel and perpendicular, unmagnetized and magnetized collisionless shocks with large (1 - 3 m) system sizes. In the first experiment, a 1 m diameter theta-pinch drove a supersonic (3 < M < 4) compressive flow perpendicular to the background magnetic field. In the second, a compact toroid ([cite TriAlpha]) was fired supersonically (4 < M < 5) parallel to the background magnetic field. Triple, Langmuir, emissive, and magnetic probes were used to measure electron density, temperature, plasma potential, and fluctuations in magnetic fields. Results showing the transition from above to below MA = 1 , measurements of electron precursors, exploration of subshock structure, evidence of instabilities in the shock formation process, and future work will be presented. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE 1256259.

Dewetting of Epitaxial Silver Film on Silicon by Thermal Annealing

NASA Astrophysics Data System (ADS)

Sanders, Charlotte E.; Kellogg, Gary L.; Shih, C.-K.

2013-03-01

It has been shown that noble metals can grow epitaxially on semiconducting and insulating substrates, despite being a non-wetting system: low temperature deposition followed by room temperature annealing leads to atomically flat film morphology. However, the resulting metastable films are vulnerable to dewetting, which has limited their utility for applications under ambient conditions. The physics of this dewetting is of great interest but little explored. We report on an investigation of the dewetting of epitaxial Ag(111) films on Si(111) and (100). Low energy electron microscopy (LEEM) shows intriguing evolution in film morphology and crystallinity, even at temperatures below 100oC. On the basis of these findings, we can begin to draw compelling inferences about film-substrate interaction and the kinetics of dewetting. Financial support is from NSF, DGE-0549417 and DMR-0906025. This work was performed, in part, at the Center for Integrated Nanotechnologies, User Facility operated for the U.S. DOE Office of Science. Sandia National Lab is managed and operated by Sandia Corp., a subsidiary of Lockheed Martin Corp., for the U.S. DOE's National Nuclear Security Administration under DE-AC04-94AL85000.

Structure of jammed configurations and their relation to unjamming times

NASA Astrophysics Data System (ADS)

Birwa, Sumit Kumar; Merrigan, Carl; Chakraborty, Bulbul; Tewari, Shubha

The distribution of the times for the cessation of flow of grains falling under gravity in a vertical hopper is known to be exponential. Recent experiments have shown, however, that the time lapse between avalanches follows a power-law distribution when the hopper is unjammed using periodic vertical vibrations. The reasons for this distribution of the unjamming times, which indicates the time needed for an applied continuous perturbation to induce another avalanche, are not well understood. We report on a numerical simulation of granular hopper flow using LAMMPS in which we seek to understand the origin and scope of this behavior. We find that cessation of flow is related to the formation of a stable arch that spans the system. However, the actual structure of the jammed configuration varies and is closely related to the unjamming time. We find that the symmetry of the arches is an important parameter in determining the strength of the jammed configurations. Using different force thresholds, we have characterized the contact networks around the arches which provides stability to the packed structure and analyzed the strength of various jammed configurations. Supported by NSF Grant DMR1409093 and DGE1068620.

Stochastic Modeling of Direct Radiation Transmission in Particle-Laden Turbulent Flows

NASA Astrophysics Data System (ADS)

Banko, Andrew; Villafane, Laura; Kim, Ji Hoon; Esmaily Moghadam, Mahdi; Eaton, John K.

2017-11-01

Direct radiation transmission in turbulent flows laden with heavy particles plays a fundamental role in systems such as clouds, spray combustors, and particle-solar-receivers. Owing to their inertia, the particles preferentially concentrate and the resulting voids and clusters lead to deviations in mean transmission from the classical Beer-Lambert law for exponential extinction. Additionally, the transmission fluctuations can exceed those of Poissonian media by an order of magnitude, which implies a gross misprediction in transmission statistics if the correlations in particle positions are neglected. On the other hand, tracking millions of particles in a turbulence simulation can be prohibitively expensive. This work presents stochastic processes as computationally cheap reduced order models for the instantaneous particle number density field and radiation transmission therein. Results from the stochastic processes are compared to Monte Carlo Ray Tracing (MCRT) simulations using the particle positions obtained from the point-particle DNS of isotropic turbulence at a Taylor Reynolds number of 150. Accurate transmission statistics are predicted with respect to MCRT by matching the mean, variance, and correlation length of DNS number density fields. Funded by the U.S. Department of Energy under Grant No. DE-NA0002373-1 and the National Science Foundation under Grant No. DGE-114747.

Unconventional Electron Pairing and Topological Superconductivity in Proximitized HgTe Quantum Wells

NASA Astrophysics Data System (ADS)

Ren, Hechen; Hart, Sean; Kosowsky, Michael; Ben-Shach, Gilad; Leubner, Philipp; Brüne, Christoph; Buhmann, Hartmut; Molenkamp, Laurens; Halperin, Bertrand; Yacoby, Amir

Coupling s-wave superconductors to systems with exotic Fermi surface spin textures has been recently proposed as a way to manipulate the nature of the paired state, in some cases even leading to a topological phase transition. Recently, we studied the behavior of Fraunhofer interference in HgTe quantum well-based Josephson junctions, in the presence of a magnetic field applied in the plane of the quantum well. Here we theoretically analyze our system and compare the predicted behavior to our experimental results. We find that the in-plane magnetic field tunes the momentum of Cooper pairs in the quantum well, directly reflecting the response of the spin-dependent Fermi surfaces. This momentum tuning depends crucially on the type of spin-orbit coupling in the system. In the high electron density regime, the induced superconductivity evolves with electron density in agreement with our model based on the Hamiltonian of Bernevig, Hughes and Zhang. This agreement provides a quantitative value for g/vF, where g is the effective g-factor and vF is the Fermi velocity. Our new understanding of the interplay between spin physics and superconductivity introduces a way to spatially engineer the order parameter from singlet to triplet pairing, and in general allows investigation of electronic spin texture at the Fermi surface of materials. NSF DMR-1206016; STC Center for Integrated Quantum Materials under NSF Grant No. DMR-1231319; NSF GRFP under Grant DGE1144152, Microsoft Corporation Project Q.

Error budgeting single and two qubit gates in a superconducting qubit

NASA Astrophysics Data System (ADS)

Chen, Z.; Chiaro, B.; Dunsworth, A.; Foxen, B.; Neill, C.; Quintana, C.; Wenner, J.; Martinis, John. M.; Google Quantum Hardware Team Team

Superconducting qubits have shown promise as a platform for both error corrected quantum information processing and demonstrations of quantum supremacy. High fidelity quantum gates are crucial to achieving both of these goals, and superconducting qubits have demonstrated two qubit gates exceeding 99% fidelity. In order to improve gate fidelity further, we must understand the remaining sources of error. In this talk, I will demonstrate techniques for quantifying the contributions of control, decoherence, and leakage to gate error, for both single and two qubit gates. I will also discuss the near term outlook for achieving quantum supremacy using a gate-based approach in superconducting qubits. This work is supported Google Inc., and by the National Science Foundation Graduate Research Fellowship under Grant No. DGE 1605114.

Ecto- and endoparasite induce similar chemical and brain neurogenomic responses in the honey bee (Apis mellifera)

PubMed Central

2013-01-01

Background Exclusion from a social group is an effective way to avoid parasite transmission. This type of social removal has also been proposed as a form of collective defense, or social immunity, in eusocial insect groups. If parasitic modification of host behavior is widespread in social insects, the underlying physiological and neuronal mechanisms remain to be investigated. We studied this phenomenon in honey bees parasitized by the mite Varroa destructor or microsporidia Nosema ceranae, which make bees leave the hive precociously. We characterized the chemical, behavioral and neurogenomic changes in parasitized bees, and compared the effects of both parasites. Results Analysis of cuticular hydrocarbon (CHC) profiles by gas chromatography coupled with mass spectrophotometry (GC-MS) showed changes in honey bees parasitized by either Nosema ceranae or Varroa destructor after 5 days of infestation. Levels of 10-HDA, an antiseptic important for social immunity, did not change in response to parasitism. Behavioral analysis of N. ceranae- or V. destructor- parasitized bees revealed no significant differences in their behavioral acts or social interactions with nestmates. Digital gene expression (DGE) analysis of parasitized honey bee brains demonstrated that, despite the difference in developmental stage at which the bee is parasitized, Nosema and Varroa-infested bees shared more gene changes with each other than with honey bee brain expression gene sets for forager or nurse castes. Conclusions Parasitism by Nosema or Varroa induces changes to both the CHC profiles on the surface of the bee and transcriptomic profiles in the brain, but within the social context of the hive, does not result in observable effects on her behavior or behavior towards her. While parasitized bees are reported to leave the hive as foragers, their brain transcription profiles suggest that their behavior is not driven by the same molecular pathways that induce foraging behavior. PMID:23866001

Aluminum Nanowire Arrays via Soft Nanoimprint Lithography

NASA Astrophysics Data System (ADS)

Naughton, Michael J.; Nesbitt, Nathan T.; Merlo, Juan M.; Rose, Aaron H.; Calm, Yitzi M.; D'Imperio, Luke A.; Courtney, Dave T.; Shepard, Steve; Kempa, Krzysztof; Burns, Michael J.

We have previously reported a method to fabricate freestanding, vertically-oriented, and lithographically-ordered Al nanowire arrays via directed assembly, and demonstrated their utility as a plasmonic waveguide. However, the process, a variation on the preparation of anodized aluminum oxide (AAO), involved imprinting Al with a hard stamp, which wore down the stamp and had a low yield of Al NWs. Here we show a new nanoimprint lithography (NIL) technique that uses a soft stamp to pattern a mask on the Al; it provides a greater yield of Al NWs and is less destructive to the stamp, providing a path to applications that require NW arrays over macroscopic areas. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. (DGE-1258923).

Towards NV-based magnetic sensing in the time domain

NASA Astrophysics Data System (ADS)

Urbach, Elana; Sumarac, Tamara; Lovchinsky, Igor; Landig, Renate; Sanchez-Yamagishi, Javier; Andersen, Trond; Park, Hongkun; Lukin, Mikhail

2017-04-01

The study of protein folding dynamics is an outstanding problem in the biological sciences. We show that nitrogen-vacancy (NV) centers in diamond can be used to dynamically sense the conformational states of individual proteins under ambient conditions. We present preliminary data on time-domain detection of electronic spin labels which were chemically attached to the proteins, as well as label-free detection of native hydrogen nuclear spins within the protein. In addition, we discuss work towards polarizing boron-11 spins in atomically-thin hexagonal boron nitride using Hartmann-Hahn double resonance, with the ultimate goal of studying many-body spin dynamics and performing quantum simulation. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE1144152.

Very-High-Energy Solar Gamma Rays From Cosmic-Ray Interactions

NASA Astrophysics Data System (ADS)

Zhou, Bei; Ng, Kenny; Beacom, John; Peter, Annika; Rott, Cartsen

2017-01-01

Cosmic-ray induced gamma rays from the Sun has been observed up to 100 GeV. However, there are no theoretical predictions beyond 10 GeV. We provide the first calculation of the hadronic disk component in TeV-PeV, where solar magnetic fields can be ignored. We also consider the leptonic gamma-ray halo, taking into account electrons from local pulsars. With Fermi and soon HAWC & LHAASO observations, our results provide new insights on local cosmic rays, solar magnetic fields, and solar dark matter studies. BZ is supported by OSU Fowler Fellowship. KN and FB are supported by NSF Grant PHY-1404311. AK is supported by NSF GRFP Grant No. DGE-1321846. CR is supported by the Korea Neutrino Research Center. KN is also supported by the OSU Presidential Fellowship.

Proteome Analysis of the Plasma Membrane of Mycobacterium Tuberculosis

PubMed Central

Arora, Shalini; Kosalai, K.; Namane, Abdelkader; Pym, Alex S.; Cole, Stewart T.

2002-01-01

The plasma membrane of Mycobacterium tuberculosis is likely to contain proteins that could serve as novel drug targets, diagnostic probes or even components of a vaccine against tuberculosis. With this in mind, we have undertaken proteome analysis of the membrane of M. tuberculosis H37Rv. Isolated membrane vesicles were extracted with either a detergent (Triton X114) or an alkaline buffer (carbonate) following two of the protocols recommended for membrane protein enrichment. Proteins were resolved by 2D-GE using immobilized pH gradient (IPG) strips, and identified by peptide mass mapping utilizing the M. tuberculosis genome database. The two extraction procedures yielded patterns with minimal overlap. Only two proteins, both HSPs, showed a common presence. MALDI–MS analysis of 61 spots led to the identification of 32 proteins, 17 of which were new to the M. tuberculosis proteome database. We classified 19 of the identified proteins as ‘membrane-associated’; 14 of these were further classified as ‘membrane-bound’, three of which were lipoproteins. The remaining proteins included four heat-shock proteins and several enzymes involved in energy or lipid metabolism. Extraction with Triton X114 was found to be more effective than carbonate for detecting ‘putative’ M. tuberculosis membrane proteins. The protocol was also found to be suitable for comparing BCG and M. tuberculosis membranes, identifying ESAT-6 as being expressed selectively in M. tuberculosis. While this study demonstrates for the first time some of the membrane proteins of M. tuberculosis, it also underscores the problems associated with proteomic analysis of a complex membrane such as that of a mycobacterium. PMID:18629250

Transcriptome analysis of mud crab (Scylla paramamosain) gills in response to Mud crab reovirus (MCRV).

PubMed

Liu, Shanshan; Chen, Guanxing; Xu, Haidong; Zou, Weibin; Yan, Wenrui; Wang, Qianqian; Deng, Hengwei; Zhang, Heqian; Yu, Guojiao; He, Jianguo; Weng, Shaoping

2017-01-01

Mud crab (Scylla paramamosain) is an economically important marine cultured species in China's coastal area. Mud crab reovirus (MCRV) is the most important pathogen of mud crab, resulting in large economic losses in crab farming. In this paper, next-generation sequencing technology and bioinformatics analysis are used to study transcriptome differences between MCRV-infected mud crab and normal control. A total of 104.3 million clean reads were obtained, including 52.7 million and 51.6 million clean reads from MCRV-infected (CA) and controlled (HA) mud crabs respectively. 81,901, 70,059 and 67,279 unigenes were gained respectively from HA reads, CA reads and HA&CA reads. A total of 32,547 unigenes from HA&CA reads called All-Unigenes were matched to at least one database among Nr, Nt, Swiss-prot, COG, GO and KEGG databases. Among these, 13,039, 20,260 and 11,866 unigenes belonged to the 3, 258 and 25 categories of GO, KEGG pathway, and COG databases, respectively. Solexa/Illumina's DGE platform was also used, and about 13,856 differentially expressed genes (DEGs), including 4444 significantly upregulated and 9412 downregulated DEGs were detected in diseased crabs compared with the control. KEGG pathway analysis revealed that DEGs were obviously enriched in the pathways related to different diseases or infections. This transcriptome analysis provided valuable information on gene functions associated with the response to MCRV in mud crab, as well as detail information for identifying novel genes in the absence of the mud crab genome database. Copyright © 2016. Published by Elsevier Ltd.

Myofibril growth during cardiac hypertrophy is regulated through dual phosphorylation and acetylation of the actin capping protein CapZ

PubMed Central

Lin, Ying-Hsi; Warren, Chad M.; Li, Jieli; McKinsey, Timothy A.; Russell, Brenda

2016-01-01

The mechanotransduction signaling pathways initiated in heart muscle by increased mechanical loading are known to lead to long-term transcriptional changes and hypertrophy, but the rapid events for adaptation at the sarcomeric level are not fully understood. The goal of this study was to test the hypothesis that actin filament assembly during cardiomyocyte growth is regulated by post-translational modifications (PTMs) of CapZβ1. In rapidly hypertrophying neonatal rat ventricular myocytes (NRVMs) stimulated by phenylephrine (PE), two-dimensional gel electrophoresis (2DGE) of CapZβ1 revealed a shift toward more negative charge. Consistent with this, mass spectrometry identified CapZβ1 phosphorylation on serine-204 and acetylation on lysine-199, two residues which are near the actin binding surface of CapZβ1. Ectopic expression of dominant negative PKCε (dnPKCε) in NRVMs blunted the PE-induced increase in CapZ dynamics, as evidenced by the kinetic constant (Kfrap) of fluorescence recovery after photobleaching (FRAP), and concomitantly reduced phosphorylation and acetylation of CapZβ1. Furthermore, inhibition of class I histone deacetylases (HDACs) increased lysine-199 acetylation on CapZβ1, which increased Kfrap of CapZ and stimulated actin dynamics. Finally, we show that PE treatment of NRVMs results in decreased binding of HDAC3 to myofibrils, suggesting a signal-dependent mechanism for the regulation of sarcomere-associated CapZβ1 acetylation. Taken together, this dual regulation through phosphorylation and acetylation of CapZβ1 provides a novel model for the regulation of myofibril growth during cardiac hypertrophy. PMID:27185186

Substance P in Flush Tears and Schirmer Strips of Healthy Participants.

PubMed

Markoulli, Maria; Gokhale, Moneisha; You, Jingjing

2017-04-01

To determine the repeatability of the flush tear collection technique and the Schirmer strip for Substance P tear analysis. The tears of 10 healthy non-contact-lens wearers were collected via Schirmer strip and microcapillary following instillation of either 20 μL (F-20) or 60 μL (F-60) of saline. Each technique was conducted on two occasions and in a randomized order. Total protein content (TPC) and Substance P concentrations were determined. The overall protein separation profile of each type of tears was examined using one-dimensional gel electrophoresis (1DGE). Collection rates were significantly faster for the F-60 compared to F-20 (17.3 ± 6.9 μL/min and 11.9 ± 5.3 μL/min, respectively, P < .001), with an average Schirmer strip length of 1.5 ± 2.1 mm/min. The coefficient of repeatability between days and eyes was greatest for the Schirmer strip, with eyes and days being significantly different (P = .03 and P = .03, respectively) for Schirmer strip Substance P. TPC was 3.8 ± 2.6 mg/mL, 3.3 ± 1.8 mg/mL, and 3.6 ± 3.0 mg/mL for F-20, F-60, and Schirmer strip techniques, respectively, with no significant difference between techniques (P = .85). Substance P concentration was 13.1 ± 14.8 ng/mL, 9.1 ± 6.1 ng/mL, and 14.9 ± 10.6 ng/mL for F-20, F-60, and Schirmer strip tears, respectively, with no significant difference between techniques (P = .57). 1DGE profile showed similar electrophoresis patterns among F-20, F-60, and basal tears. The F-60 method allows faster collection than F-20, but the latter results in better repeatability than both the F-60 and Schirmer sampling techniques. All three techniques return the same concentrations of TPC and Substance P. This indicates that tear collection using the F-20 may be more appropriate when conducting comparative analysis, whereas the F-60 may be more appropriate when more volume is required.

Numerical Simulations of Dynamical Mass Transfer in Binaries

NASA Astrophysics Data System (ADS)

Motl, P. M.; Frank, J.; Tohline, J. E.

1999-05-01

We will present results from our ongoing research project to simulate dynamically unstable mass transfer in near contact binaries with mass ratios different from one. We employ a fully three-dimensional self-consistent field technique to generate synchronously rotating polytropic binaries. With our self-consistent field code we can create equilibrium binaries where one component is, by radius, within about 99 of filling its Roche lobe for example. These initial configurations are evolved using a three-dimensional, Eulerian hydrodynamics code. We make no assumptions about the symmetry of the subsequent flow and the entire binary system is evolved self-consistently under the influence of its own gravitational potential. For a given mass ratio and polytropic index for the binary components, mass transfer via Roche lobe overflow can be predicted to be stable or unstable through simple theoretical arguments. The validity of the approximations made in the stability calculations are tested against our numerical simulations. We acknowledge support from the U.S. National Science Foundation through grants AST-9720771, AST-9528424, and DGE-9355007. This research has been supported, in part, by grants of high-performance computing time on NPACI facilities at the San Diego Supercomputer Center, the Texas Advanced Computing Center and through the PET program of the NAVOCEANO DoD Major Shared Resource Center in Stennis, MS.

The Urine Proteome as a Biomarker of Radiation Injury: Submitted to Proteomics- Clinical Applications Special Issue: "Renal and Urinary Proteomics (Thongboonkerd)"

PubMed

Sharma, Mukut; Halligan, Brian D; Wakim, Bassam T; Savin, Virginia J; Cohen, Eric P; Moulder, John E

2008-06-18

Terrorist attacks or nuclear accidents could expose large numbers of people to ionizing radiation, and early biomarkers of radiation injury would be critical for triage, treatment and follow-up of such individuals. However, no such biomarkers have yet been proven to exist. We tested the potential of high throughput proteomics to identify protein biomarkers of radiation injury after total body X-ray irradiation in a rat model. Subtle functional changes in the kidney are suggested by an increased glomerular permeability for macromolecules measured within 24 hours after TBI. Ultrastructural changes in glomerular podocytes include partial loss of the interdigitating organization of foot processes. Analysis of urine by LC-MS/MS and 2D-GE showed significant changes in the urine proteome within 24 hours after TBI. Tissue kallikrein 1-related peptidase, cysteine proteinase inhibitor cystatin C and oxidized histidine were found to be increased while a number of proteinase inhibitors including kallikrein-binding protein and albumin were found to be decreased post-irradiation. Thus, TBI causes immediately detectable changes in renal structure and function and in the urinary protein profile. This suggests that both systemic and renal changes are induced by radiation and it may be possible to identify a set of biomarkers unique to radiation injury.

Localization Protection and Symmetry Breaking in One-dimensional Potts Chains

NASA Astrophysics Data System (ADS)

Friedman, Aaron; Vasseur, Romain; Potter, Andrew; Parameswaran, Siddharth

Recent work on the 3-state Potts and Z3 clock models has demonstrated that their ordered phases are connected by duality to a phase that hosts topologically protected parafermionic zero modes at the system's boundary. The analogy with Kitaev's example of the one-dimensional Majorana chain (similarly related by duality to the Ising model) suggests that such zero modes may also be stabilized in highly excited states by many-body localization (MBL). However, the Potts model has a non-Abelian S3 symmetry believed to be incompatible with MBL; hence any MBL state must spontaneously break this symmetry, either completely or into one of its abelian subgroups (Z2 or Z3), with the topological phase corresponding to broken Z3 symmetry. We therefore study the excited state phase structure of random three-state Potts and clock models in one dimension using exact diagonalization and real-space renormalization group techniques. We also investigate the interesting possibility of a direct excited-state transition between MBL phases that break either Z3 or Z2 symmetry, forbidden within Landau theory. NSF DGE-1321846 (AJF), NSF DMR-1455366 and President's Research Catalyst Award No. CA-15-327861 from the University of California Office of the President (SAP), LDRD Program of LBNL (RV), NSF PHY11-25915 at the KITP (AJF, RV, SAP).

The Urine Proteome as a Biomarker of Radiation Injury

PubMed Central

Sharma, Mukut; Halligan, Brian D.; Wakim, Bassam T.; Savin, Virginia J.; Cohen, Eric P.; Moulder, John E.

2009-01-01

Terrorist attacks or nuclear accidents could expose large numbers of people to ionizing radiation, and early biomarkers of radiation injury would be critical for triage, treatment and follow-up of such individuals. However, no such biomarkers have yet been proven to exist. We tested the potential of high throughput proteomics to identify protein biomarkers of radiation injury after total body X-ray irradiation in a rat model. Subtle functional changes in the kidney are suggested by an increased glomerular permeability for macromolecules measured within 24 hours after TBI. Ultrastructural changes in glomerular podocytes include partial loss of the interdigitating organization of foot processes. Analysis of urine by LC-MS/MS and 2D-GE showed significant changes in the urine proteome within 24 hours after TBI. Tissue kallikrein 1-related peptidase, cysteine proteinase inhibitor cystatin C and oxidized histidine were found to be increased while a number of proteinase inhibitors including kallikrein-binding protein and albumin were found to be decreased post-irradiation. Thus, TBI causes immediately detectable changes in renal structure and function and in the urinary protein profile. This suggests that both systemic and renal changes are induced by radiation and it may be possible to identify a set of biomarkers unique to radiation injury. PMID:19746194

Optimal Management of Water, Nutrient and Carbon Cycles of Green Urban Spaces

NASA Astrophysics Data System (ADS)

Revelli, R.; Pelak, N. F., III; Porporato, A. M.

2016-12-01

The urban ecosystem is a complex, metastable system with highly coupled flows of mass, energy, people and capital. Their sustainability is in part linked to the existence of green spaces which provide important ecosystem services, whose sustainable management requires quantification of their benefits in terms of impacts on water, carbon and energy fluxes. An exploration of problems of optimal management of such green urban spaces and the related biogeochemical fluxes is presented, extending probabilistic ecohydrological models of the soil-plant system to the urban context, where biophysical and ecological conditions tend to be radically different from the surrounding rural and natural environment (e.g. heat islands, air and water pollution, low quality soils, etc…). The coupled soil moisture, nutrient and plant dynamics are modeled to compute water requirements, carbon footprint, nutrient demand and losses, and related fluxes under different design, management and climate scenarios. The goal is to provide operative rules for a sustainable water use through focused irrigation and fertilization strategies, optimal choice of plants, soil and cultivation conditions, accounting for the typical hydroclimatic variability that occur in the urban environment. This work is part of a project that has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 701914. The work is also cofounded by USDA Agricultural Research Service cooperative agreement 58-6408-3-027; National Science Foundation (NSF) grants: EAR-1331846, EAR-1316258, and the DGE-1068871 and FESD EAR-1338694.

Comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri identifies potential genes related to triterpenoid saponin biosynthesis.

PubMed

Jeena, Gajendra Singh; Fatima, Shahnoor; Tripathi, Pragya; Upadhyay, Swati; Shukla, Rakesh Kumar

2017-06-28

Bacopa monnieri commonly known as Brahmi is utilized in Ayurveda to improve memory and many other human health benefits. Bacosides enriched standardized extract of Bacopa monnieri is being marketed as a memory enhancing agent. In spite of its well known pharmacological properties it is not much studied in terms of transcripts involved in biosynthetic pathway and its regulation that controls the secondary metabolic pathway in this plant. The aim of this study was to identify the potential transcripts and provide a framework of identified transcripts involved in bacosides production through transcriptome assembly. We performed comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri in two independent biological replicate and obtained 22.48 million and 22.0 million high quality processed reads in shoot and root respectively. After de novo assembly and quantitative assessment total 26,412 genes got annotated in root and 18,500 genes annotated in shoot sample. Quality of raw reads was determined by using SeqQC-V2.2. Assembled sequences were annotated using BLASTX against public database such as NR or UniProt. Searching against the KEGG pathway database indicated that 37,918 unigenes from root and 35,130 unigenes from shoot were mapped to 133 KEGG pathways. Based on the DGE data we found that most of the transcript related to CYP450s and UDP-glucosyltransferases were specifically upregulated in shoot tissue as compared to root tissue. Finally, we have selected 43 transcripts related to secondary metabolism including transcription factor families which are differentially expressed in shoot and root tissues were validated by qRT-PCR and their expression level were monitored after MeJA treatment and wounding for 1, 3 and 5 h. This study not only represents the first de novo transcriptome analysis of Bacopa monnieri but also provides information about the identification, expression and differential tissues specific distribution of transcripts related to triterpenoid sapogenin which is one of the most important pharmacologically active secondary metabolite present in Bacopa monnieri. The identified transcripts in this study will establish a foundation for future studies related to carrying out the metabolic engineering for increasing the bacosides biosynthesis and its regulation for human health benefits.

Using an integral-field unit spectrograph to study radical species in cometary coma

NASA Astrophysics Data System (ADS)

Lewis, Benjamin; Pierce, Donna M.; Vaughan, Charles M.; Cochran, Anita

2015-01-01

We have observed several comets using an integral-field unit spectrograph (the George and Cynthia Mitchell Spectrograph) on the 2.7m Harlan J. Smith telescope at McDonald Observatory. Full-coma spectroscopic images were obtained for various radical species (C2, C3, CN, NH2). Various coma enhancements were used to identify and characterize coma morphological features. The azimuthal average profiles and the Haser model were used to determine production rates and possible parent molecules. Here, we present the work completed to date, and we compare our results to other comet taxonomic surveys. This work was funded by the National Science Foundation Graduate K-12 (GK-12) STEM Fellows program (Award No. DGE-0947419), NASA's Planetary Atmospheres program (Award No. NNX14AH18G), and the Fund for Astrophysical Research, Inc.

Using an integral-field unit spectrograph to study radical species in cometary coma

NASA Astrophysics Data System (ADS)

Lewis, Benjamin; Pierce, Donna; Cochran, Anita; Vaughan, Charles

2014-11-01

We have observed several comets using an integral-field unit spectrograph (the George and Cynthia Mitchell Spectrograph) on the 2.7m Harlan J. Smith telescope at McDonald Observatory. Full-coma spectroscopic images were obtained for various radical species (C2, C3, CN, NH2). Various coma enhancements were used to identify and characterize coma morphological features. The azimuthal average profiles and the Haser model were used to determine production rates and possible parent molecules. Here, we present the work completed to date, and we compare our results to other comet taxonomic surveys. This work was funded by the National Science Foundation Graduate K-12 (GK-12) STEM Fellows program (Award No. DGE-0947419), NASA’s Planetary Atmospheres program (Award No. NNX14AH18G), and the Fund for Astrophysical Research, Inc.

Mock X-ray Observations of Localized LMC Outflows

NASA Astrophysics Data System (ADS)

Tomesh, Teague; Bustard, Chad; Zweibel, Ellen

2018-01-01

The Milky Way’s nearest neighbor, the Large Magellanic Cloud (LMC), is a perfect testing ground for modeling a variety of astrophysical phenomena. Specifically, the LMC provides a unique opportunity for the study of possible localized outflows driven by star formation and their x-ray signatures. We have developed FLASH simulations of theoretical outflows originating in the LMC that we have used to generate predicted observations of X-ray luminosity. This X-ray emission can be a useful probe of the hot gas in these winds which may couple to the cool gas and drive it from the disk. Future observations of the LMC may provide us with valuable checks on our model. This work is partially supported by the National Science Foundation (NSF) Graduate Research Fellowship Program under grant No. DGE-125625 and NSF grant No. AST-1616037.

Finding Effective Models in Transition Metals using Quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Williams, Kiel; Wagner, Lucas K.

There is a gap between high-accuracy ab-initio calculations, like those produced from Quantum Monte Carlo (QMC), and effective lattice models such as the Hubbard model. We have developed a method that combines data produced from QMC with fitting techniques taken from data science, allowing us to determine which degrees of freedom are required to connect ab-initio and model calculations. We test this approach for transition metal atoms, where spectroscopic reference data exists. We report on the accuracy of several derived effective models that include different degrees of freedom, and comment on the quality of the parameter values we obtain from our fitting procedure. We gratefully acknowledge funding from the National Science Foundation Graduate Research Fellowship Program under Grant Number DGE-1144245 (K.T.W.) and from SciDAC Grant DE-FG02-12ER46875 (L.K.W.).

A Polymer-Dispersed Liquid Crystal-Based Dynamic Gain Equalizer

NASA Astrophysics Data System (ADS)

Barge, M.; Battarel, D.; de Bougrenet de La Tocnaye, J. L.

2005-08-01

This paper presents results obtained with a spatial light modulator (SLM) using a polymer-dispersed liquid-crystal (LC) material to provide dynamic gain equalization (DGE) for wavelength-division multiplexing (WDM) networks. We show the benefit of using a nonchannelized approach to adjust some physical parameters such as the ripple and the maximum obtainable attenuation slope for the spectra to be equalized. Particular attention is paid here to polarization dependence that can result from parasitic anisotropic multiple path interferences as well as induced anisotropy due to a planar transverse field when using a free-space SLM structure. In this frame, we demonstrate an original approach using a depolarizing prism that is only appropriate to such choice of material and that mitigates these effects. Finally, material engineering to widen the operating temperature range is also shortly presented in this paper.

Investigation of the thermal stability of 1T'-MoTe2 multilayers via Raman spectroscopy

NASA Astrophysics Data System (ADS)

Herman, Irving P.; Wang, Dennis; Smyser, Kori; Rhodes, Daniel; Pasupathy, Abhay N.

The distorted octahedral (1T') form of MoTe2 has garnered much interest in recent years because of its potential applications as a quantum spin hall insulator. Here we study the structural stability of 1T'-MoTe2 multilayers encapsulated by hexagonal boron nitride (hBN) above room temperature by tracking the evolution of its Raman spectrum and cross-checking the results with atomic force microscopy (AFM). Our data indicate the presence of both linear and nonlinear redshifts in peak positions upon heating and, furthermore, suggest the irreversible degradation of the original compound into tellurium nanocrystals at higher temperatures. We discuss the implications of these findings for related optical and transport experiments involving this material and how encapsulation may help extend the lifetime of such devices. NSF IGERT (DGE-1069240).

Differential gene expression profiling through transcriptome approach of Saccharum spontaneum L. under low temperature stress reveals genes potentially involved in cold acclimation.

PubMed

Selvarajan, Dharshini; Mohan, Chakravarthi; Dhandapani, Vignesh; Nerkar, Gauri; Jayanarayanan, Ashwin Narayan; Vadakkancherry Mohanan, Manoj; Murugan, Naveenarani; Kaur, Lovejot; Chennappa, Mahadevaiah; Kumar, Ravinder; Meena, Minturam; Ram, Bakshi; Chinnaswamy, Appunu

2018-04-01

Sugarcane ( Saccharum sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8-9 months mainly due to winter's low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant S. spontaneum IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using trinity and annotated with UNIPROT, KEGG, GO, COG and SUCEST databases, and transcriptome was validated using qRT-PCR. The differential gene expression (DGE) analysis showed that 2583 genes were upregulated and 3302 genes were down-regulated upon low temperature stress. A total of 170 cold responsive transcriptional factors belonging to 30 families were differentially regulated. CBF6 (C-binding factor), a DNA binding transcriptional activation protein associated with cold acclimation and freezing tolerance was differentially upregulated. Many low temperature responsive genes involved in various metabolic pathways, viz. cold sensing through membrane fluidity, calcium and lipid signaling genes, MAP kinases, phytohormone signaling and biosynthetic genes, antioxidative enzymes, membrane and cellular stabilizing genes, genes involved in biosynthesis of polyunsaturated fatty acids, chaperones, LEA proteins, soluble sugars, osmoprotectants, lignin and pectin biosynthetic genes were also differentially upregulated. Potential cold responsive genes and transcriptional factors involved in cold tolerance mechanism in cold tolerant S. spontaneum IND 00-1037 were identified. Together, this study provides insights into the cold tolerance to low temperature stress in S. spontaneum , thus opening applications in the genetic improvement of cold stress tolerance in sugarcane.

RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum—A. cepa monosomic addition lines

PubMed Central

Abdelrahman, Mostafa; El-Sayed, Magdi; Sato, Shusei; Hirakawa, Hideki; Ito, Shin-ichi; Tanaka, Keisuke; Mine, Yoko; Sugiyama, Nobuo; Suzuki, Minoru; Yamauchi, Naoki

2017-01-01

The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium’s defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A. cepa Aggregatum group, AA) are powerful genetic resources that enable us to understand many physiological traits of Allium. In the present study, we were able to isolate and identify Alliospiroside A saponin compound in A. fistulosum with extra chromosome 2A from shallot (FF2A) and its role in the defense mechanism against Fusarium pathogens. Furthermore, to gain molecular insight into the Allium saponin biosynthesis pathway, high-throughput RNA-Seq of the root, bulb, and leaf of AA, MALs, and FF was carried out using Illumina's HiSeq 2500 platform. An open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated based on RNA-Seq data. The resulting assembled transcripts were functionally annotated, revealing 50 unigenes involved in saponin biosynthesis. Differential gene expression (DGE) analyses of AA and MALs as compared with FF (as a control) revealed a strong up-regulation of the saponin downstream pathway, including cytochrome P450, glycosyltransferase, and beta-glucosidase in chromosome 2A. An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance. PMID:28800607

Transcriptomic profiling-based mutant screen reveals three new transcription factors mediating menadione resistance in Neurospora crassa.

PubMed

Zhu, Jufen; Yu, Xinxu; Xie, Baogui; Gu, Xiaokui; Zhang, Zhenying; Li, Shaojie

2013-06-01

To gain insight into the regulatory mechanisms of oxidative stress responses in filamentous fungi, the genome-wide transcriptional response of Neurospora crassa to menadione was analysed by digital gene expression (DGE) profiling, which identified 779 upregulated genes and 576 downregulated genes. Knockout mutants affecting 130 highly-upregulated genes were tested for menadione sensitivity, which revealed that loss of the transcription factor siderophore regulation (SRE) (a transcriptional repressor for siderophore biosynthesis), catatase-3, cytochrome c peroxidase or superoxide dismutase 1 copper chaperone causes hypersensitivity to menadione. Deletion of sre dramatically increased transcription of the siderophore biosynthesis gene ono and the siderophore iron transporter gene sit during menadione stress, suggesting that SRE is required for repression of iron uptake under oxidative stress conditions. Contrary to its phenotype, the sre deletion mutant showed higher transcriptional levels of genes encoding reactive oxygen species (ROS) scavengers than wild type during menadione stress, which implies that the mutant suffers a higher level of oxidative stress than wild type. Uncontrolled iron uptake in the sre mutant might exacerbate cellular oxidative stress. This is the first report of a negative regulator of iron assimilation participating in the fungal oxidative stress response. In addition to SRE, eight other transcription factor genes were also menadione-responsive but their single gene knockout mutants showed wild-type menadione sensitivity. Two of them, named as mit-2 (menadione induced transcription factor-2) and mit-4 (menadione induced transcription factor-4), were selected for double mutant analysis. The double mutant was hypersensitive to menadione. Similarly, the double mutation of mit-2 and sre also had additive effects on menadione sensitivity, suggesting multiple transcription factors mediate oxidative stress resistance in an additive manner. Copyright © 2013 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines.

PubMed

Abdelrahman, Mostafa; El-Sayed, Magdi; Sato, Shusei; Hirakawa, Hideki; Ito, Shin-Ichi; Tanaka, Keisuke; Mine, Yoko; Sugiyama, Nobuo; Suzuki, Yutaka; Yamauchi, Naoki; Shigyo, Masayoshi

2017-01-01

The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium's defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A. cepa Aggregatum group, AA) are powerful genetic resources that enable us to understand many physiological traits of Allium. In the present study, we were able to isolate and identify Alliospiroside A saponin compound in A. fistulosum with extra chromosome 2A from shallot (FF2A) and its role in the defense mechanism against Fusarium pathogens. Furthermore, to gain molecular insight into the Allium saponin biosynthesis pathway, high-throughput RNA-Seq of the root, bulb, and leaf of AA, MALs, and FF was carried out using Illumina's HiSeq 2500 platform. An open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated based on RNA-Seq data. The resulting assembled transcripts were functionally annotated, revealing 50 unigenes involved in saponin biosynthesis. Differential gene expression (DGE) analyses of AA and MALs as compared with FF (as a control) revealed a strong up-regulation of the saponin downstream pathway, including cytochrome P450, glycosyltransferase, and beta-glucosidase in chromosome 2A. An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance.

Cosmic Ray Acceleration from Multiple Galactic Wind Shocks

NASA Astrophysics Data System (ADS)

Cotter, Cory; Bustard, Chad; Zweibel, Ellen

2018-01-01

Cosmic rays still have an unknown origin. Many mechanisms have been suggested for their acceleration including quasars, pulsars, magnetars, supernovae, supernova remnants, and galactic termination shocks. The source of acceleration may be a mixture of these and a different mixture in different energy regimes. Using numerical simulations, we investigate multiple shocks in galactic winds as potential cosmic rays sources. By having shocks closer to the parent galaxy, more particles may diffuse back to the disk instead of being blown out in the wind, as found in Bustard, Zweibel, and Cotter (2017, ApJ) and also Merten, Bustard, Zweibel, and Tjus (to be submitted to ApJ). Specifically, this flux of cosmic rays could contribute to the unexplained "shin" region between the well-known "knee" and "ankle" of the cosmic ray spectrum. We would like to acknowledge support from the National Science Foundation (NSF) Graduate Research Fellowship Program under grant No. DGE-125625 and NSF grant No. AST-1616037.

Concentrations of Simulated Dark Matter Halos

NASA Astrophysics Data System (ADS)

Child, Hillary

2017-01-01

We present the concentration-mass (c-M) relation of dark matter halos in two new high-volume high-resolution cosmological N-body simulations, Q Continuum and Outer Rim. Concentration describes the density of the central regions of halos; it is highest for low-mass halos at low redshift, decreasing at high mass and redshift. The shape of the c-M relation is an important probe of cosmology. We discuss the redshift dependence of the c-M relation, several different methods to determine concentrations of simulated halos, and potential sources of bias in concentration measurements. To connect to lensing observations, we stack halos, which also allows us to assess the suitability of the Navarro-Frenk-White profile and other profiles, such as Einasto, with an additional shape parameter. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1144082.

Molecular Dynamical Simulation of Thermal Conductivity in Amorphous Structures

NASA Astrophysics Data System (ADS)

Deangelis, Freddy; Henry, Asegun

While current descriptions of thermal transport exists for well-ordered materials such as crystal latices, new methods are needed to describe thermal transport in disordered materials, including amorphous solids. Because such structures lack periodic, long-range order, a group velocity cannot be defined for thermal modes of vibration; thus, the phonon gas model cannot be applied to these structures. Instead, a new framework must be applied to analyze such materials. Using a combination of density functional theory and molecular dynamics, we have analyzed thermal transport in amorphous structures, chiefly amorphous germanium. The analysis allows us to categorize vibrational modes as propagons, diffusons, or locons, and to determine how they contribute to thermal conductivity within amorphous structures. This method is also being extended to other disordered structures such as amorphous polymers. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1148903.

Scalable Methods for Eulerian-Lagrangian Simulation Applied to Compressible Multiphase Flows

NASA Astrophysics Data System (ADS)

Zwick, David; Hackl, Jason; Balachandar, S.

2017-11-01

Multiphase flows can be found in countless areas of physics and engineering. Many of these flows can be classified as dispersed two-phase flows, meaning that there are solid particles dispersed in a continuous fluid phase. A common technique for simulating such flow is the Eulerian-Lagrangian method. While useful, this method can suffer from scaling issues on larger problem sizes that are typical of many realistic geometries. Here we present scalable techniques for Eulerian-Lagrangian simulations and apply it to the simulation of a particle bed subjected to expansion waves in a shock tube. The results show that the methods presented here are viable for simulation of larger problems on modern supercomputers. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1315138. This work was supported in part by the U.S. Department of Energy under Contract No. DE-NA0002378.

Simulating incompressible flow on moving meshfree grids using General Finite Differences (GFD)

NASA Astrophysics Data System (ADS)

Vasyliv, Yaroslav; Alexeev, Alexander

2016-11-01

We simulate incompressible flow around an oscillating cylinder at different Reynolds numbers using General Finite Differences (GFD) on a meshfree grid. We evolve the meshfree grid by treating each grid node as a particle. To compute velocities and accelerations, we consider the particles at a particular instance as Eulerian observation points. The incompressible Navier-Stokes equations are directly discretized using GFD with boundary conditions enforced using a sharp interface treatment. Cloud sizes are set such that the local approximations use only 16 neighbors. To enforce incompressibility, we apply a semi-implicit approximate projection method. To prevent overlapping particles and formation of voids in the grid, we propose a particle regularization scheme based on a local minimization principle. We validate the GFD results for an oscillating cylinder against the lattice Boltzmann method and find good agreement. Financial support provided by National Science Foundation (NSF) Graduate Research Fellowship, Grant No. DGE-1148903.

The Hubbard Dimer: A Complete DFT Solution to a Many-Body Problem

NASA Astrophysics Data System (ADS)

Smith, Justin; Carrascal, Diego; Ferrer, Jaime; Burke, Kieron

2015-03-01

In this work we explain the relationship between density functional theory and strongly correlated models using the simplest possible example, the two-site asymmetric Hubbard model. We discuss the connection between the lattice and real-space and how this is a simple model for stretched H2. We can solve this elementary example analytically, and with that we can illuminate the underlying logic and aims of DFT. While the many-body solution is analytic, the density functional is given only implicitly. We overcome this difficulty by creating a highly accurate parameterization of the exact function. We use this parameterization to perform benchmark calculations of correlation kinetic energy, the adiabatic connection, etc. We also test Hartree-Fock and the Bethe Ansatz Local Density Approximation. We also discuss and illustrate the derivative discontinuity in the exchange-correlation energy and the infamous gap problem in DFT. DGE-1321846, DE-FG02-08ER46496.

Phytochemical Evaluation of Moth Bean (Vigna aconitifolia L.) Seeds and Their Divergence

PubMed Central

Gupta, Neha; Shrivastava, Nidhi; Singh, Pramod Kumar; Bhagyawant, Sameer S.

2016-01-01

In the present study, phytochemical contents of 25 moth bean (Vigna aconitifolia) seed accessions were evaluated. This includes protease inhibitors, phytic acid, radical scavenging activity, and tannins. The studies revealed significant variation in the contents of theses phytochemicals. Presence of photochemical composition was correlated with seed storage proteins like albumin and globulin. Qualitative identification of total seed storage protein abundance across two related moth bean accessions using two-dimensional gel electrophoresis (2D-GE) was performed. Over 20 individual protein fractions were distributed over the gel as a series of spots in two moth bean accessions. Seed proteome accumulated spots of high intensity over a broad range of pI values of 3–10 in a molecular weight range of 11–170 kDa. In both seed accessions maximum protein spots are seen in the pI range of 6–8. PMID:27239343

Phytochemical Evaluation of Moth Bean (Vigna aconitifolia L.) Seeds and Their Divergence.

PubMed

Gupta, Neha; Shrivastava, Nidhi; Singh, Pramod Kumar; Bhagyawant, Sameer S

2016-01-01

In the present study, phytochemical contents of 25 moth bean (Vigna aconitifolia) seed accessions were evaluated. This includes protease inhibitors, phytic acid, radical scavenging activity, and tannins. The studies revealed significant variation in the contents of theses phytochemicals. Presence of photochemical composition was correlated with seed storage proteins like albumin and globulin. Qualitative identification of total seed storage protein abundance across two related moth bean accessions using two-dimensional gel electrophoresis (2D-GE) was performed. Over 20 individual protein fractions were distributed over the gel as a series of spots in two moth bean accessions. Seed proteome accumulated spots of high intensity over a broad range of pI values of 3-10 in a molecular weight range of 11-170 kDa. In both seed accessions maximum protein spots are seen in the pI range of 6-8.

Stability of Granular Packings Jammed under Gravity: Avalanches and Unjamming

NASA Astrophysics Data System (ADS)

Merrigan, Carl; Birwa, Sumit; Tewari, Shubha; Chakraborty, Bulbul

Granular avalanches indicate the sudden destabilization of a jammed state due to a perturbation. We propose that the perturbation needed depends on the entire force network of the jammed configuration. Some networks are stable, while others are fragile, leading to the unpredictability of avalanches. To test this claim, we simulated an ensemble of jammed states in a hopper using LAMMPS. These simulations were motivated by experiments with vibrated hoppers where the unjamming times followed power-law distributions. We compare the force networks for these simulated states with respect to their overall stability. The states are classified by how long they remain stable when subject to continuous vibrations. We characterize the force networks through both their real space geometry and representations in the associated force-tile space, extending this tool to jammed states with body forces. Supported by NSF Grant DMR1409093 and DGE1068620.

Discovering Hidden Controlling Parameters using Data Analytics and Dimensional Analysis

NASA Astrophysics Data System (ADS)

Del Rosario, Zachary; Lee, Minyong; Iaccarino, Gianluca

2017-11-01

Dimensional Analysis is a powerful tool, one which takes a priori information and produces important simplifications. However, if this a priori information - the list of relevant parameters - is missing a relevant quantity, then the conclusions from Dimensional Analysis will be incorrect. In this work, we present novel conclusions in Dimensional Analysis, which provide a means to detect this failure mode of missing or hidden parameters. These results are based on a restated form of the Buckingham Pi theorem that reveals a ridge function structure underlying all dimensionless physical laws. We leverage this structure by constructing a hypothesis test based on sufficient dimension reduction, allowing for an experimental data-driven detection of hidden parameters. Both theory and examples will be presented, using classical turbulent pipe flow as the working example. Keywords: experimental techniques, dimensional analysis, lurking variables, hidden parameters, buckingham pi, data analysis. First author supported by the NSF GRFP under Grant Number DGE-114747.

Perturbative Normal Form Theory for the 2D Random-Field Ising Model

NASA Astrophysics Data System (ADS)

Hayden, Lorien; Raju, Archishman; Sethna, James

Bifurcation theory is important to explain scaling in many systems. For the equilibrium random-field Ising model (RFIM) in 2D, the exponentially diverging correlation length can be derived directly from the RG flows which form a pitchfork bifurcation: dw/dl = -ɛ/2 w +w3 (Bray and Moore 1985). Our perturbative normal form theory (PNFT) predicts a term w5 to be critical in describing the behavior - it cannot be removed through an analytic change of coordinates. The new form of the correlation length produced has been observed to occur in leading order without explanation (Meinke and Middleton 2005). Performing simulations of the non-equilibrium RFIM on a Voronoi lattice uncovers a transcritical bifurcation of the form dw/dl = -ɛ/2 w +w2 + Bw3 . The RG flows determined by PNFT in this case lead directly to a form for the appropriate invariant scaling combination: s exp (- 1 / σνw) (1/w + B) C + B / σν . Using this scaling combination yields a collapse which was not possible to achieve using standard methods such as Widom scaling arguments. Further, the scaling extends over a decade in the magnitude of the disorder and explains behavior down to avalanche sizes of three, the edge of complexity. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No . DGE-1144153 and a Cornell Fellowship.

A pilot scale ultrasonic system to enhance extraction processes with dense gases

NASA Astrophysics Data System (ADS)

Riera, E.; Blasco, M.; Tornero, A.; Casas, E.; Roselló, C.; Simal, S.; Acosta, V. M.; Gallego-Juárez, J. A.

2012-05-01

The use of dense gases (supercritical fluids) as extracting agents has been attracting wide interest for years. In particular, supercritical carbon dioxide is considered nowadays as a green and very useful solvent. Nevertheless, the extraction process has a slow dynamics. Power ultrasound represents an efficient way for accelerating and enhancing the kinetics of the process by producing strong agitation and turbulence, compressions and decompressions, and heating in the media. For this purpose, a device prototype for using ultrasound in supercritical media was developed, tested and validated in extraction processes of oil from grounded almonds (55% oil content, wet basis and 3-4 mm particle size) in a 5 L extraction unit. An amount of 1500 g of grounded almonds was placed in a cylindrical basket during the trials inside the dense gas extractor (DGE) where solvent was introduced at different flow rates, pressures and temperatures. In all cases the ultrasonic energy confirmed the enhancement and acceleration of the almond oil extraction kinetics using supercritical CO2. Presently the power ultrasound effect in such a process is being deeply analyzed in a 5 L extraction unit before scaling-up a new ultrasonic system. This technology, still under development, has been designed for a bigger dense gas pilot-plant consisting of two extractors (20 L capacity), two separation units and has the possibility of operating at a pressure up to 50 MPa. The goal of this work is to study the effect of high-power ultrasound coupled to dense gas extraction inside the basket with the product, and to present a prototype for the use of power ultrasound in extraction processes with dense gases inside a new 20 L extractor unit.

The water footprint of Austria for different diets.

PubMed

Vanham, D

2013-01-01

This paper analyses the Austrian water footprint of consumption (WF(cons)) for different diets: the current diet, a healthy diet (based upon the dietary recommendations issued by the German nutrition society, or DGE), a vegetarian diet and a combined diet between both latter diets. As in many western countries, the current Austrian diet consists of too many products from the groups sugar, crop oils, meat, animal fats, milk, milk products and eggs and not enough products from the groups cereals, rice, potatoes, vegetables and fruit. Especially the consumption of animal products accounts for high WF amounts. These diets result in a substantial reduction (range 922-1,362 l per capita per day (lcd)) of the WF(cons) for agricultural products, which is currently 3,655 lcd. However, the Austrian water footprint of agricultural production (WF(prod) = 2,066 lcd) still remains lower than even the WF(cons) for a vegetarian diet (2,293 lcd). As a result the country is a net virtual water importer regarding agricultural products for all analysed scenarios.

Morphological Control of Au Dendrite Electrocatalysts for CO2 Reduction

NASA Astrophysics Data System (ADS)

Nesbitt, Nathan T.; Ma, Ming; Carter, Brittany E.; D'Imperio, Luke A.; Naughton, Jeffrey R.; Courtney, Dave T.; Shepard, Steve; Burns, Michael J.; Smith, Wilson A.; Naughton, Michael J.

Au has demonstrated the highest catalytic selectivity, activity, and stability for CO2 reduction to CO of any metal, but the mechanism for this performance remains unclear. Studies of nanoparticle films have shown that higher index facets have improved performance, but the preeminent nanoparticle films, from oxide-derived Au, lack well-defined facets and morphological stability to illuminate their enabling mechanism. More recent work has shown Au needles with a sub 5 nm radius of curvature have excellent performance and stability, independent of crystal facet. The same studies, however, still show calculations expecting a facet dependance. Here we demonstrate a facile and novel dendrite fabrication process with tunable morphology. The dendrites show high catalytic selectivity, activity, and stability for CO2 reduction to CO, along with morphological stability after 18 hours of operation, allowing correlation between morphology and performance. The influence of exposed facets will be discussed. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. (DGE-1258923).

New variational bounds on convective transport. I. Formulation and analysis

NASA Astrophysics Data System (ADS)

Tobasco, Ian; Souza, Andre N.; Doering, Charles R.

2016-11-01

We study the maximal rate of scalar transport between parallel walls separated by distance h, by an incompressible fluid with scalar diffusion coefficient κ. Given velocity vector field u with intensity measured by the Péclet number Pe =h2 < | ∇ u |2 >1/2 / κ (where < . > is space-time average) the challenge is to determine the largest enhancement of wall-to-wall scalar flux over purely diffusive transport, i.e., the Nusselt number Nu . Variational formulations of the problem are presented and it is determined that Nu <= cPe 2 / 3 , where c is an absolute constant, as Pe -> ∞ . Moreover, this scaling for optimal transport-possibly modulo logarithmic corrections-is asymptotically sharp: admissible steady flows with Nu >=c' Pe 2 / 3 /[ log Pe ] 2 are constructed. The structure of (nearly) maximally transporting flow fields is discussed. Supported in part by National Science Foundation Graduate Research Fellowship DGE-0813964, awards OISE-0967140, PHY-1205219, DMS-1311833, and DMS-1515161, and the John Simon Guggenheim Memorial Foundation.

Incompressible flow simulations on regularized moving meshfree grids

NASA Astrophysics Data System (ADS)

Vasyliv, Yaroslav; Alexeev, Alexander

2017-11-01

A moving grid meshfree solver for incompressible flows is presented. To solve for the flow field, a semi-implicit approximate projection method is directly discretized on meshfree grids using General Finite Differences (GFD) with sharp interface stencil modifications. To maintain a regular grid, an explicit shift is used to relax compressed pseudosprings connecting a star node to its cloud of neighbors. The following test cases are used for validation: the Taylor-Green vortex decay, the analytic and modified lid-driven cavities, and an oscillating cylinder enclosed in a container for a range of Reynolds number values. We demonstrate that 1) the grid regularization does not impede the second order spatial convergence rate, 2) the Courant condition can be used for time marching but the projection splitting error reduces the convergence rate to first order, and 3) moving boundaries and arbitrary grid distortions can readily be handled. Financial support provided by the National Science Foundation (NSF) Graduate Research Fellowship, Grant No. DGE-1148903.

Rethinking Physics for Biologists: A design-based research approach

NASA Astrophysics Data System (ADS)

Sawtelle, Vashti

2015-03-01

Biology majors at the University of Maryland are required to take courses in biology, chemistry, and physics - but they often see these courses as disconnected. Over the past three years the NEXUS/Physics course has been working to develop an interdisciplinary learning environment that bridges the disciplinary domains of biology and physics. Across the three years we have gone from teaching in a small class with one instructor to teaching in a large lecture hall with multiple instructors. We have used a design-based research approach to support critical reflection of the course at multiple-time scales. In this presentation I will detail our process of collecting systematic data, listening to and valuing students' reasoning, and bridging diverse perspectives led. I will demonstrate how this process led to improved curricular design, refined assessment objectives, and new design heuristics. This work is supported by NSF-TUES DUE 11-22818, the HHMI NEXUS grant, and a NSF Graduate Research Fellowship (DGE 0750616).

Geometrical structure of Neural Networks: Geodesics, Jeffrey's Prior and Hyper-ribbons

NASA Astrophysics Data System (ADS)

Hayden, Lorien; Alemi, Alex; Sethna, James

2014-03-01

Neural networks are learning algorithms which are employed in a host of Machine Learning problems including speech recognition, object classification and data mining. In practice, neural networks learn a low dimensional representation of high dimensional data and define a model manifold which is an embedding of this low dimensional structure in the higher dimensional space. In this work, we explore the geometrical structure of a neural network model manifold. A Stacked Denoising Autoencoder and a Deep Belief Network are trained on handwritten digits from the MNIST database. Construction of geodesics along the surface and of slices taken from the high dimensional manifolds reveal a hierarchy of widths corresponding to a hyper-ribbon structure. This property indicates that neural networks fall into the class of sloppy models, in which certain parameter combinations dominate the behavior. Employing this information could prove valuable in designing both neural network architectures and training algorithms. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No . DGE-1144153.

The Gemini Planet Imager Exoplanet Survey

NASA Astrophysics Data System (ADS)

Nielsen, Eric L.; Macintosh, Bruce; Graham, James R.; Barman, Travis S.; Doyon, Rene; Fabrycky, Daniel; Fitzgerald, Michael P.; Kalas, Paul; Konopacky, Quinn M.; Marchis, Franck; Marley, Mark S.; Marois, Christian; Patience, Jenny; Perrin, Marshall D.; Oppenheimer, Rebecca; Song, Inseok; GPIES Team

2017-01-01

The Gemini Planet Imager Exoplanet Survey (GPIES) is one of the largest most sensitive direct imaging searches for exoplanets conducted to date, and having observed more than 300 stars the survey is halfway complete. We present highlights from the first half of the survey, including the discovery and characterization of the young exoplanet 51 Eri b and the brown dwarf HR 2562 B, new imaging of multiple disks, and resolving the young stellar binary V343 Nor for the first time. GPI has also provided new spectra and orbits of previous known planets and brown dwarfs and polarization measurements of a wide range of disks. Finally, we discuss the constraints placed by the first half of the GPIES campaign on the population of giant planets at orbital separations beyond that of Jupiter. Supported by NSF grants AST-0909188 and AST-1313718, AST-1411868, AST 141378, NNX11AF74G, and DGE-1232825, and by NASA grants NNX15AD95G/NEXSS and NNX11AD21G.

Comparative Biochemical and Proteomic Analyses of Soybean Seed Cultivars Differing in Protein and Oil Content.

PubMed

Min, Chul Woo; Gupta, Ravi; Kim, So Wun; Lee, So Eui; Kim, Yong Chul; Bae, Dong Won; Han, Won Young; Lee, Byong Won; Ko, Jong Min; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Sun Tae

2015-08-19

This study develops differential protein profiles of soybean (Glycine max) seeds (cv. Saedanbaek and Daewon) varying in protein (47.9 and 39.2%) and oil (16.3 and 19.7%) content using protamine sulfate (PS) precipitation method coupled with a 2D gel electrophoresis (2DGE) approach. Of 71 detected differential spots between Daewon and Saedanbaek, 48 were successfully identified by MALDI-TOF/TOF. Gene ontology analysis revealed that up-regulated proteins in Saedanbaek were largely associated with nutrient reservoir activity (42.6%), which included mainly seed-storage proteins (SSPs; subunits of glycinin and β-conglycinin). Similar results were also obtained in two cultivars of wild soybean (G. soja cv. WS22 and WS15) differing in protein content. Western blots confirmed higher accumulation of SSPs in protein-rich Saedanbaek. Findings presented and discussed in this study highlight a possible involvement of the urea cycle for increased accumulation of SSPs and hence the higher protein content in soybean seeds.

Optimization of Large Gel 2D Electrophoresis for Proteomic Studies of Skeletal Muscle

PubMed Central

Reed, Patrick W.; Densmore, Allison; Bloch, Robert J.

2013-01-01

We describe improved methods for large format, 2-dimensional gel electrophoresis (2-DE) that improve protein solubility and recovery, minimize proteolysis, and reduce the loss of resolution due to contaminants and manipulations of the gels, and thus enhance quantitative analysis of protein spots. Key modifications are: (i) the use of 7M urea + 2 M thiourea, instead of 9M urea, in sample preparation and in the tops of the gel tubes; (ii) standardized deionization of all solutions containing urea with a mixed bed ion exchange resin and removal of urea from the electrode solutions; and (iii) use of a new gel tank and cooling device that eliminate the need to run two separating gels in the SDS dimension. These changes make 2D-GE analysis more reproducible and sensitive, with minimal artifacts. Application of this method to the soluble fraction of muscle tissues reliably resolves ~1800 protein spots in adult human skeletal muscle and over 2800 spots in myotubes. PMID:22589104

Ground States of Random Spanning Trees on a D-Wave 2X

NASA Astrophysics Data System (ADS)

Hall, J. S.; Hobl, L.; Novotny, M. A.; Michielsen, Kristel

The performances of two D-Wave 2 machines (476 and 496 qubits) and of a 1097-qubit D-Wave 2X were investigated. Each chip has a Chimera interaction graph calG . Problem input consists of values for the fields hj and for the two-qubit interactions Ji , j of an Ising spin-glass problem formulated on calG . Output is returned in terms of a spin configuration {sj } , with sj = +/- 1 . We generated random spanning trees (RSTs) uniformly distributed over all spanning trees of calG . On the 476-qubit D-Wave 2, RSTs were generated on the full chip with Ji , j = - 1 and hj = 0 and solved one thousand times. The distribution of solution energies and the average magnetization of each qubit were determined. On both the 476- and 1097-qubit machines, four identical spanning trees were generated on each quadrant of the chip. The statistical independence of these regions was investigated. In another study, on the D-Wave 2X, one hundred RSTs with random Ji , j ∈ { - 1 , 1 } and hj = 0 were generated on the full chip. Each RST problem was solved one hundred times and the number of times the ground state energy was found was recorded. This procedure was repeated for square subgraphs, with dimensions ranging from 7 ×7 to 11 ×11. Supported in part by NSF Grants DGE-0947419 and DMR-1206233. D-Wave time provided by D-Wave Systems and by the USRA Quantum Artificial Intelligence Laboratory Research Opportunity.

Dicer and Argonaute Genes Involved in RNA Interference in the Entomopathogenic Fungus Metarhizium robertsii.

PubMed

Meng, Huimin; Wang, Zhangxun; Wang, Yulong; Zhu, Hong; Huang, Bo

2017-04-01

RNA interference (RNAi) is a gene-silencing mechanism that plays an important role in gene regulation in a number of eukaryotic organisms. Two core components, Dicer and Argonaute, are central in the RNAi machinery. However, the physiological roles of Dicer and Argonaute in the entomopathogenic fungus Metarhizium robertsii have remained unclear. Here, the roles of genes encoding Dicer ( M. robertsii dcl1 [ Mrdcl1 ] and Mrdcl2 ) and Argonaute ( Mrago1 and Mrago2 ) proteins in M. robertsii were investigated. The results showed that the Dicer-like protein MrDCL2 and Argonaute protein MrAGO1 are the major components of the RNAi process occurring in M. robertsii The Dicer and Argonaute genes were not involved in the regulation of growth and diverse abiotic stress response in M. robertsii under the tested conditions. Moreover, our results showed that the Dicer and Argonaute gene mutants demonstrated reduced abilities to produce conidia, compared to the wild type (WT) and the gene-rescued mutant. In particular, the conidial yields in the Δ dcl2 and Δ ago1 mutants were reduced by 55.8% and 59.3%, respectively, compared with those from the control strains. Subsequently, for the WT and Δ dcl2 mutant strains, digital gene expression (DGE) profiling analysis of the stage of mycelium growth and conidiogenesis revealed that modest changes occur in development or metabolism processes, which may explain the reduction in conidiation in the Δ dcl2 mutant. In addition, we further applied high-throughput sequencing technology to identify small RNAs (sRNAs) that are differentially expressed in the WT and the Δ dcl2 mutant and found that 4 known microRNA-like small RNAs (milRNAs) and 8 novel milRNAs were Mrdcl2 dependent in M. robertsii IMPORTANCE The identification and characterization of components in RNAi have contributed significantly to our understanding of the mechanism and functions of RNAi in eukaryotes. Here, we found that Dicer and Argonaute genes play an important role in regulating conidiation in M. robertsii Our study also demonstrates that diverse small RNA pathways exist in M. robertsii The study provides a theoretical platform for exploration of the functions of Dicer and Argonaute genes involved in RNAi in fungi. Copyright © 2017 American Society for Microbiology.

Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4

PubMed Central

2012-01-01

Background Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is considered the most lethal disease of Cavendish bananas in the world. The disease can be managed in the field by planting resistant Cavendish plants generated by somaclonal variation. However, little information is available on the genetic basis of plant resistance to Foc TR4. To a better understand the defense response of resistant banana plants to the Fusarium wilt pathogen, the transcriptome profiles in roots of resistant and susceptible Cavendish banana challenged with Foc TR4 were compared. Results RNA-seq analysis generated more than 103 million 90-bp clean pair end (PE) reads, which were assembled into 88,161 unigenes (mean size = 554 bp). Based on sequence similarity searches, 61,706 (69.99%) genes were identified, among which 21,273 and 50,410 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 33,243 (37.71%) unigenes to 119 KEGG pathways. A total of 5,008 genes were assigned to plant-pathogen interactions, including disease defense and signal transduction. Digital gene expression (DGE) analysis revealed large differences in the transcriptome profiles of the Foc TR4-resistant somaclonal variant and its susceptible wild-type. Expression patterns of genes involved in pathogen-associated molecular pattern (PAMP) recognition, activation of effector-triggered immunity (ETI), ion influx, and biosynthesis of hormones as well as pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, cell wall modification genes and genes with other functions were analyzed and compared. The results indicated that basal defense mechanisms are involved in the recognition of PAMPs, and that high levels of defense-related transcripts may contribute to Foc TR4 resistance in banana. Conclusions This study generated a substantial amount of banana transcript sequences and compared the defense responses against Foc TR4 between resistant and susceptible Cavendish bananas. The results contribute to the identification of candidate genes related to plant resistance in a non-model organism, banana, and help to improve the current understanding of host-pathogen interactions. PMID:22863187

Roles of a maize phytochrome-interacting factors protein ZmPIF3 in regulation of drought stress responses by controlling stomatal closure in transgenic rice without yield penalty.

PubMed

Gao, Yong; Wu, Meiqin; Zhang, Menjiao; Jiang, Wei; Liang, Enxing; Zhang, Dongping; Zhang, Changquan; Xiao, Ning; Chen, Jianmin

2018-06-05

ZmPIF3 plays an important role in ABA-mediated regulation of stomatal closure in the control of water loss, and can improve both drought tolerance and did not affect the grain yield in the transgenic rice. Phytochrome-interacting factors (PIFs) are a subfamily of basic helix-loop-helix (bHLH) transcription factors and play important roles in regulating plant growth and development. In our previous study, overexpression of a maize PIFs family gene, ZmPIF3, improved drought tolerance in transgenic rice. In this study, measurement of water loss rate, transpiration rate, stomatal conductance, guard cell aperture, density and length of ZmPIF3 transgenic plants showed that ZmPIF3 can enhance water-saving and drought-resistance by decreasing stomatal aperture and reducing transpiration in both transgenic rice and transgenic Arabidopsis. Scrutiny of sensitivity to ABA showed that ZmPIF3 transgenic rice was hypersensitive to ABA, while the endogenous ABA level was not significantly changed. These results indicate that ZmPIF3 plays a major role in the ABA signaling pathway. In addition, DGE results further suggest that ZmPIF3 participates in the ABA signaling pathway and regulates stomatal aperture in rice. Comparison analysis of the phenotype, physiology, and transcriptome of ZmPIF3 transgenic rice compared to control plants further suggests that ZmPIF3 is a positive regulator of ABA signaling and enhances water-saving and drought-resistance traits by reducing stomatal openings to control water loss. Moreover, investigation of the agronomic traits of ZmPIF3 transgenic rice from four cultivating seasons showed that ZmPIF3 expression increased the tiller and panicle number and did not affect the grain yield in the transgenic rice. These results demonstrate that ZmPIF3 is a promising candidate gene in the transgenic breeding of water-saving and drought-resistant rice plants and crop improvement.

Optical MEMS: boom, bust, and beyond

NASA Astrophysics Data System (ADS)

Payne, Richard S.

2005-01-01

Optical Telecommunications bandwidth, spurred by the growth of the internet, experienced unprecedented growth in the late 1990's. The creation of new enterprises was vast and the expansion of established component, system and services companies was also breathtaking. This period of speculative growth was followed in 2001-2004 by one of the most significant market crashes in history. While $20B of venture capital was invested in optical telecom in the last 10 years, the vast majority of that has been written off in the last 4. Countless start-ups inaugurated with great fanfare at the end of the 20th century were unceremoniously shut down at the start of the 21st century.(1) As in all speculative bubbles innovative technologies were born and were buried. Nonetheless, new capabilities emerge from the chaos and disruption; one such example is the advent of Optical MEMS (MOEMS). Its development was vigorously pursued in both academic and corporate laboratories during the boom and, in the author's view; MOEMS constitutes a powerful and versatile tool set that will be an invaluable residual of the last few years. In Telecommunications, MOEMS have been proven to be the technology of choice for many optical switching and wavelength management applications.(2) Variable Optical Attenuators (VOA), Wavelength Blockers (WB), Dynamic Gain Equalizers (DGE), and most recently Wavelength Selective Switches (WSS) are being used in the numerous recent network deployments. Moreover, agile networks of the future will have MOEMS at every node. This presentation will provide an overview of the history of MOEMS in Telecommunications, discuss their byproducts and project the future of the technology.

Optical MEMS: boom, bust and beyond

NASA Astrophysics Data System (ADS)

Ramani, Chandra Mouli

2005-10-01

Optical Telecommunications bandwidth, spurred by the growth of the internet, experienced unprecedented growth in the late 1990's. The creation of new enterprises was vast and the expansion of established component, system and services companies was also breathtaking. This period of speculative growth was followed in 2001-2004 by one of the most significant market crashes in history. While $20B of venture capital was invested in optical telecom in the last 10 years, the vast majority of that has been written off in the last four. Countless start-ups inaugurated with great fanfare at the end of the 20th century were unceremoniously shut down at the start of the 21st. (1) As in all speculative bubbles, innovative technologies were born and buried. Nonetheless, new capabilities emerge from the chaos and disruption; one such example is the advent of Optical MEMS (MOEMS). Its development was vigorously pursued in both academic and corporate laboratories during the boom and, in the author's view; MOEMS constitutes a powerful and versatile tool set that is an invaluable residual of the last few years. In Telecommunications, MOEMS has proven to be the technology of choice for many optical switching and wavelength management applications. (2) Variable Optical Attenuators (VOA), Wavelength Blockers (WB), Dynamic Gain Equalizers (DGE), and most recently Wavelength Selective Switches (WSS) are being used in the numerous recent network deployments. Moreover, agile networks of the future will have MOEMS at every node. This presentation will provide an overview of the history of MOEMS in Telecommunications, discuss its byproducts and project the future of the technology.

A prototype web-GIS application for risk analysis of natural hazards in Switzerland

NASA Astrophysics Data System (ADS)

Aye, Zar Chi; Nicolet, Pierrick; Jaboyedoff, Michel; Derron, Marc-Henri; Gerber, Christian; Lévy, Sebastien

2016-04-01

Following changes in the system of Swiss subsidy in January 2008, the Swiss cantons and the Federal Office for the Environment (FOEN) were forced to prioritize different natural hazard protection projects based on their cost-effectiveness, as a response to limited financial resources (Bründl et al., 2009). For this purpose, applications such as EconoMe (OFEV, 2016) and Valdorisk (DGE, 2016) were developed for risk evaluation and prioritization of mitigation projects. These tools serve as a useful decision-making instrument to the community of practitioners and responsible authorities for natural hazard risk management in Switzerland. However, there are several aspects which could be improved, in particular, the integration and visualization of spatial information interactively through a web-GIS interface for better risk planning and evaluation. Therefore, in this study, we aim to develop an interactive web-GIS application based on the risk concepts applied in Switzerland. The purpose of this tool is to provide a rapid evaluation of risk before and after protection measures, and to test the efficiency of measures by using a simplified cost-benefit analysis within the context of different protection projects. This application allows to integrate different layers which are necessary to calculate risk, in particular, hazard intensity (vector) maps for different scenarios (such as 30, 100 and 300 years of return periods based on Swiss guidelines), exposed objects (such as buildings) and vulnerability information of these objects. Based on provided information and additional parameters, risk is calculated automatically and results are visualized within the web-GIS interface of the application. The users can modify these input information and parameters to create different risk scenarios. Based on the resultant risk scenarios, the users can propose and visualize (preliminary) risk reduction measures before realizing the actual design and dimensions of such protective measures in the area. After designing measures, the users can re-calculate risk by updating hazard intensity and object layers. This is achieved by manual editing of shape (vector) layers in the web-GIS interface interactively. Within the application, a cost-benefit analysis tool is also integrated to support the decision-making process for the selection of different protection measures. Finally, the resultant risk information (vector layers and data) can be exported in the form of shapefiles and excel sheets. A prototype application is realized using open-source geospatial software and technologies. Boundless framework with its client-side SDK environment is applied for the rapid prototyping. Free and open source components such as PostGIS spatial database, GeoServer and GeoWebCache, GeoExt and OpenLayers are used for the development of the platform. This developed prototype is demonstrated with a case study area located in Les Diablerets, Switzerland. This research work is carried out within a project funded by the Canton of Vaud, Switzerland. References: Bründl, M., Romang, H. E., Bischof, N., and Rheinberger, C. M.: The risk concept and its application in natural hazard risk management in Switzerland, Nat. Hazards Earth Syst. Sci., 9, 801-813, 2009. DGE: Valdorisk - Direction Générale de l'Environnement, www.vd.ch, accessed 9 January 2016, 2016. OFEV: EconoMe - Office fédéral de l'environnement, www.econome.admin.ch, accessed 9 January 2016, 2016.

Structural and interaction parameters of thermosensitive native α-elastin biohybrid microgel

NASA Astrophysics Data System (ADS)

Balaceanu, Andreea; Singh, Smriti; Demco, Dan E.; Möller, Martin

2014-09-01

The structural and water interaction parameters for native, α-elastin biohybrid microgel crosslinked with hydrophilic and hydrophobic crosslinkers are obtained from the volume phase transition temperature behaviour, 1H high-resolution magic-angle sample spinning transverse magnetization relaxation NMR, and modified Flory-Rehner swelling theory. Firstly, considering a homogeneous morphology the number of subchains in the biohybrid microgel, the residual water in deswollen state as a function of crosslink density and the temperature dependence of the Flory biopolymer-water interaction parameters are reported for the biohybrid microgels prepared with hydrophilic (PEG-DGE) and hydrophobic (BS3) crosslinkers. The Flory-Rehner classical approach is subsequently modified taking into account the heterogeneities observed by NMR transverse relaxation measurements. Two differently mobile regions are determined, a hydrophobic domain and a crosslinking domain with relative reduced mobility. For the first time, the influence of chain mobility on the Flory interaction parameter is investigated through a modified Flory state equation. The contributions of amino-acids located in the hydrophobic and crosslinking domains in the polypeptide sequence are separated while analyzing the biopolymer-water interaction.

Do the Math - The Role of Physicists in the Climate Movement

NASA Astrophysics Data System (ADS)

Nesbitt, Nathan

2014-03-01

``It's simple math: we can emit 565 more gigatons of carbon dioxide and stay below 2°C of warming - anything more than that risks catastrophe for life on earth. The only problem? Burning the fossil fuel that corporations now have in their reserves would result in emitting 2,795 gigatons of carbon dioxide - five times the safe amount.\\xE2\\x80[2] Physicists stand in a powerful position to help the world wiggle out of this circumstance: our profession not only has the technical capacity to work on renewable energy development but also is popularly recognized as a source of scientific authority. This ability to influence public perception and politics is arguably even more important than our technological skills in the fight to stop rapid climate change. I will discuss several strategic campaigns presently underway at universities across the country, such as fossil fuel divestment, and how the physics community can become a valuable asset. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. (DGE-1258923).

Application of Biot-Savart Solver to Predict Axis Switching Phenomena in Finite-Span Vortices Expelled from a Synthetic Jet

NASA Astrophysics Data System (ADS)

Straccia, Joseph; Farnsworth, John

2016-11-01

The Biot-Savart law is a simple yet powerful inviscid and incompressible relationship between the velocity induced at a point and the circulation, orientation and distance of separation of a vortex line. The authors have developed an algorithm for obtaining numerical solutions of the Biot-Savart relationship to predict the self-induced velocity on a vortex line of arbitrary shape. In this work the Biot-Savart solver was used to predict the self-induced propagation of non-circular, finite-span vortex rings expelled from synthetic jets with rectangular orifices of varying aspect ratios. The solver's prediction of the time varying shape of the vortex ring and frequency of axis switching was then compared with Particle Image Velocimetry (PIV) data from a synthetic jet expelled into a quiescent flow i.e. zero cross flow condition. Conclusions about the effectiveness and limitations of this simple, inviscid relationship are drawn from this experimental data. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE 1144083.

New variational bounds on convective transport. II. Computations and implications

NASA Astrophysics Data System (ADS)

Souza, Andre; Tobasco, Ian; Doering, Charles R.

2016-11-01

We study the maximal rate of scalar transport between parallel walls separated by distance h, by an incompressible fluid with scalar diffusion coefficient κ. Given velocity vector field u with intensity measured by the Péclet number Pe =h2 < | ∇ u |2 >1/2 / κ (where < . > is space-time average) the challenge is to determine the largest enhancement of wall-to-wall scalar flux over purely diffusive transport, i.e., the Nusselt number Nu . Variational formulations of the problem are studied numerically and optimizing flow fields are computed over a range of Pe . Implications of this optimal wall-to-wall transport problem for the classical problem of Rayleigh-Bénard convection are discussed: the maximal scaling Nu Pe 2 / 3 corresponds, via the identity Pe2 = Ra (Nu - 1) where Ra is the usual Rayleigh number, to Nu Ra 1 / 2 as Ra -> ∞ . Supported in part by National Science Foundation Graduate Research Fellowship DGE-0813964, awards OISE-0967140, PHY-1205219, DMS-1311833, and DMS-1515161, and the John Simon Guggenheim Memorial Foundation.

Applied Physics Education: PER focused on Physics-Intensive Careers

NASA Astrophysics Data System (ADS)

Zwickl, Benjamin

2017-01-01

Physics education research is moving beyond classroom learning to study the application of physics education within STEM jobs and PhD-level research. Workforce-related PER is vital to supporting physics departments as they educate students for a diverse range of careers. Results from an on-going study involving interviews with entry-level employees, academic researchers, and supervisors in STEM jobs describe the ways that mathematics, physics, and communication are needed for workplace success. Math and physics are often used for solving ill-structured problems that involve data analysis, computational modeling, or hands-on work. Communication and collaboration are utilized in leadership, sales, and as way to transfer information capital throughout the organization through documentation, emails, memos, and face-to-face discussions. While managers and advisors think a physics degree typically establishes technical competency, communication skills are vetted through interviews and developed on the job. Significant learning continues after graduation, showing the importance of cultivating self-directed learning habits and the critical role of employers as educators of specialized technical abilities through on-the-job training. Supported by NSF DGE-1432578.

Targeting virulence: salmochelin modification tunes the antibacterial activity spectrum of β-lactams for pathogen-selective killing of Escherichia coli † †Electronic supplementary information (ESI) available: Tables of bacterial strains employed in this study, iron content of the antimicrobial activity medium, characterization of GlcEnt–Amp/Amx 7–10, GlcEnt-PEG3-N3 12–13, and BLAST search for iroN sequence. Figures of HPLC traces of MceC- and IroB-catalyzed glucosylation of Ent-PEG3-N3 11, optical absorption spectra of GlcEnt–Amp/Amx 7–10, additional antimicrobial activity assays, time-kill kinetics, competition assays for FepA and IroN recognition, mixed-species antimicrobial activity assays, Lcn2 effect on antibacterial activity of GlcEnt–Amp/Amx 7–10, and cytotoxicity assays against T84 cells. See DOI: 10.1039/c5sc00962f Click here for additional data file.

PubMed Central

Chairatana, Phoom; Zheng, Tengfei

2015-01-01

New antibiotics are required to treat bacterial infections and counteract the emergence of antibiotic resistance. Pathogen-specific antibiotics have several advantages over broad-spectrum drugs, which include minimal perturbation to the commensal microbiota. We present a strategy for targeting antibiotics to bacterial pathogens that utilises the salmochelin-mediated iron uptake machinery of Gram-negative Escherichia coli. Salmochelins are C-glucosylated derivatives of the siderophore enterobactin. The biosynthesis and utilisation of salmochelins are important for virulence because these siderophores allow pathogens to acquire iron and evade the enterobactin-scavenging host-defense protein lipocalin-2. Inspired by the salmochelins, we report the design and chemoenzymatic preparation of glucosylated enterobactin–β-lactam conjugates that harbour the antibiotics ampicillin (Amp) and amoxicillin (Amx), hereafter GlcEnt–Amp/Amx. The GlcEnt scaffolds are based on mono- and diglucosylated Ent where one catechol moiety is functionalized at the C5 position for antibiotic attachment. We demonstrate that GlcEnt–Amp/Amx provide up to 1000-fold enhanced antimicrobial activity against uropathogenic E. coli relative to the parent β-lactams. Moreover, GlcEnt–Amp/Amx based on a diglucosylated Ent (DGE) platform selectively kill uropathogenic E. coli that express the salmochelin receptor IroN in the presence of non-pathogenic E. coli and other bacterial strains that include the commensal microbe Lactobacillus rhamnosus GG. Moreover, GlcEnt–Amp/Amx evade the host-defense protein lipocalin-2, and exhibit low toxicity to mammalian cells. Our work establishes that siderophore–antibiotic conjugates provide a strategy for targeting virulence, narrowing the activity spectrum of antibiotics in clinical use, and achieving selective delivery of antibacterial cargos to pathogenic bacteria on the basis of siderophore receptor expression. PMID:28717471

Optical MEMS: past, present and future

NASA Astrophysics Data System (ADS)

Ramani, Chandra Mouli

2005-09-01

Spurred by the growth of the internet, Optical Telecommunications bandwidth, experienced unprecedented growth during late 1990's. During this time of great economic expansion, the creation of new enterprises was vast and the expansion of established component, system and services companies was breathtaking. Unfortunately, this positive economic state was short-lived. This period was followed in 2001-2004 by one of the most significant market crashes in history. During those 10 years of economic growth, about $20B in venture capital was invested in the optical telecom industry, most of this investment was lost in recent years. Many start-up industries which experienced unprecedented growth at the end of the 20th century were lost at the start of the 21st. (1) During this time many, innovative technologies were born and buried. However, many new capabilities emerged from this period of unrest; one such example is the advent of Optical MEMS (MOEMS). Many academics and corporate laboratories pursued the development of MOEMS during the economic boom and, in the author's view; MOEMS surfaced as a powerful and versatile tool set that has proved invaluable and in the last few years during economic downturn, stood the test of time. In the Telecommunications industry, for optical switching and wavelength management applications MOEMS has proven to be the technology of choice. (2) Variable Optical Attenuators (VOA), Wavelength Blockers (WB), Dynamic Gain Equalizers (DGE), and most recently Wavelength Selective Switches (WSS) are being used in the numerous recent network deployments. Moreover, agile networks of the future will have MOEMS at every node. This presentation will provide an overview of the history of MOEMS in Telecommunications, discuss its byproducts and offer a window into the future of the technology.

Surfing with capillary waves: a survival strategy for trapped bees

NASA Astrophysics Data System (ADS)

Roh, Chris; Gharib, Morteza

2017-11-01

Honeybees are able to propel themselves at the water surface. A rapid vibration (30-220 Hz) of wings at the air-water interface results in a locomotion speed of 3-4 cm/s. A mechanism for generating thrust required for achieving and maintaining such speed must be different from their mechanism of flight inasmuch as they are in a different fluid environment. In this study, we present the thrust generating mechanism of the honeybee at the air-water interface. A close observation of the wing's interaction with the water surface showed that the wing does not penetrate nor detach from the water surface. Moreover, the stroke speed of the wing exceeds the minimum capillary wave speed, which signifies that the wing constantly generates the capillary wave by pulling on the surface with its wetted underside. Observation of such interaction suggests that honeybee's locomotion at the water surface resembles surfing on the self-generated capillary wave. A further evidence of described mechanism is explored by constructing a similarly sized mechanical model. This material is based upon work supported by the National Science Foundation under Grant No. CBET-1511414; additional support by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1144469.

Identifying Meteorological Controls on Open and Closed Mesoscale Cellular Convection as Associated with Marine Cold Air Outbreaks

NASA Astrophysics Data System (ADS)

McCoy, Isabel; Wood, Robert; Fletcher, Jennifer

Marine low clouds are key influencers of the climate and contribute significantly to uncertainty in model climate sensitivity due to their small scale and complex processes. Many low clouds occur in large-scale cellular patterns, known as open and closed mesoscale cellular convection (MCC), which have significantly different radiative and microphysical properties. Investigating MCC development and meteorological controls will improve our understanding of their impacts on the climate. We conducted an examination of time-varying meteorological conditions associated with satellite-determined open and closed MCC. The spatial and temporal patterns of MCC clouds were compared with key meteorological control variables calculated from ERA-Interim Reanalysis to highlight dependencies and major differences. This illustrated the influence of environmental stability and surface forcing as well as the role of marine cold air outbreaks (MCAO, the movement of cold air from polar-regions across warmer waters) in MCC cloud formation. Such outbreaks are important to open MCC development and may also influence the transition from open to closed MCC. Our results may lead to improvements in the parameterization of cloudiness and advance the simulation of marine low clouds. National Science Foundation Graduate Research Fellowship Grant (DGE-1256082).

Coherence and Dynamics of a High- β Metallo-dielectric Nanolasers

NASA Astrophysics Data System (ADS)

Pan, Si Hui Athena

Metal-clad nanolasers with high spontaneous emission factors (β) represent a class of ultra-compact light emitters with applications in fiber-optic communications, optical computing, imaging and sensing. In-depth studies on both the coherence and dynamical properties of these emitters are necessary before practical applications can be realized. However, the coherence characterization of a high- β nanolaser using the conventional measurement of output versus input intensity (L-L curve) is inherently difficult. We conducted the second order intensity correlation measurement, or g2 (τ) - a more definitive method to confirm coherence - on a high- β metallo-dielectric nanolaser. Our result indicates that full coherence is achieved at three times the threshold conventionally defined by the kink in the L-L curve. Additionally, we observed that the g2 (τ) peak width shrinks below and broadens above threshold. Rate-equation analyses reveal that the above-threshold broadening is due to dynamical hysteresis. We propose that this dynamical phenomenon can be exploited to determine the lasing regimes of a unity- β nanolaser, whose threshold is inherently ambiguous and difficult to observe. National Science Foundation (NSF); Office of Naval Research; Army Research Office; Cymer; NSF Graduate Research Fellowship (DGE-1144086).

Cloud Properties and Radiative Heating Rates for TWP

DOE Data Explorer

Comstock, Jennifer

2013-11-07

A cloud properties and radiative heating rates dataset is presented where cloud properties retrieved using lidar and radar observations are input into a radiative transfer model to compute radiative fluxes and heating rates at three ARM sites located in the Tropical Western Pacific (TWP) region. The cloud properties retrieval is a conditional retrieval that applies various retrieval techniques depending on the available data, that is if lidar, radar or both instruments detect cloud. This Combined Remote Sensor Retrieval Algorithm (CombRet) produces vertical profiles of liquid or ice water content (LWC or IWC), droplet effective radius (re), ice crystal generalized effective size (Dge), cloud phase, and cloud boundaries. The algorithm was compared with 3 other independent algorithms to help estimate the uncertainty in the cloud properties, fluxes, and heating rates (Comstock et al. 2013). The dataset is provided at 2 min temporal and 90 m vertical resolution. The current dataset is applied to time periods when the MMCR (Millimeter Cloud Radar) version of the ARSCL (Active Remotely-Sensed Cloud Locations) Value Added Product (VAP) is available. The MERGESONDE VAP is utilized where temperature and humidity profiles are required. Future additions to this dataset will utilize the new KAZR instrument and its associated VAPs.

Vertex stability and topological transitions in vertex models of foams and epithelia

NASA Astrophysics Data System (ADS)

Spencer, Meryl; Jabeen, Zahera; Lubensky, David

Vertex models are widely used to computationally simulate dry foams and epithelial tissues. This class of models describes the shape and motion of cells as a function of the forces on vertices where 3 or more cells meet. Despite the widespread use of these models, relatively little is known about their basic theoretical properties. One outstanding issue is the stability of fourfold vertices. In real foams, fourfold vertices are always unstable, but it has been unclear whether vertex models necessarily reflect this behavior. In biological tissues, fourfold vertices arise as an intermediate in T1 transitions, which are one of the fundamental processes by which tissues change topology, and stable fourfold vertices have recently been observed in several different epithelia. We show that, when all edges have the same tension, stationary fourfold vertices in vertex models must always break up. However, when tensions depend on edge orientation, as they might in a planar-polarized tissue, fourfold vertices can become stable. These findings pave the way for studies of more biologically realistic models that couple topological transitions to the dynamics of regulatory proteins. NSF Grant No. DMR-1056456 and NSF-GRFP Grant No. DGE-1256260.

Optoelectronic Control of Spin and Pseudospin in Layered WSe2

NASA Astrophysics Data System (ADS)

Jones, Aaron

2014-03-01

Coherent manipulation of spin-like quantum numbers facilitates the development of new quantum technologies. Layered transition metal dichalcogenides provide an ideal laboratory to exploit such dynamic control of spin, pseudospin, and their interplay. Here, we discuss two examples based on monolayer and bilayer WSe2. Due to the inversion asymmetry in monolayer WSe2, valley pseudospins, which index the degenerate extrema of the energy-momentum bands, possess circularly polarized optical selection rules. In addition to the generation of valley polarization through optical pumping of valley excitons, we demonstrate the creation of a coherent superposition between valley states in monolayer WSe2 by linearly polarized excitation. On the other hand, bilayer WSe2 provides an additional quantum degree of freedom, the layer pseudospin, which corresponds to layer polarization. In AB stacked bilayers, we find the real spin is locked to layer pseudospin for a given valley, which results in the suppression of spin relaxation and electrical control of spin Zeeman splitting without an applied magnetic field. Additionally, we obtain spectroscopic evidence of interlayer and intralayer trion species, an important step toward coherent optical control in van der Waals 2D heterostructures. Aaron Jones partially supported by NSF Grant No. DGE-0718124.

Experimental Investigation of the Electrothermal Instability on Planar Foil Ablation Experiments

NASA Astrophysics Data System (ADS)

Steiner, Adam; Patel, Sonal; Yager-Elorriaga, David; Jordan, Nicholas; Gilgenbach, Ronald; Lau, Y. Y.

2014-10-01

The electrothermal instability (ETI) is an important early-time physical effect on pulsed power foil ablation experiments due to its ability to seed the destructive magneto-Rayleigh-Taylor (MRT) instability. ETI occurs whenever electrical resistivity has temperature dependence; when resistivity increases with temperature, as with solid metal liners or foils, ETI forms striation structures perpendicular to current flow. These striations provide an initial perturbation for the MRT instability, which is the dominant late-time instability in planar foil ablations. The MAIZE linear transformer driver was used to drive current pulses of approximately 600 kA into 400 nm-thick aluminum foils in order to study ETI in planar geometry. Shadowgraph images of the aluminum plasmas were taken for multiple shots at various times within approximately 50 ns of current start. Fourier analysis extracted the approximate wavelengths of the instability structures on the plasma-vacuum interface. Surface metrology of pre-shot foils was performed to provide a comparison between surface roughness features and resulting plasma structure. This work was supported by US DoE. S.G. Patel and A.M. Steiner supported by NPSC funded by Sandia. D.A. Yager supported by NSF fellowship Grant # DGE 1256260.

Hybrid X-pinch Experiments on a MA Linear Transformer Driver

NASA Astrophysics Data System (ADS)

Patel, S. G.; Yager-Elorriaga, D. A.; Steiner, A. M.; Gilgenbach, R. M.; Jordan, N. M.; Chalenski, D. A.; Lau, Y. Y.

2013-10-01

X-pinch experiments have been conducted on the Linear Transformer Driver (LTD) at the University of Michigan. The x-pinch consists of a single wire separated by conical electrodes between two current return plates. The LTD was charged to +/-70 kV resulting in approximately 0.5 MA passing through a 35 μm Al wire. Multiple, short x-ray bursts were detected over the 400 ns current pulse. Ultimately the x-pinch will be located in parallel with a planar foil in order to backlight the Magneto-Rayleigh-Taylor instability. A smaller 100 kA driver is also in development and may be used to independently energize the x-pinch. The x-pinch chamber has been constructed and the results of these experiments will be presented. This work was supported by DoE award number DE-SC0002590, NSF grant number PHY 0903340, and US DoE through Sandia National Labs award numbers 240985 and 76822 to the U of Michigan. S.G Patel and A.M Steiner are supported by NPSC funded by Sandia National Labs. D.A. Yager-Elorriaga is supported by an NSF fellowship under grant number DGE 1256260.

Magneto Rayleigh-Taylor, Sausage, and Kink Instability Experiments on a MegaAmpere Linear Transformer Driver

NASA Astrophysics Data System (ADS)

Yager-Elorriaga, D. A.; Steiner, A. M.; Patel, S. G.; Jordan, N. M.; Gilgenbach, R. M.; Lau, Y. Y.; Weis, M. R.; Zhang, P.

2015-11-01

At the Michigan Accelerator for Inductive Z-Pinch Experiments (MAIZE) facility, a 1-MA Linear Transformer Driver (LTD) is being used to deliver 500-600 kA to cylindrical liners in order to study the magneto Rayleigh-Taylor (MRT), sausage, and kink instabilities in imploding and exploding Al plasmas. The liners studied in this experiment had thicknesses of 400 nm to 30 μm, heights of 1-2 cm, and diameters of 1-6 mm. The plasmas were imaged using 4-time-frame, laser shadowgraphy and shearing-interferometry at 532 nm. For imploding liners, the measured acceleration was found to be less than predicted from the current pulse, indicating significant diffusion of the azimuthal magnetic field. A simple experimental configuration is presented for ``end-on'' laser probing in the r- θ plane in order to study the interior of the liner. Finally, the effects of axial magnetic fields are determined by modifying the return current posts and incorporating external coils. Experimental growth rates are determined and discussed. This work was supported by DOE award DE-SC0012328. S.G. Patel supported by Sandia National Labs. D.A. Yager was supported by NSF fellowship grant DGE 1256260.

Magnon drag thermopower and thermomagnetic properties of single-crystal iron

NASA Astrophysics Data System (ADS)

Watzman, Sarah; Jin, Hyungyu; Heremans, Joseph

2015-03-01

Lucassen et al. demonstrate that magnon drag involves a spin-transfer mechanism closely related to the recently discovered spin-Seebeck effect. This talk will first present results of experiments mapping out the thermopower and magnetothermopower of single-crystal iron and prove that its thermopower is indeed dominated by magnon drag, as suggested by Blatt et al. in 1967. Measurements will then be presented on the magnetic field and temperature dependence of the full thermomagnetic tensor of iron's thermopower in the xxx, xyx, and xyz geometries (the first index gives the direction of the heat flux, the second the measured electric field, the third the applied magnetic field). Results of magneto-thermopower and Nernst coefficients will be reported for single-crystal samples oriented with x =[100]. The Nernst coefficients of elemental iron contain a contribution of a direct spin-transfer mechanism, which should be present in the absence of an interface between a ferromagnet and a normal metal. This mechanism could be put to use in high temperature ferromagnetic metallic thermoelectric alloys. This work is supported by the NSF GRFP under Grant No. DGE-0822215 and the ARO MURI under Grant No. W911NF-14-1-0016.

Semi-Numerical Studies of the Three-Meter Spherical Couette Experiment Utilizing Data Assimilation

NASA Astrophysics Data System (ADS)

Burnett, S. C.; Rojas, R.; Perevalov, A.; Lathrop, D. P.

2017-12-01

The model of the Earth's magnetic field has been investigated in recent years through experiments and numerical models. At the University of Maryland, experimental studies are implemented in a three-meter spherical Couette device filled with liquid sodium. The inner and outer spheres of this apparatus mimic the planet's inner core and core-mantle boundary, respectively. These experiments incorporate high velocity flows with Reynolds numbers 108. In spherical Couette geometry, the numerical scheme applied to this work features finite difference methods in the radial direction and pseudospectral spherical harmonic transforms elsewhere [Schaeffer, N. G3 (2013)]. Adding to the numerical model, data assimilation integrates the experimental outer-layer magnetic field measurements. This semi-numerical model can then be compared to the experimental results as well as forecasting magnetic field changes. Data assimilation makes it possible to get estimates of internal motions of the three-meter experiment that would otherwise be intrusive or impossible to obtain in experiments or too computationally expensive with a purely numerical code. If we can provide accurate models of the three-meter device, it is possible to attempt to model the geomagnetic field. We gratefully acknowledge the support of NSF Grant No. EAR1417148 & DGE1322106.

Semi-Numerical Studies of the Three-Meter Spherical Couette Experiment Utilizing Data Assimilation

NASA Astrophysics Data System (ADS)

Burnett, Sarah; Rojas, Ruben; Perevalov, Artur; Lathrop, Daniel; Ide, Kayo; Schaeffer, Nathanael

2017-11-01

The model of the Earth's magnetic field has been investigated in recent years through experiments and numerical models. At the University of Maryland, experimental studies are implemented in a three-meter spherical Couette device filled with liquid sodium. The inner and outer spheres of this apparatus mimic the planet's inner core and core-mantle boundary, respectively. These experiments incorporate high velocity flows with Reynolds numbers 108 . In spherical Couette geometry, the numerical scheme applied to this work features finite difference methods in the radial direction and pseudospectral spherical harmonic transforms elsewhere. Adding to the numerical model, data assimilation integrates the experimental outer-layer magnetic field measurements. This semi-numerical model can then be compared to the experimental results as well as forecasting magnetic field changes. Data assimilation makes it possible to get estimates of internal motions of the three-meter experiment that would otherwise be intrusive or impossible to obtain in experiments or too computationally expensive with a purely numerical code. If we can provide accurate models of the three-meter device, it is possible to attempt to model the geomagnetic field. We gratefully acknowledge the support of NSF Grant No. EAR1417148 & DGE1322106.

Recombinant expression of extracellular domain of mutant Epidermal Growth Factor Receptor in prokaryotic and baculovirus expression systems.

PubMed

Vettath, Sunitha Kodengil; Shivashankar, Gaganashree; Menon, Krishnakumar N; Vijayachandran, Lakshmi S

2018-04-15

Epidermal Growth Factor Receptor variant III (EGFRvIII) is a tumor specific antigen detected in various tumors including gliomas, breast cancer, lung cancer, head and neck squamous cell carcinoma (HNSCC). Screening of EGFRvIII targeting drug molecules can be accelerated by developing drug screening platforms using recombinantly expressed protein. Choice of expression system is one of the major factors deciding the success of recombinant expression of a protein. In our study, we have tried to express and purify the extracellular domain (ECD) of this highly unstable protein using bacterial and baculovirus expression systems to select the expression system suited for our purpose. Even though the protein was successfully expressed in prokaryotic system, purification could be done only under denaturing conditions. But in the baculovirus expression system, the protein was expressed in soluble form and could be purified under native conditions, with single step of purification. Based on our results, we conclude that insect cells are better choice over E. coli cells for expressing EGFRvIII ECD in soluble form. This study provides insights for other researchers involved in expression of similar unstable membrane proteins, on selecting the best expression system and challenges involved. Copyright © 2018 Elsevier B.V. All rights reserved.

Tunable Control of an Escherichia coli Expression System for the Overproduction of Membrane Proteins by Titrated Expression of a Mutant lac Repressor.

PubMed

Kim, Seong Keun; Lee, Dae-Hee; Kim, Oh Cheol; Kim, Jihyun F; Yoon, Sung Ho

2017-09-15

Most inducible expression systems suffer from growth defects, leaky basal induction, and inhomogeneous expression levels within a host cell population. These difficulties are most prominent with the overproduction of membrane proteins that are toxic to host cells. Here, we developed an Escherichia coli inducible expression system for membrane protein production based on titrated expression of a mutant lac repressor (mLacI). Performance of the mLacI inducible system was evaluated in conjunction with commonly used lac operator-based expression vectors using a T7 or tac promoter. Remarkably, expression of a target gene can be titrated by the dose-dependent addition of l-rhamnose, and the expression levels were homogeneous in the cell population. The developed system was successfully applied to overexpress three membrane proteins that were otherwise difficult to produce in E. coli. This gene expression control system can be easily applied to a broad range of existing protein expression systems and should be useful in constructing genetic circuits that require precise output signals.

Climate Change & Social Justice: Why We Should Care

NASA Astrophysics Data System (ADS)

Nesbitt, Nathan T.

2015-03-01

In the past several years the global impacts brought about by climate change have become increasingly apparent through the advent of numerous natural disasters. In these events the social costs of climate change have materialized demonstrating high costs in lives, livelihoods, and equity. Due to geographic bad-luck many of the countries most affected by climate change are those that contributed least, a challenge that's exacerbated by a lack of robust infrastructure in these countries. Wealthy nations remain at risk themselves and incidents such as Hurricanes Sandy & Katrina have demonstrated that in times of crisis even institutions like the Red Cross will abandon the poor to their deaths. As necessary action on climate change would cost the fossil fuel industry 20 trillion, money in politics has stymied action. Recently, however, a groundswell grassroots movement (e.g. People's Climate March in NYC) and great strides in energy technology and policy have begun to create necessary change. Reports quantifying the impacts of climate change will be discussed, as well as an update on the current state of the global climate justice movement. The important contributions from scientists to this movement will be highlighted. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. (DGE-1258923).

Microstructure Effects on Spall Strength of Titanium-based Bulk Metallic Glass Composites

NASA Astrophysics Data System (ADS)

Diaz, Rene; Hofmann, Douglas; Thadhani, Naresh; Georgia Tech Team; GT-JPL Collaboration

2017-06-01

The spall strength of Ti-based metallic glass composites is investigated as a function of varying volume fractions (0-80%) of in-situ formed crystalline dendrites. With increasing dendrite content, the topology changes such that neither the harder glass nor the softer dendrites dominate the microstructure. Plate-impact experiments were performed using the 80-mm single-stage gas gun over impact stresses up to 18 GPa. VISAR interferometry was used to obtain rear free-surface velocity profiles revealing the velocity pullback spall failure signals. The spall strengths were higher than for Ti-6Al-4V alloy, and remained high up to impact stress. The influence of microstructure on the spall strength is indicated by the constants of the power law fit with the decompression strain rate. Differences in fracture behavior reveal void nucleation as a dominant mechanism affecting the spall strength. The microstructure with neither 100% glass nor with very high crystalline content, provides the most tortuous path for fracture and therefore highest spall strength. The results allow projection of spall strength predictions for design of in-situ formed metallic glass composites. ARO Grant # W911NF-09 ``1-0403 NASA JPL Contract # 1492033 ``Prime # NNN12AA01C; NSF GRFP Grant #DGE-1148903; and NDSE & G.

Detached eddy simulation for turbulent fluid-structure interaction of moving bodies using the constraint-based immersed boundary method

NASA Astrophysics Data System (ADS)

Nangia, Nishant; Bhalla, Amneet P. S.; Griffith, Boyce E.; Patankar, Neelesh A.

2016-11-01

Flows over bodies of industrial importance often contain both an attached boundary layer region near the structure and a region of massively separated flow near its trailing edge. When simulating these flows with turbulence modeling, the Reynolds-averaged Navier-Stokes (RANS) approach is more efficient in the former, whereas large-eddy simulation (LES) is more accurate in the latter. Detached-eddy simulation (DES), based on the Spalart-Allmaras model, is a hybrid method that switches from RANS mode of solution in attached boundary layers to LES in detached flow regions. Simulations of turbulent flows over moving structures on a body-fitted mesh incur an enormous remeshing cost every time step. The constraint-based immersed boundary (cIB) method eliminates this operation by placing the structure on a Cartesian mesh and enforcing a rigidity constraint as an additional forcing in the Navier-Stokes momentum equation. We outline the formulation and development of a parallel DES-cIB method using adaptive mesh refinement. We show preliminary validation results for flows past stationary bodies with both attached and separated boundary layers along with results for turbulent flows past moving bodies. This work is supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1324585.

Direct Observation of Electron-Phonon Coupling and Slow Vibrational Relaxation in Organic-Inorganic Hybrid Perovskites

NASA Astrophysics Data System (ADS)

Hurtado Parra, Sebastian; Straus, Daniel; Iotov, Natasha; Fichera, Bryan; Gebhardt, Julian; Rappe, Andrew; Subotnik, Joseph; Kikkawa, James; Kagan, Cherie

Quantum and dielectric confinement effects in Ruddlesden-Popper 2D hybrid perovskites create excitons with a binding energy exceeding 150 meV. We exploit the large exciton binding energy to study exciton and carrier dynamics as well as electron-phonon coupling (EPC) in hybrid perovskites using absorption and photoluminescence (PL) spectroscopies. At temperatures <75 K, we resolve splitting of the excitonic absorption and PL into multiple regularly spaced resonances every 40-46 meV, consistent with EPC to phonons located on the organic cation. We also resolve resonances with a 14 meV spacing, in accord with coupling to phonons with mixed organic and inorganic character. These assignments are supported by density-functional theory calculations. Hot exciton PL and time-resolved PL measurements show that vibrational relaxation occurs on a picosecond time scale competitive with that for PL. At temperatures >75 K, excitonic absorption and PL exhibit homogeneous broadening. While absorption remains homogeneous, PL becomes inhomogeneous at temperatures <75K, which we speculate is caused by the formation and subsequent dynamics of a polaronic exciton. This work is supported by the U.S. Department of Energy, Office of Basic Energy Sciences Grant DE-SC0002158 and the National Science Foundation Graduate Research Fellowship Grant DGE-1321851.

Convection of wall shear stress events in a turbulent boundary layer

NASA Astrophysics Data System (ADS)

Pabon, Rommel; Mills, David; Ukeiley, Lawrence; Sheplak, Mark

2017-11-01

The fluctuating wall shear stress is measured in a zero pressure gradient turbulent boundary layer of Reτ 1700 simultaneously with velocity measurements using either hot-wire anemometry or particle image velocimetry. These experiments elucidate the patterns of large scale structures in a single point measurement of the wall shear stress, as well as their convection velocity at the wall. The wall shear stress sensor is a CS-A05 one-dimensional capacitice floating element from Interdisciplinary Consulting Corp. It has a nominal bandwidth from DC to 5 kHz and a floating element size of 1 mm in the principal sensing direction (streamwise) and 0.2 mm in the cross direction (spanwise), allowing the large scales to be well resolved in the current experimental conditions. In addition, a two sensor array of CS-A05 aligned in the spanwise direction with streamwise separations O (δ) is utilized to capture the convection velocity of specific scales of the shear stress through a bandpass filter and peaks in the correlation. Thus, an average wall normal position for the corresponding convecting event can be inferred at least as high as the equivalent local streamwise velocity. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1315138.

A Hybrid Physics-Based Data-Driven Approach for Point-Particle Force Modeling

NASA Astrophysics Data System (ADS)

Moore, Chandler; Akiki, Georges; Balachandar, S.

2017-11-01

This study improves upon the physics-based pairwise interaction extended point-particle (PIEP) model. The PIEP model leverages a physical framework to predict fluid mediated interactions between solid particles. While the PIEP model is a powerful tool, its pairwise assumption leads to increased error in flows with high particle volume fractions. To reduce this error, a regression algorithm is used to model the differences between the current PIEP model's predictions and the results of direct numerical simulations (DNS) for an array of monodisperse solid particles subjected to various flow conditions. The resulting statistical model and the physical PIEP model are superimposed to construct a hybrid, physics-based data-driven PIEP model. It must be noted that the performance of a pure data-driven approach without the model-form provided by the physical PIEP model is substantially inferior. The hybrid model's predictive capabilities are analyzed using more DNS. In every case tested, the hybrid PIEP model's prediction are more accurate than those of physical PIEP model. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1315138 and the U.S. DOE, NNSA, ASC Program, as a Cooperative Agreement under Contract No. DE-NA0002378.

Spatio-temporal characteristics of large scale motions in a turbulent boundary layer from direct wall shear stress measurement

NASA Astrophysics Data System (ADS)

Pabon, Rommel; Barnard, Casey; Ukeiley, Lawrence; Sheplak, Mark

2016-11-01

Particle image velocimetry (PIV) and fluctuating wall shear stress experiments were performed on a flat plate turbulent boundary layer (TBL) under zero pressure gradient conditions. The fluctuating wall shear stress was measured using a microelectromechanical 1mm × 1mm floating element capacitive shear stress sensor (CSSS) developed at the University of Florida. The experiments elucidated the imprint of the organized motions in a TBL on the wall shear stress through its direct measurement. Spatial autocorrelation of the streamwise velocity from the PIV snapshots revealed large scale motions that scale on the order of boundary layer thickness. However, the captured inclination angle was lower than that determined using the classic method by means of wall shear stress and hot-wire anemometry (HWA) temporal cross-correlations and a frozen field hypothesis using a convection velocity. The current study suggests the large size of these motions begins to degrade the applicability of the frozen field hypothesis for the time resolved HWA experiments. The simultaneous PIV and CSSS measurements are also used for spatial reconstruction of the velocity field during conditionally sampled intense wall shear stress events. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1315138.

On the topological stability of continuous functions in certain spaces related to Fourier series

NASA Astrophysics Data System (ADS)

Lebedev, Vladimir V.

2010-04-01

We show that the following properties of a continuous function f on the circle \\mathbb T are equivalent: the sequence \\widehat{f\\circ h} of the Fourier coefficients of the superposition f\\circ h belongs to the weak l^1 for every homeomorphism h of the circle onto itself; f is a function of bounded quadratic variation. We obtain similar results for spaces of functions whose sequence of Fourier coefficients belongs to the weak l^p, 1, for spaces A_p of functions f with \\widehat{f}\\in l^p, for the Sobolev spaces W_2^\\lambda, and for other spaces of functions on \\mathbb T. Under rather general assumptions on a space \\mathbb X of functions on the circle, we give a necessary condition for a given continuous function f to stay in \\mathbb X for every change of variable. We also consider the multidimensional case, which is essentially different from the one-dimensional case. In particular, we show that if p<2 and f is a continuous function on the torus \\mathbb T^d, d\\ge2, such that f\\circ h\\in A_p(\\mathbb T^d) for every homeomorphism h\\colon \\mathbb T^d\\to\\mathbb T^d, then f is constant.

Experimental Investigation of the Effects of an Axial Magnetic Field on the Magneto-Rayleigh-Taylor Instability in Ablating Planar Foils

NASA Astrophysics Data System (ADS)

Yager-Elorriaga, D. A.; Patel, S. G.; Steiner, A. M.; Jordan, N. M.; Weiss, M. R.; Gilgenbach, R. M.; Lau, Y. Y.

2014-10-01

Experiments are underway to study the effects an axial magnetic field on the magneto-Rayleigh-Taylor instability (MRT) in ablating planar foils on the 1-MA LTD at the Michigan Accelerator for Inductive Z-pinch Experiments (MAIZE) facility at the University of Michigan. For 600 kA drive current, a 15 T axial magnetic field is produced using helical return current posts. During the current pulse, the magnetic field may diffuse into the foil, creating a sheared magnetic field along with the possibility of shear stabilization of the MRT instability. Theoretical investigation at UM has shown that a sheared azimuthal magnetic field coupled with an axial magnetic field reduces the MRT growth rate in general. In order to study this effect, the amount of magnetic shear is controlled by offsetting the initial position of the foil. A 775 nm Ti:sapphire laser will be used to shadowgraph the foil in order to measure the MRT growth rate. By comparing these results to previous experiments at UM, the effects of magnetic shear and an axial magnetic field will be determined. This work was supported by US DoE. S.G. Patel and A.M. Steiner supported by NPSC funded by Sandia. D.A. Yager-Elorriaga supported by NSF fellowship Grant DGE 1256260.

Spectroscopic Measurements of Planar Foil Plasmas Driven by a MA LTD

NASA Astrophysics Data System (ADS)

Patel, Sonal; Yager-Elorriaga, David; Steiner, Adam; Jordan, Nick; Gilgenbach, Ronald; Lau, Y. Y.

2014-10-01

Planar foil ablation experiments are being conducted on the Linear Transformer Driver (LTD) at the University of Michigan. The experiment consists of a 400 nm-thick, Al planar foil and a current return post. An optical fiber is placed perpendicular to the magnetic field and linear polarizers are used to isolate the pi and sigma lines. The LTD is charged to +/-70 kV with approximately 400-500 kA passing through the foil. Laser shadowgraphy has previously imaged the plasma and measured anisotropy in the Magneto Rayleigh-Taylor (MRT) instability. Localized magnetic field measurements using Zeeman splitting during the current rise is expected to yield some insight into this anisotropy. Initial experiments use Na D lines of Al foils seeded with sodium to measure Zeeman splitting. Several ion lines are also currently being studied, such as Al III and C IV, to probe the higher temperature core plasma. In planned experiments, several lens-coupled optical fibers will be placed across the foil, and local magnetic field measurements will be taken to measure current division within the plasma. This work was supported by US DoE. S.G. Patel and A.M. Steiner supported by NPSC funded by Sandia. D.A. Yager supported by NSF fellowship Grant DGE 1256260.

Transport of Indirect Excitons in High Magnetic Fields

NASA Astrophysics Data System (ADS)

Dorow, C. J.; Kuznetsova, Y. Y.; Calman, E. V.; Butov, L. V.; Wilkes, J.; Campman, K. L.; Gossard, A. C.

Spatially- and spectrally-resolved photoluminescence measurements of indirect excitons in high magnetic fields are presented. The high magnetic field regime for excitons is realized when the cyclotron splitting compares to the exciton binding energy. Due to small mass and binding energy, the high magnetic field regime for excitons is achievable in lab, requiring a few Tesla. Long indirect exciton lifetimes allow large exciton transport distances before recombination, giving an opportunity to study transport and relaxation kinetics of indirect magnetoexcitons via optical imaging. Indirect excitons in several Landau level states are realized. 0e -0h indirect magnetoexcitons (formed from electrons and holes at zeroth Landau levels) travel over large distances and form an emission ring around the excitation spot. In contrast, the 1e -1h and 2e -2h states do not exhibit long transport distances, and the spatial profiles of the emission closely follow the laser excitation. The 0e -0h indirect magnetoexciton transport distance reduces with increasing magnetic field. Accompanying theoretical work explains these effects in terms of magnetoexciton energy relaxation and effective mass enhancement. Supported by NSF Grant No. 1407277. J.W. was supported by the EPSRC (Grant EP/L022990/1). C.J.D. was supported by the NSF Graduate Research Fellowship Program under Grant No. DGE-1144086.

Impact of Ethylene diurea (EDU) on growth, yield and proteome of two winter wheat varieties under high ambient ozone phytotoxicity.

PubMed

Gupta, Sunil K; Sharma, Marisha; Majumder, Baisakhi; Maurya, Vivek K; Lohani, Meenakshi; Deeba, Farah; Pandey, Vivek

2018-04-01

The present study evaluated the impact of high ambient O 3 on morphological, physiological and biochemical traits and leaf proteome in two high-yielding varieties of wheat using ethylene diurea (EDU) as foliar spray (200 and 300 ppm). Average ambient ozone concentration was 60 ppb which was more than sufficient to cause phytotoxic effects. EDU treatment resulted in less lipid peroxidation along with increased chlorophyll content, biomass and yield. EDU alleviated the negative effects of ozone by enhancing activities of antioxidants and antioxidative enzymes. Two dimensional electrophoresis (2DGE) analysis revealed massive changes in protein abundance in Kundan at vegetative stage (50% proteins were increased, 20% were decreased) and at flowering stage (25% increased, 18% decreased). In PBW 343 at both the developmental stages about 15% proteins were increased whereas 20% were decreased in abundance. Higher abundance of proteins related to carbon metabolism, defense and photorespiration conferred tolerance to EDU treated Kundan. In PBW343, EDU provided incomplete protection as evidenced by low abundance of many primary metabolism related proteins. Proteomic changes in response to EDU treatment in two varieties are discussed in relation to growth and yield. Copyright © 2018 Elsevier Ltd. All rights reserved.

High Surface Area Dendrite Nanoelectrodes for Electrochemistry

NASA Astrophysics Data System (ADS)

Nesbitt, Nathan; Glover, Jennifer; Goyal, Saurabh; Simidjiysky, Svetoslav; Naughton, Michael

2014-03-01

Solution-based electrodeposition of metal using a low ion concentration, surface passivation agents, and/or electrochemical crystal conditioning has allowed for the formation of high surface area metal electrodes, useful for Raman spectroscopy and electrochemical sensors. Additionally, high frequency electrical oscillations have been used to electrically connect co-planar electrodes, a process called directed electrochemical nanowire assembly (DENA). These approaches aim to control the crystal face that metal atoms in solution will nucleate onto, thus causing anisotropic growth of metal crystals. However, DENA has not been used to create high surface area electrodes, and no study has been conducted on the effect of micron-scale surface topography on the initial nucleation of metal crystals on the electrode surface. When DENA is used to create a high surface area electrode, such a texture has a strong impact on the subsequent topography of the three dimensional dendritic structures by limiting the areal density of crystals on the electrode surface. Such structures both demonstrate unique physics concerning the nucleation of metal dendrites, and offer a unique and highly facile fabrication method of high surface area electrodes, useful for chemical and biological sensing. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. (DGE-1258923).

Large scale structures in a turbulent boundary layer and their imprint on wall shear stress

NASA Astrophysics Data System (ADS)

Pabon, Rommel; Barnard, Casey; Ukeiley, Lawrence; Sheplak, Mark

2015-11-01

Experiments were performed on a turbulent boundary layer developing on a flat plate model under zero pressure gradient flow. A MEMS differential capacitive shear stress sensor with a 1 mm × 1 mm floating element was used to capture the fluctuating wall shear stress simultaneously with streamwise velocity measurements from a hot-wire anemometer traversed in the wall normal direction. Near the wall, the peak in the cross correlation corresponds to an organized motion inclined 45° from the wall. In the outer region, the peak diminishes in value, but is still significant at a distance greater than half the boundary layer thickness, and corresponds to a structure inclined 14° from the wall. High coherence between the two signals was found for the low-frequency content, reinforcing the belief that large scale structures have a vital impact on wall shear stress. Thus, estimation of the wall shear stress from the low-frequency velocity signal will be performed, and is expected to be statistically significant in the outer boundary layer. Additionally, conditionally averaged mean velocity profiles will be presented to assess the effects of high and low shear stress. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1315138.

Spike frequency adaptation is a possible mechanism for control of attractor preference in auto-associative neural networks

NASA Astrophysics Data System (ADS)

Roach, James; Sander, Leonard; Zochowski, Michal

Auto-associative memory is the ability to retrieve a pattern from a small fraction of the pattern and is an important function of neural networks. Within this context, memories that are stored within the synaptic strengths of networks act as dynamical attractors for network firing patterns. In networks with many encoded memories, some attractors will be stronger than others. This presents the problem of how networks switch between attractors depending on the situation. We suggest that regulation of neuronal spike-frequency adaptation (SFA) provides a universal mechanism for network-wide attractor selectivity. Here we demonstrate in a Hopfield type attractor network that neurons minimal SFA will reliably activate in the pattern corresponding to a local attractor and that a moderate increase in SFA leads to the network to converge to the strongest attractor state. Furthermore, we show that on long time scales SFA allows for temporal sequences of activation to emerge. Finally, using a model of cholinergic modulation within the cortex we argue that dynamic regulation of attractor preference by SFA could be critical for the role of acetylcholine in attention or for arousal states in general. This work was supported by: NSF Graduate Research Fellowship Program under Grant No. DGE 1256260 (JPR), NSF CMMI 1029388 (MRZ) and NSF PoLS 1058034 (MRZ & LMS).

A theory for protein dynamics: Global anisotropy and a normal mode approach to local complexity

NASA Astrophysics Data System (ADS)

Copperman, Jeremy; Romano, Pablo; Guenza, Marina

2014-03-01

We propose a novel Langevin equation description for the dynamics of biological macromolecules by projecting the solvent and all atomic degrees of freedom onto a set of coarse-grained sites at the single residue level. We utilize a multi-scale approach where molecular dynamic simulations are performed to obtain equilibrium structural correlations input to a modified Rouse-Zimm description which can be solved analytically. The normal mode solution provides a minimal basis set to account for important properties of biological polymers such as the anisotropic global structure, and internal motion on a complex free-energy surface. This multi-scale modeling method predicts the dynamics of both global rotational diffusion and constrained internal motion from the picosecond to the nanosecond regime, and is quantitative when compared to both simulation trajectory and NMR relaxation times. Utilizing non-equilibrium sampling techniques and an explicit treatment of the free-energy barriers in the mode coordinates, the model is extended to include biologically important fluctuations in the microsecond regime, such as bubble and fork formation in nucleic acids, and protein domain motion. This work supported by the NSF under the Graduate STEM Fellows in K-12 Education (GK-12) program, grant DGE-0742540 and NSF grant DMR-0804145, computational support from XSEDE and ACISS.

Learning with touchscreen devices: game strategies to improve geometric thinking

NASA Astrophysics Data System (ADS)

Soldano, Carlotta; Arzarello, Ferdinando

2016-03-01

The aim of this paper is to reflect on the importance of the students' game-strategic thinking during the development of mathematical activities. In particular, we hypothesise that this type of thinking helps students in the construction of logical links between concepts during the "argumentation phase" of the proving process. The theoretical background of our study lies in the works of J. Hintikka, a Finnish logician, who developed a new type of logic, based on game theory, called the logic of inquiry. In order to experiment with this new approach to the teaching and learning of mathematics, we have prepared five game-activities based on geometric theorems in which two players play against each other in a multi-touch dynamic geometric environment (DGE). In this paper, we present the design of the first game-activity and the relationship between it and the logic of inquiry. Then, adopting the theoretical framework of the instrumental genesis by Vérillon and Rabardel (EJPE 10: 77-101, 1995), we will present and analyse significant actions and dialogues developed by students while they are solving the game. We focus on the presence of a particular way of playing the game introduced by the students, the "reflected game", and highlight its functions for the development of the task.

Baculovirus expression system and method for high throughput expression of genetic material

DOEpatents

Clark, Robin; Davies, Anthony

2001-01-01

The present invention provides novel recombinant baculovirus expression systems for expressing foreign genetic material in a host cell. Such expression systems are readily adapted to an automated method for expression foreign genetic material in a high throughput manner. In other aspects, the present invention features a novel automated method for determining the function of foreign genetic material by transfecting the same into a host by way of the recombinant baculovirus expression systems according to the present invention.

Construction and development of an auto-regulatory gene expression system in Bacillus subtilis.

PubMed

Guan, Chengran; Cui, Wenjing; Cheng, Jintao; Zhou, Li; Guo, Junling; Hu, Xu; Xiao, Guoping; Zhou, Zhemin

2015-09-21

Bacillus subtilis is an all-important Gram-positive bacterium of valuable biotechnological utility that has been widely used to over-produce industrially and pharmaceutically relevant proteins. There are a variety of expression systems in terms of types of transcriptional patterns, among which the auto-inducible and growth-phase-dependent promoters are gaining increasing favor due to their inducer-independent feature, allowing for the potential to industrially scale-up. To expand the applicability of the auto-inducible expression system, a novel auto-regulatory expression system coupled with cell density was constructed and developed in B. subtilis using the quorum-sensing related promoter srfA (PsrfA). The promoter of the srf operon was used to construct an expression plasmid with the green fluorescent protein (GFP) downstream of PsrfA. The expression displayed a cell-density-dependent pattern in that GFP had a fairly low expression level at the early exponential stage and was highly expressed at the late exponential as well as the stationary stages. Moreover, the recombinant system had a similar expression pattern in wild-type B. subtilis 168, WB600, and WB800, as well as in B. subtilis 168 derivative strain 1681, with the complete deletion of PsrfA, indicating the excellent compatibility of this system. Noticeably, the expression strength of PsrfA was enhanced by optimizing the -10 and -35 core sequence by substituting both sequences with consensus sequences. Importantly, the expression pattern was successfully developed in an auto-regulatory cell-density coupling system by the simple addition of glucose in which GFP could not be strongly expressed until glucose was depleted, resulting in a greater amount of the GFP product and increased cell density. The expression system was eventually tested by the successful over-production of aminopeptidase to a desired level. The auto-regulatory cell density coupling system that is mediated by PsrfA is a novel expression system that has an expression pattern that is split between cell-growth and over-expression, leading to an increase in cell density and elevating the overall expression levels of heterologously expressed proteins. The broad applicability of this system and inducer-free expression property in B. subtilis facilitate the industrial scale-up and medical applications for the over-production of a variety of desired proteins.

Engineering low-temperature expression systems for heterologous production of cold-adapted enzymes.

PubMed

Bjerga, Gro Elin Kjæreng; Lale, Rahmi; Williamson, Adele Kim

2016-01-01

Production of psychrophilic enzymes in the commonly used mesophilic expression systems is hampered by low intrinsic stability of the recombinant enzymes at the optimal host growth temperatures. Unless strategies for low-temperature expression are advanced, research on psychrophilic enzymes may end up being biased toward those that can be stably produced in commonly used mesophilic host systems. Two main strategies are currently being explored for the development of low-temperature expression in bacterial hosts: (i) low-temperature adaption of existing mesophilic expression systems, and (ii) development of new psychrophilic hosts. These developments include genetic engineering of the expression cassettes to optimize the promoter/operator systems that regulate heterologous expression. In this addendum we present our efforts in the development of such low-temperature expression systems, and speculate about future advancements in the field and potential applications.

21 CFR 862.1163 - Cardiac allograft gene expression profiling test system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Cardiac allograft gene expression profiling test... Chemistry Test Systems § 862.1163 Cardiac allograft gene expression profiling test system. (a) Identification. A cardiac allograft gene expression profiling test system is a device that measures the...

Integrating T7 RNA Polymerase and Its Cognate Transcriptional Units for a Host-Independent and Stable Expression System in Single Plasmid.

PubMed

Liang, Xiao; Li, Chenmeng; Wang, Wenya; Li, Qiang

2018-05-18

Metabolic engineering and synthetic biology usually require universal expression systems for stable and efficient gene expression in various organisms. In this study, a host-independent and stable T7 expression system had been developed by integrating T7 RNA polymerase and its cognate transcriptional units in single plasmid. The expression of T7 RNA polymerase was restricted below its lethal threshold using a T7 RNA polymerase antisense gene cassette, which allowed long periods of cultivation and protein production. In addition, by designing ribosome binding sites, we further tuned the expression capacity of this novel T7 system within a wide range. This host-independent expression system efficiently expressed genes in five different Gram-negative strains and one Gram-positive strain and was also shown to be applicable in a real industrial d- p-hydroxyphenylglycine production system.

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

Yu, V; Nguyen, D; Tran, A

Purpose: To develop and clinically implement 4π radiotherapy, an inverse optimization platform that maximally utilizes non-coplanar intensity modulated radiotherapy (IMRT) beams to significantly improve critical organ sparing. Methods: A 3D scanner was used to digitize the human and phantom subject surfaces, which were positioned in the computer assisted design (CAD) model of a TrueBeam machine to create a virtual geometrical model, based on which, the feasible beam space was calculated for different tumor locations. Beamlets were computed for all feasible beams using convolution/superposition. A column generation algorithm was employed to optimize patient specific beam orientations and fluence maps. Optimal routingmore » through all selected beams were calculated by a level set method. The resultant plans were converted to XML files and delivered to phantoms in the TrueBeam developer mode. Finally, 4π plans were recomputed in Eclipse and manually delivered to recurrent GBM patients. Results: Compared to IMRT utilizing manually selected beams and volumetric modulated arc therapy plans, markedly improved dosimetry was observed using 4π for the brain, head and neck, liver, lung, and prostate patients. The improvements were due to significantly improved conformality and reduced high dose spillage to organs mediolateral to the PTV. The virtual geometrical model was experimentally validated. Safety margins with 99.9% confidence in collision avoidance were included to the model based model accuracy estimates determined via 300 physical machine to phantom distance measurements. Automated delivery in the developer mode was completed in 10 minutes and collision free. Manual 4 π treatment on the GBM cases resulted in significant brainstem sparing and took 35–45 minutes including multiple images, which showed submillimeter cranial intrafractional motion. Conclusion: The mathematical modeling utilized in 4π is accurate to create and guide highly complex non-coplanar IMRT treatments that consistently and significantly outperform human-operator-created plans. Deliverability of such plans is clinically demonstrated. This work is funded by Varian Medical Systems and the NSF Graduate Research Fellowship DGE-1144087.« less

Towards an animal model of ovarian cancer: cataloging chicken blood proteins using combinatorial peptide ligand libraries coupled with shotgun proteomic analysis for translational research.

PubMed

Ma, Yingying; Sun, Zeyu; de Matos, Ricardo; Zhang, Jing; Odunsi, Kunle; Lin, Biaoyang

2014-05-01

Epithelial ovarian cancer is the most deadly gynecological cancer around the world, with high morbidity in industrialized countries. Early diagnosis is key in reducing its morbidity rate. Yet, robust biomarkers, diagnostics, and animal models are still limited for ovarian cancer. This calls for broader omics and systems science oriented diagnostics strategies. In this vein, the domestic chicken has been used as an ovarian cancer animal model, owing to its high rate of developing spontaneous epithelial ovarian tumors. Chicken blood has thus been considered a surrogate reservoir from which cancer biomarkers can be identified. However, the presence of highly abundant proteins in chicken blood has compromised the applicability of proteomics tools to study chicken blood owing to a lack of immunodepletion methods. Here, we demonstrate that a combinatorial peptide ligand library (CPLL) can efficiently remove highly abundant proteins from chicken blood samples, consequently doubling the number of identified proteins. Using an integrated CPLL-1DGE-LC-MSMS workflow, we identified a catalog of 264 unique proteins. Functional analyses further suggested that most proteins were coagulation and complement factors, blood transport and binding proteins, immune- and defense-related proteins, proteases, protease inhibitors, cellular enzymes, or cell structure and adhesion proteins. Semiquantitative spectral counting analysis identified 10 potential biomarkers from the present chicken ovarian cancer model. Additionally, many human homologs of chicken blood proteins we have identified have been independently suggested as diagnostic biomarkers for ovarian cancer, further triangulating our novel observations reported here. In conclusion, the CPLL-assisted proteomic workflow using the chicken ovarian cancer model provides a feasible platform for translational research to identify ovarian cancer biomarkers and understand ovarian cancer biology. To the best of our knowledge, we report here the most comprehensive survey of the chicken blood proteome to date.

A plasmid-based Escherichia coli gene expression system with cell-to-cell variation below the extrinsic noise limit

PubMed Central

2017-01-01

Experiments in synthetic biology and microbiology can benefit from protein expression systems with low cell-to-cell variability (noise) and expression levels precisely tunable across a useful dynamic range. Despite advances in understanding the molecular biology of microbial gene regulation, many experiments employ protein-expression systems exhibiting high noise and nearly all-or-none responses to induction. I present an expression system that incorporates elements known to reduce gene expression noise: negative autoregulation and bicistronic transcription. I show by stochastic simulation that while negative autoregulation can produce a more gradual response to induction, bicistronic expression of a repressor and gene of interest can be necessary to reduce noise below the extrinsic limit. I synthesized a plasmid-based system incorporating these principles and studied its properties in Escherichia coli cells, using flow cytometry and fluorescence microscopy to characterize induction dose-response, induction/repression kinetics and gene expression noise. By varying ribosome binding site strengths, expression levels from 55–10,740 molecules/cell were achieved with noise below the extrinsic limit. Individual strains are inducible across a dynamic range greater than 20-fold. Experimental comparison of different regulatory networks confirmed that bicistronic autoregulation reduces noise, and revealed unexpectedly high noise for a conventional expression system with a constitutively expressed transcriptional repressor. I suggest a hybrid, low-noise expression system to increase the dynamic range. PMID:29084263

ATNT: an enhanced system for expression of polycistronic secondary metabolite gene clusters in Aspergillus niger.

PubMed

Geib, Elena; Brock, Matthias

2017-01-01

Fungi are treasure chests for yet unexplored natural products. However, exploitation of their real potential remains difficult as a significant proportion of biosynthetic gene clusters appears silent under standard laboratory conditions. Therefore, elucidation of novel products requires gene activation or heterologous expression. For heterologous gene expression, we previously developed an expression platform in Aspergillus niger that is based on the transcriptional regulator TerR and its target promoter P terA . In this study, we extended this system by regulating expression of terR  by the doxycycline inducible Tet-on system. Reporter genes cloned under the control of the target promoter P terA remained silent in the absence of doxycycline, but were strongly expressed when doxycycline was added. Reporter quantification revealed that the coupled system results in about five times higher expression rates compared to gene expression under direct control of the Tet-on system. As production of secondary metabolites generally requires the expression of several biosynthetic genes, the suitability of the self-cleaving viral peptide sequence P2A was tested in this optimised expression system. P2A allowed polycistronic expression of genes required for Asp-melanin formation in combination with the gene coding for the red fluorescent protein tdTomato. Gene expression and Asp-melanin formation was prevented in the absence of doxycycline and strongly induced by addition of doxycycline. Fluorescence studies confirmed the correct subcellular localisation of the respective enzymes. This tightly regulated but strongly inducible expression system enables high level production of secondary metabolites most likely even those with toxic potential. Furthermore, this system is compatible with polycistronic gene expression and, thus, suitable for the discovery of novel natural products.

Complex Expression of the Cellulolytic Transcriptome of Saccharophagus degradans † ▿

PubMed Central

Zhang, Haitao; Hutcheson, Steven W.

2011-01-01

Saccharophagus degradans is an aerobic marine bacterium that can degrade cellulose by the induced expression of an unusual cellulolytic system composed of multiple endoglucanases and glucosidases. To understand the regulation of the cellulolytic system, transcript levels for the genes predicted to contribute to the cellulolytic system were monitored by quantitative real-time PCR (qRT-PCR) during the transition to growth on cellulose. Four glucanases of the cellulolytic system exhibited basal expression during growth on glucose. All but one of the predicted cellulolytic system genes were induced strongly during growth on Avicel, with three patterns of expression observed. One group showed increased expression (up to 6-fold) within 4 h of the nutritional shift, with the relative expression remaining constant over the next 22 h. A second group of genes was strongly induced between 4 and 10 h after nutritional transfer, with relative expression declining thereafter. The third group of genes was slowly induced and was expressed maximally after 24 h. Cellodextrins and cellobiose, products of the predicted basally expressed endoglucanases, stimulated expression of representative cellulase genes. A model is proposed by which the activity of basally expressed endoglucanases releases cellodextrins from Avicel that are then perceived and transduced to initiate transcription of each of the regulated cellulolytic system genes forming an expression pattern. PMID:21705539

Proposal of Self-Learning and Recognition System of Facial Expression

NASA Astrophysics Data System (ADS)

Ogawa, Yukihiro; Kato, Kunihito; Yamamoto, Kazuhiko

We describe realization of more complicated function by using the information acquired from some equipped unripe functions. The self-learning and recognition system of the human facial expression, which achieved under the natural relation between human and robot, are proposed. The robot with this system can understand human facial expressions and behave according to their facial expressions after the completion of learning process. The system modelled after the process that a baby learns his/her parents’ facial expressions. Equipping the robot with a camera the system can get face images and equipping the CdS sensors on the robot’s head the robot can get the information of human action. Using the information of these sensors, the robot can get feature of each facial expression. After self-learning is completed, when a person changed his facial expression in front of the robot, the robot operates actions under the relevant facial expression.

A new maltose-inducible high-performance heterologous expression system in Bacillus subtilis.

PubMed

Yue, Jie; Fu, Gang; Zhang, Dawei; Wen, Jianping

2017-08-01

To improve heterologous proteins production, we constructed a maltose-inducible expression system in Bacillus subtilis. An expression system based on the promoter for maltose utilization constructed in B. subtilis. Successively, to improve the performance of the P malA -derived system, mutagenesis was employed by gradually shortening the length of P malA promoter and altering the spacing between the predicted MalR binding site and the -35 region. Furthermore, deletion of the maltose utilization genes (malL and yvdK) improved the P malA promoter activity. Finally, using this efficient maltose-inducible expression system, we enhanced the production of luciferase and D-aminoacylase, compared with the P hpaII system. A maltose-inducible expression system was constructed and evaluated. It could be used for high level expression of heterologous proteins production.

[Prokaryotic expression systems].

PubMed

Porowińska, Dorota; Wujak, Magdalena; Roszek, Katarzyna; Komoszyński, Michał

2013-03-01

For overproduction of recombinant proteins both eukaryotic and prokaryotic expression systems are used. Choosing the right system depends, among other things, on the growth rate and culture of host cells, level of the target gene expression and posttranslational processing of the synthesized protein. Regardless of the type of expression system, its basic elements are the vector and the expression host. The most widely used system for protein overproduction, both on a laboratory and industrial scale, is the prokaryotic system. This system is based primarily on the bacteria E. coli, although increasingly often Bacillus species are used. The prokaryotic system allows one to obtain large quantities of recombinant proteins in a short time. A simple and inexpensive bacterial cell culture and well-known mechanisms of transcription and translation facilitate the use of these microorganisms. The simplicity of genetic modifications and the availability of many bacterial mutants are additional advantages of the prokaryotic system. In this article we characterize the structural elements of prokaryotic expression vectors. Also strategies for preparation of the target protein gene that increase productivity, facilitate detection and purification of recombinant protein and provide its activity are discussed. Bacterial strains often used as host cells in expression systems as well as the potential location of heterologous proteins are characterized. Knowledge of the basic elements of the prokaryotic expression system allows for production of biologically active proteins in a short time and in satisfactory quantities. 

Dual transcriptional-translational cascade permits cellular level tuneable expression control

PubMed Central

Morra, Rosa; Shankar, Jayendra; Robinson, Christopher J.; Halliwell, Samantha; Butler, Lisa; Upton, Mathew; Hay, Sam; Micklefield, Jason; Dixon, Neil

2016-01-01

The ability to induce gene expression in a small molecule dependent manner has led to many applications in target discovery, functional elucidation and bio-production. To date these applications have relied on a limited set of protein-based control mechanisms operating at the level of transcription initiation. The discovery, design and reengineering of riboswitches offer an alternative means by which to control gene expression. Here we report the development and characterization of a novel tunable recombinant expression system, termed RiboTite, which operates at both the transcriptional and translational level. Using standard inducible promoters and orthogonal riboswitches, a multi-layered modular genetic control circuit was developed to control the expression of both bacteriophage T7 RNA polymerase and recombinant gene(s) of interest. The system was benchmarked against a number of commonly used E. coli expression systems, and shows tight basal control, precise analogue tunability of gene expression at the cellular level, dose-dependent regulation of protein production rates over extended growth periods and enhanced cell viability. This novel system expands the number of E. coli expression systems for use in recombinant protein production and represents a major performance enhancement over and above the most widely used expression systems. PMID:26405200

Evaluation of novel inducible promoter/repressor systems for recombinant protein expression in Lactobacillus plantarum.

PubMed

Heiss, Silvia; Hörmann, Angelika; Tauer, Christopher; Sonnleitner, Margot; Egger, Esther; Grabherr, Reingard; Heinl, Stefan

2016-03-10

Engineering lactic acid bacteria (LAB) is of growing importance for food and feed industry as well as for in vivo vaccination or the production of recombinant proteins in food grade organisms. Often, expression of a transgene is only desired at a certain time point or period, e.g. to minimize the metabolic burden for the host cell or to control the expression time span. For this purpose, inducible expression systems are preferred, though cost and availability of the inducing agent must be feasible. We selected the plasmid free strain Lactobacillus plantarum 3NSH for testing and characterization of novel inducible promoters/repressor systems. Their feasibility in recombinant protein production was evaluated. Expression of the reporter protein mCherry was monitored with the BioLector(®) micro-fermentation system. Reporter gene mCherry expression was compared under the control of different promoter/repressor systems: PlacA (an endogenous promoter/repressor system derived from L. plantarum 3NSH), PxylA (a promoter/repressor system derived from Bacillus megaterium DSMZ 319) and PlacSynth (synthetic promoter and codon-optimized repressor gene based on the Escherichia coli lac operon). We observed that PlacA was inducible solely by lactose, but not by non-metabolizable allolactose analoga. PxylA was inducible by xylose, yet showed basal expression under non-induced conditions. Growth on galactose (as compared to exponential growth phase on glucose) reduced basal mCherry expression at non-induced conditions. PlacSynth was inducible with TMG (methyl β-D-thiogalactopyranoside) and IPTG (isopropyl β-D-1-thiogalactopyranoside), but also showed basal expression without inducer. The promoter PlacSynth was used for establishment of a dual plasmid expression system, based on T7 RNA polymerase driven expression in L. plantarum. Comparative Western blot supported BioLector(®) micro-fermentation measurements. Conclusively, overall expression levels were moderate (compared to a constitutive promoter). We evaluated different inducible promoters, as well as an orthologous expression system, for controlled gene expression in L. plantarum. Furthermore, here we provide proof of concept for a T7 RNA polymerase based expression system for L. plantarum. Thereby we expanded the molecular toolbox for an industrial relevant and generally regarded as safe (GRAS) strain.

High-yield, in vitro protein expression using a continuous-exchange, coupled transcription/ translation system.

PubMed

Martin, G A; Kawaguchi, R; Lam, Y; DeGiovanni, A; Fukushima, M; Mutter, W

2001-10-01

The Rapid Translation System (RTS 500) (Roche Molecular Biochemicals) is a high-yield protein expression system that utilizes an enhanced E. coli lysate for an in vitro transcription/translation reaction. In contrast to conventional transcription/translation, this system allows protein expression to continue for more than 24 h. We demonstrated the utility of the RTS 500 by expressing different soluble and active proteins that generally pose problems in cell-based expression systems. We first expressed GFP-lunasin, a fusion protein that, because of its toxicity, has been impossible to produce in whole cells. The second protein we expressed, human interleukin-2 (IL-2), is generally difficult to produce, either as the native molecule or as a GSTfusion protein, in a soluble form in bacteria. Finally, we demonstrated the capacity of the RTS 500 to co-express proteins, by the simultaneous production of GFP and CAT in a single reaction. This new technology appears to be particularly usefulfor the convenient production of preparative amounts (100-900 microg) of proteins that are toxic or insoluble in cell-based systems.

Impact of Alloy Fluctuations on Radiative and Auger Recombination in InGaN Quantum Wells

NASA Astrophysics Data System (ADS)

Jones, Christina; Teng, Chu-Hsiang; Yan, Qimin; Ku, Pei-Cheng; Kioupakis, Emmanouil

Light-emitting diodes (LEDs) based on indium gallium nitride (InGaN) are important for efficient solid-state lighting (2014 Nobel Prize in Physics). Despite its many successes, InGaN suffers from issues that reduce the efficiency of devices at high power, such as the green gap and efficiency droop. The origin of the droop has been attributed to Auger recombination, mediated by carrier scattering due to phonons and alloy disorder. Additionally, InGaN exhibits atomic-scale composition fluctuations that localize carriers and may affect the efficiency. In this work, we study the effect of local composition fluctuations on the radiative recombination rate, Auger recombination rate, and efficiency of InGaN/GaN quantum wells. We apply k.p calculations to simulate band edges and wave functions of quantum wells with fluctuating alloy distributions based on atom probe tomography data, and we evaluate double and triple overlaps of electron and hole wave functions. We compare results for quantum wells with fluctuating alloy distributions to those with uniform alloy compositions and to published work. Our results demonstrate that alloy-composition fluctuations aggravate the efficiency-droop and green-gap problems and further reduce LED efficiency at high power. We acknowledge the NSF CAREER award DMR-1254314, the NSF Graduate Research Fellowship Program DGE-1256260, and the DOE NERSC facility (DE-AC02-05CH11231).

Radiative and Auger recombination of degenerate carriers in InN

NASA Astrophysics Data System (ADS)

McAllister, Andrew; Bayerl, Dylan; Kioupakis, Emmanouil

Group-III nitrides find applications in many fields - energy conversion, sensors, and solid-state lighting. The band gaps of InN, GaN and AlN alloys span the infrared to ultraviolet spectral range. However, nitride optoelectronic devices suffer from a drop in efficiency as carrier density increases. A major component of this decrease is Auger recombination, but its influence is not fully understood, particularly for degenerate carriers. For nondegenerate carriers the radiative rate scales as the carrier density squared, while the Auger rate scales as the density cubed. However, it is unclear how these power laws decrease as carriers become degenerate. Using first-principles calculations we studied the dependence of the radiative and Auger recombination rates on carrier density in InN. We found a more complex dependence on the Auger rate than expected. The power law of the Auger rate changes at different densities depending on the type of Auger process involved and the type of carriers that have become degenerate. In contrast, the power law of the radiative rate changes when either carrier type becomes degenerate. This creates problems in designing devices, as Auger remains a major contributor to carrier recombination at densities for which radiative recombination is suppressed by phase-space filling. This work was supported by NSF (GRFP DGE 1256260 and CAREER DMR-1254314). Computational resources provided by the DOE NERSC facility (DE-AC02-05CH11231).

An Experimental Evaluation of Blockage Corrections for Current Turbines

NASA Astrophysics Data System (ADS)

Ross, Hannah; Polagye, Brian

2017-11-01

Flow confinement has been shown to significantly alter the performance of turbines that extract power from water currents. These performance effects are related to the degree of constraint, defined by the ratio of turbine projected area to channel cross-sectional area. This quantity is referred to as the blockage ratio. Because it is often desirable to adjust experimental observations in water channels to unconfined conditions, analytical corrections for both wind and current turbines have been derived. These are generally based on linear momentum actuator disk theory but have been applied to turbines without experimental validation. This work tests multiple blockage corrections on performance and thrust data from a cross-flow turbine and porous plates (experimental analogues to actuator disks) collected in laboratory flumes at blockage ratios ranging between 10 and 35%. To isolate the effects of blockage, the Reynolds number, Froude number, and submergence depth were held constant while the channel width was varied. Corrected performance data are compared to performance in a towing tank at a blockage ratio of less than 5%. In addition to examining the accuracy of each correction, underlying assumptions are assessed to determine why some corrections perform better than others. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1256082 and the Naval Facilities Engineering Command (NAVFAC).

Implication of Taylor's hypothesis on amplitude modulation

NASA Astrophysics Data System (ADS)

Howland, Michael; Yang, Xiang

2017-11-01

Amplitude modulation is a physical phenomenon which describes the non-linear inter-scale interaction between large and small scales in a turbulent wall-bounded flow. The amplitude of the small scale fluctuations are modulated by the large scale flow structures. Due to the increase of amplitude modulation as a function of Reynolds number (Reτ = δuτ / ν), this phenomenon is frequently studied using experimental temporal 1D signals, taken using hot-wire anemometry. Typically, Taylor's frozen turbulence hypothesis has been invoked where the convection by velocity fluctuations is neglected and the mean velocity is used as the convective velocity. At high Reynolds numbers, turbulent fluctuations are comparable to the mean velocity in the near wall region (y+ O(10)), and as a result, using a constant global convective velocity systematically locally compresses or stretches a velocity signal when converting from temporal to spatial domain given a positive or negative fluctuation respectively. Despite this, temporal hot-wire data from wind tunnel or field experiments of high Reynolds number boundary layer flows can still be used for measuring modulation provided that the local fluid velocity is used as the local convective velocity. MH is funded through the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1656518 and the Stanford Graduate Fellowship. XY is funded by the US AFOSR, Grant No. 1194592-1-TAAHO monitored by Dr. Ivett Leyva.

Analysis of Lagrangian stretching in turbulent channel flow using a database task-parallel particle tracking approach

NASA Astrophysics Data System (ADS)

Meneveau, Charles; Johnson, Perry; Hamilton, Stephen; Burns, Randal

2016-11-01

An intrinsic property of turbulent flows is the exponential deformation of fluid elements along Lagrangian paths. The production of enstrophy by vorticity stretching follows from a similar mechanism in the Lagrangian view, though the alignment statistics differ and viscosity prevents unbounded growth. In this paper, the stretching properties of fluid elements and vorticity along Lagrangian paths are studied in a channel flow at Reτ = 1000 and compared with prior, known results from isotropic turbulence. To track Lagrangian paths in a public database containing Direct Numerical Simulation (DNS) results, the task-parallel approach previously employed in the isotropic database is extended to the case of flow in a bounded domain. It is shown that above 100 viscous units from the wall, stretching statistics are equal to their isotropic values, in support of the local isotropy hypothesis. Normalized by dissipation rate, the stretching in the buffer layer and below is less efficient due to less favorable alignment statistics. The Cramér function characterizing cumulative Lagrangian stretching statistics shows that overall the channel flow has about half of the stretching per unit dissipation compared with isotropic turbulence. Supported by a National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1232825, and by National Science Foundation Grants CBET-1507469, ACI-1261715, OCI-1244820 and by JHU IDIES.

Vortex dynamics of very low aspect ratio rectangular orifice synthetic jets

NASA Astrophysics Data System (ADS)

Straccia, Joseph; Farnsworth, John; Experimental Aerodynamics Laboratory Team

2017-11-01

The vast majority of prior synthetic jet research has focused on actuators with either circular orifices or rectangular orifices with high aspect ratios (AR), i.e. AR >=25. The results reported in these studies have also been biased towards bulk and time averaged statistics of the jet, viewing them in a steady sense as a source of momentum addition. Recent work has revealed that the unsteady vortex dynamics in a synthetic jet can be very relevant to how the jet interacts with and influences the base flow. In this study the synthetic jet issued into a quiescent fluid by an actuator with low orifice aspect ratios (i.e. AR =2-18) was studied using Stereoscopic Particle Image Velocimetry (SPIV) with a special focus on the vortex dynamics. The progression of vortex ring axis switching is presented and a distinct difference between the axis switching dynamics of very low AR (AR <=6) and moderate AR (AR =6-24) vortex rings is discussed. The high resolution SPIV vector fields are also used to extract details of the vortex core structure which are compared to theoretical vortex models. Furthermore, the influence of axis switching on the circulation magnitude around the vortex ring is reported in addition to how circulation varies with time as the ring advects. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. (DGE 1144083).

Strengthening Communication and Scientific Reasoning Skills of Graduate Students Through the INSPIRE Program

NASA Astrophysics Data System (ADS)

Pierce, Donna M.; McNeal, K. S.; Radencic, S. P.; Schmitz, D. W.; Cartwright, J.; Hare, D.; Bruce, L. M.

2012-10-01

Initiating New Science Partnerships in Rural Education (INSPIRE) is a five-year partnership between Mississippi State University and three nearby school districts. The primary goal of the program is to strengthen the communication and scientific reasoning skills of graduate students in geosciences, physics, chemistry, and engineering by placing them in area middle school and high school science and mathematics classrooms for ten hours a week for an entire academic year as they continue to conduct their thesis or dissertation research. Additional impacts include increased content knowledge for our partner teachers and improvement in the quality of classroom instruction using hands-on inquiry-based activities that incorporate ideas used in the research conducted by the graduate students. Current technologies, such as Google Earth, GIS, Celestia, benchtop SEM and GCMS, are incorporated into many of the lessons. Now in the third year of our program, we will present the results of our program to date, including an overview of documented graduate student, teacher, and secondary student achievements, the kinds of activities the graduate students and participating teachers have developed for classroom instruction, and the accomplishments resulting from our four international partnerships. INSPIRE is funded by the Graduate K-12 (GK-12) STEM Fellowship Program (Award No. DGE-0947419), which is part of the Division for Graduate Education of the National Science Foundation.

Jet Morphology and Coma Analysis of 103P/Hartley 2: Temporal Evolution and Interspecies Comparisons

NASA Astrophysics Data System (ADS)

Vaughan, Charles M.; Pierce, Donna M.; Cochran, Anita L.

2014-11-01

We present our results on an expanded study of the jet and coma behavior of comet 103P/Hartley 2 (a continuation of original results presented in Vaughan et al. 2012). We observed Hartley 2 pre- and post-perihelion in 2010 using the George and Cynthia Mitchell Spectrograph on the 2.7 m telescope at McDonald Observatory. Data for CN, C2, C3, CH, and NH2 were collected over six nights from 15 July to 10 November. The spectral data were used to create coma maps for each of the observed species, and the maps were processed using radial and azimuthal division techniques to create enhanced images of the coma to examine coma morphological features. To compliment the ongoing investigation of Hartley 2 as studied by the EPOXI flyby mission, we use findings from other researchers (Belton et al. 2012; Syal et al. 2012; Thomas et al. 2012) to identify dust jet locations on the nucleus and compare the computed jet directions to the radical densities in the coma at our observation times. We also calculate production rates and mixing ratios with water for suspected parent species. This work was funded by the National Science Foundation Graduate K-12 (GK-12) STEM Fellows program (Award No. DGE-0947419) and NASA’s Planetary Atmospheres program (Award No. NNX14AH18G).

Visualization of defect-induced excitonic properties of the edges and grain boundaries in synthesized monolayer molybdenum disulfide

NASA Astrophysics Data System (ADS)

Newaz, Akm; Yore, A. E.; Miller, A.; Crumrine, W.; Redd, B.; Tuck, J. A.; Wang, Bin; Smithe, K. K. H.; Pop, E.

Understanding nanoscale optical behavior of the edges and grain boundaries of synthetically grown transition metal dichalcogenides (TMDCs) is vital for optimizing their optoelectronic properties. Here we present our experimental work on spatial photoluminescence (PL) scanning of large size (>= 50 μ m) monolayer MoS2 grown by chemical vapor deposition (CVD) using a diffraction limited blue laser beam spot (wavelength 405 nm) with a beam diameter as small as 200 nm allowing us to probe nanoscale excitonic phenomena which was not observed before. We have found several important features: (i) there exists a sub-micron width strip ( 500 nm) along the edges that fluoresces 1000 % brighter than the region far inside; (ii) there is another brighter wide region consisting of parallel fluorescing lines ending at the corners of the zig-zag peripheral edges; (iii) there is a giant blue shifted A-excitonic peak, as large as 120 meV, in the PL spectra from the edges. Using density functional theory calculations, we attribute this giant blue shift to the adsorption of oxygen dimers at the edges, which reduces the excitonic binding energy. Our results offer an attractive route to tailor optical properties at the TMDC edges through defect engineering. AFOSR Grant FA9550-14-1-0251, NSF EFRI 2-DARE Grant 1542883, NSF Graduate Research Fellowship under Grant DGE-114747.

Ventilation Inception and Washout, Scaling, and Effects on Hydrodynamic Performance of a Surface Piercing Strut

NASA Astrophysics Data System (ADS)

Harwood, Casey; Young, Yin Lu; Ceccio, Steven

2014-11-01

High-lift devices that operate at or near a fluid free surface (such as surface-piercing or shallowly-submerged propellers and hydrofoils) are prone to a multiphase flow phenomenon called ventilation, wherein non-condensable gas is entrained in the low-pressure flow, forming a cavity around the body and dramatically altering the global hydrodynamic forces. Experiments are being conducted at the University of Michigan's towing tank using a canonical surface-piercing strut to investigate atmospheric ventilation. The goals of the work are (i) to gain an understanding of the dominant physics in fully wetted, partially ventilated, and fully ventilated flow regimes, (ii) to quantify the effects of governing dimensionless parameters on the transition between flow regimes, and (iii) to develop scaling relations for the transition between flow regimes. Using theoretical arguments and flow visualization techniques, new criteria are developed for classifying flow regimes and transition mechanisms. Unsteady transition mechanisms are described and mapped as functions of the governing non-dimensional parameters. A theoretical scaling relationship is developed for ventilation washout, which is shown to adequately capture the experimentally-observed washout boundary. This material is based upon work supported by the National Science Foundation Graduate Student Research Fellowship under Grant No. DGE 1256260. Support also comes from the Naval Engineering Education Center (Award No. N65540-10-C-003).

Neutron scattering study of the freezing of water near a cupric oxide surface

NASA Astrophysics Data System (ADS)

Torres, J.; Buck, Z. N.; Zhang, F. Z.; Chen, T.; Winholtz, R. A.; Kaiser, H.; Ma, H. B.; Taub, H.; Tyagi, M.

Oscillating heat pipes (OHP) offer promising two-phase heat transfer for a variety of applications, including cooling of electronic devices.2 Recently, it has been shown that a hydrophilic CuO coating on either the evaporator or condenser sections of a flat-plate OHP can significantly enhance its thermal performance.3 This finding has motivated us to assess the strength of the CuO/H2O interaction by investigating the freezing behavior of H2O in proximity to a CuO surface. Using the High-Flux Backscattering Spectrometer at NIST, we have measured the intensity of neutrons scattered elastically from a well-hydrated sample of CuO-coated Cu foils that mimic the oxide surfaces in a flat-plate OHP. We observe abrupt freezing of bulk-like H2O above the CuO surface at 270 K followed by continuous freezing of the interfacial H2O down to 265 K. This freezing behavior is qualitatively similar to that found for water near a zwitterionic single-supported bilayer lipid membrane.3 Further studies are planned to compare the diffusion coefficients of the interfacial water for the coated and uncoated OHPs.22F.Z. Zhang et al., submitted to J. Heat Transfer. 3M. Bai et al., Europhys. Lett. 98, 48006 (2012); Miskowiec et al., Europhys. Lett. 107, 28008 (2014). Supported by NSF Grant Nos. DMR-0944772 and DGE-1069091.

A moving control volume method for smooth computation of hydrodynamic forces and torques on immersed bodies

NASA Astrophysics Data System (ADS)

Nangia, Nishant; Patankar, Neelesh A.; Bhalla, Amneet P. S.

2017-11-01

Fictitious domain methods for simulating fluid-structure interaction (FSI) have been gaining popularity in the past few decades because of their robustness in handling arbitrarily moving bodies. Often the transient net hydrodynamic forces and torques on the body are desired quantities for these types of simulations. In past studies using immersed boundary (IB) methods, force measurements are contaminated with spurious oscillations due to evaluation of possibly discontinuous spatial velocity of pressure gradients within or on the surface of the body. Based on an application of the Reynolds transport theorem, we present a moving control volume (CV) approach to computing the net forces and torques on a moving body immersed in a fluid. The approach is shown to be accurate for a wide array of FSI problems, including flow past stationary and moving objects, Stokes flow, and high Reynolds number free-swimming. The approach only requires far-field (smooth) velocity and pressure information, thereby suppressing spurious force oscillations and eliminating the need for any filtering. The proposed moving CV method is not limited to a specific IB method and is straightforward to implement within an existing parallel FSI simulation software. This work is supported by NSF (Award Numbers SI2-SSI-1450374, SI2-SSI-1450327, and DGE-1324585), the US Department of Energy, Office of Science, ASCR (Award Number DE-AC02-05CH11231), and NIH (Award Number HL117163).

Combinatorial Screening for Transgenic Yeasts with High Cellulase Activities in Combination with a Tunable Expression System

PubMed Central

Ito, Yoichiro; Yamanishi, Mamoru; Ikeuchi, Akinori; Imamura, Chie; Matsuyama, Takashi

2015-01-01

Combinatorial screening used together with a broad library of gene expression cassettes is expected to produce a powerful tool for the optimization of the simultaneous expression of multiple enzymes. Recently, we proposed a highly tunable protein expression system that utilized multiple genome-integrated target genes to fine-tune enzyme expression in yeast cells. This tunable system included a library of expression cassettes each composed of three gene-expression control elements that in different combinations produced a wide range of protein expression levels. In this study, four gene expression cassettes with graded protein expression levels were applied to the expression of three cellulases: cellobiohydrolase 1, cellobiohydrolase 2, and endoglucanase 2. After combinatorial screening for transgenic yeasts simultaneously secreting these three cellulases, we obtained strains with higher cellulase expressions than a strain harboring three cellulase-expression constructs within one high-performance gene expression cassette. These results show that our method will be of broad use throughout the field of metabolic engineering. PMID:26692026

78 FR 71676 - Submission for Review: 3206-0201, Federal Employees Health Benefits (FEHB) Open Season Express...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-29

... (FEHB) Open Season Express Interactive Voice Response (IVR) System and Open Season Web site AGENCY: U.S... Benefits (FEHB) Open Season Express Interactive Voice Response (IVR) System and the Open Season Web site... Season Express Interactive Voice Response (IVR) System, and the Open Season Web site, Open Season Online...

Seeing red; the development of pON.mCherry, a broad-host range constitutive expression plasmid for Gram-negative bacteria.

PubMed

Gebhardt, Michael J; Jacobson, Rachael K; Shuman, Howard A

2017-01-01

The development of plasmid-mediated gene expression control in bacteria revolutionized the field of bacteriology. Many of these expression control systems rely on the addition of small molecules, generally metabolites or non-metabolized analogs thereof, to the growth medium to induce expression of the genes of interest. The paradigmatic example of an expression control system is the lac system from Escherichia coli, which typically relies on the Ptac promoter and the Lac repressor, LacI. In many cases, however, constitutive gene expression is desired, and other experimental approaches require the coordinated control of multiple genes. While multiple systems have been developed for use in E. coli and its close relatives, the utility and/or functionality of these tools does not always translate to other species. For example, for the Gram-negative pathogen, Legionella pneumophila, a causative agent of Legionnaires' Disease, the aforementioned Ptac system represents the only well-established expression control system. In order to enhance the tools available to study bacterial gene expression in L. pneumophila, we developed a plasmid, pON.mCherry, which confers constitutive gene expression from a mutagenized LacI binding site. We demonstrate that pON.mCherry neither interferes with other plasmids harboring an intact LacI-Ptac expression system nor alters the growth of Legionella species during intracellular growth. Furthermore, the broad-host range plasmid backbone of pON.mCherry allows constitutive gene expression in a wide variety of Gram-negative bacterial species, making pON.mCherry a useful tool for the greater research community.

A highly tunable system for the simultaneous expression of multiple enzymes in Saccharomyces cerevisiae.

PubMed

Ito, Yoichiro; Yamanishi, Mamoru; Ikeuchi, Akinori; Matsuyama, Takashi

2015-01-16

Control of the expression levels of multiple enzymes in transgenic yeasts is essential for the effective production of complex molecules through fermentation. Here, we propose a tunable strategy for the control of expression levels based on the design of terminator regions and other gene-expression control elements in Saccharomyces cerevisiae. Our genome-integrated system, which is capable of producing high expression levels over a wide dynamic range, will broadly enable metabolic engineering and synthetic biology. We demonstrated that the activities of multiple cellulases and the production of ethanol were doubled in a transgenic yeast constructed with our system compared with those achieved with a standard expression system.

Engineering Extracellular Expression Systems in Escherichia coli Based on Transcriptome Analysis and Cell Growth State.

PubMed

Gao, Wen; Yin, Jun; Bao, Lichen; Wang, Qun; Hou, Shan; Yue, Yali; Yao, Wenbing; Gao, Xiangdong

2018-05-18

Escherichia coli extracellular expression systems have a number of advantages over other systems, such as lower pyrogen levels and a simple purification process. Various approaches, such as the generation of leaky mutants via chromosomal engineering, have been explored for this expression system. However, extracellular protein yields in leaky mutants are relatively low compared to that in intracellular expression systems and therefore need to be improved. In this work, we describe the construction, characterization, and mechanism of enhanced extracellular expression in Escherichia coli. On the basis of the localizations, functions, and transcription levels of cell envelope proteins, we systematically elucidated the effects of multiple gene deletions on cell growth and extracellular expression using modified CRISPR/Cas9-based genome editing and a FlAsH labeling assay. High extracellular yields of heterologous proteins of different sizes were obtained by screening multiple gene mutations. The enhancement of extracellular secretion was associated with the derepression of translation and translocation. This work utilized universal methods in the design of extracellular expression systems for genes not directly associated with protein synthesis that were used to generate strains with higher protein expression capability. We anticipate that extracellular expression systems may help to shed light on the poorly understood aspects of these secretion processes as well as to further assist in the construction of engineered prokaryotic cells for efficient extracellular production of heterologous proteins.

Non-conventional expression systems for the production of vaccine proteins and immunotherapeutic molecules

PubMed Central

Legastelois, Isabelle; Buffin, Sophie; Peubez, Isabelle; Mignon, Charlotte; Sodoyer, Régis; Werle, Bettina

2017-01-01

ABSTRACT The increasing demand for recombinant vaccine antigens or immunotherapeutic molecules calls into question the universality of current protein expression systems. Vaccine production can require relatively low amounts of expressed materials, but represents an extremely diverse category consisting of different target antigens with marked structural differences. In contrast, monoclonal antibodies, by definition share key molecular characteristics and require a production system capable of very large outputs, which drives the quest for highly efficient and cost-effective systems. In discussing expression systems, the primary assumption is that a universal production platform for vaccines and immunotherapeutics will unlikely exist. This review provides an overview of the evolution of traditional expression systems, including mammalian cells, yeast and E.coli, but also alternative systems such as other bacteria than E. coli, transgenic animals, insect cells, plants and microalgae, Tetrahymena thermophila, Leishmania tarentolae, filamentous fungi, cell free systems, and the incorporation of non-natural amino acids. PMID:27905833

TH-EF-BRB-03: Significant Cord and Esophagus Dose Reduction by 4π Non-Coplanar Spine Stereotactic Body Radiation Therapy and Stereotactic Radiosurgery

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

Yu, V; Tran, A; Nguyen, D

Purpose: To demonstrate significant organ-at-risk (OAR) sparing achievable with 4π non-coplanar radiotherapy on spine SBRT and SRS patients. Methods: Twenty-five stereotactic spine cases previously treated with VMAT (n = 23) or IMRT (n = 2) were included in this study. A computer-aided-design model of a Linac with a 3D-scanned human surface was utilized to determine the feasible beam space throughout the 4π steradian and beam specific source-to-target-distances (STD) required for collision avoidance. 4π radiotherapy plans integrating beam orientation and fluence map optimization were then created using a column-generation algorithm. Twenty optimal beams were selected for each case. To evaluate themore » tradeoff between dosimetric benefit and treatment complexity, 4π plans including only isocentrically deliverable beams were also created. Beam angles of all standard and isocentric 4π plans were imported into Eclipse to recalculate the dose using the same calculation engine as the clinical plans for unbiased comparison. OAR and PTV dose statistics for the clinical, standard-4π, and isocentric-4π plans were compared. Results: Comparing standard-4π to clinical plans, particularly significant average percent reduction in the [mean, maximum] dose of the cord and esophagus of [41%, 21.7%], and [38.7%, 36.4%] was observed, along with global decrease in all other OAR dose statistics. The average cord volume receiving more than 50% prescription dose was substantially decreased by 76%. In addition, improved PTV coverage was demonstrated with a maximum dose reduction of 0.93% and 1.66% increase in homogeneity index (D95/D5). All isocentric-4π plans achieved dosimetric performance equivalent to that of the standard-4π plans with higher delivery complexity. Conclusion: 4π radiotherapy significantly improves stereotactic spine treatment dosimetry. With the substantial OAR dose sparing, PTV dose escalation is considerably safer. Isocentric-4π is sufficient to achieve the dosimetric gain. The successful implementation of 4π using an FDA approved planning system paves the way for a prospective clinical trial. Varian Medical Systems, NIH R43CA183390 and R01CA188300, NSF graduate research fellowship DGE-1144087.« less

Recognizing Action Units for Facial Expression Analysis

PubMed Central

Tian, Ying-li; Kanade, Takeo; Cohn, Jeffrey F.

2010-01-01

Most automatic expression analysis systems attempt to recognize a small set of prototypic expressions, such as happiness, anger, surprise, and fear. Such prototypic expressions, however, occur rather infrequently. Human emotions and intentions are more often communicated by changes in one or a few discrete facial features. In this paper, we develop an Automatic Face Analysis (AFA) system to analyze facial expressions based on both permanent facial features (brows, eyes, mouth) and transient facial features (deepening of facial furrows) in a nearly frontal-view face image sequence. The AFA system recognizes fine-grained changes in facial expression into action units (AUs) of the Facial Action Coding System (FACS), instead of a few prototypic expressions. Multistate face and facial component models are proposed for tracking and modeling the various facial features, including lips, eyes, brows, cheeks, and furrows. During tracking, detailed parametric descriptions of the facial features are extracted. With these parameters as the inputs, a group of action units (neutral expression, six upper face AUs and 10 lower face AUs) are recognized whether they occur alone or in combinations. The system has achieved average recognition rates of 96.4 percent (95.4 percent if neutral expressions are excluded) for upper face AUs and 96.7 percent (95.6 percent with neutral expressions excluded) for lower face AUs. The generalizability of the system has been tested by using independent image databases collected and FACS-coded for ground-truth by different research teams. PMID:25210210

Comparison of two eukaryotic systems for the expression of VP6 protein of rotavirus specie A: transient gene expression in HEK293-T cells and insect cell-baculovirus system.

PubMed

da Silva Junior, Haroldo Cid; da Silva E Mouta Junior, Sérgio; de Mendonça, Marcos César Lima; de Souza Pereira, Mirian Claudia; da Rocha Nogueira, Alanderson; de Azevedo, Maria Luiza Borges; Leite, José Paulo Gagliardi; de Moraes, Márcia Terezinha Baroni

2012-09-01

The VP6 protein of rotavirus A (RVA) is a target antigen used for diagnostic assays and also for the development of new RVA vaccines. We have compared the expression of VP6 protein in human embryonic kidney (HEK293-T) cells with results obtained using a well-established insect cell-baculovirus system. The recombinant VP6 (rVP6) expressed in HEK293-T cells did not present degradation and also retained the ability to form trimers. In the insect cell-baculovirus system, rVP6 was expressed at higher levels and with protein degradation as well as partial loss of ability to form trimers was observed. Therefore, HEK293-T cells represent a less laborious alternative system than insect cells for expression of rVP6 from human RVA.

Implementation of the agmatine-controlled expression system for inducible gene expression in Lactococcus lactis.

PubMed

Linares, Daniel M; Alvarez-Sieiro, Patricia; del Rio, Beatriz; Ladero, Victor; Redruello, Begoña; Martin, Ma Cruz; Fernandez, Maria; Alvarez, Miguel A

2015-12-30

Lactococcus lactis has been safely consumed in fermented foods for millennia. This Gram-positive bacterium has now become of industrial importance as an expression host for the overproduction of lipopolysaccharide-free recombinant proteins used as food ingredients, therapeutic proteins and biotechnological enzymes. This paper reports an agmatine-controlled expression (ACE) system for L. lactis, comprising the lactococcal agmatine-sensor/transcriptional activator AguR and its target promoter P(aguB). The usefulness and efficiency of this system was checked via the reporter gene gfp and by producing PEP (Myxococcus xanthus prolyl-endopeptidase), an enzyme of biomedical interest able to degrade the immunotoxic peptides produced during the gastrointestinal breakdown of gluten. The ACE system developed in this work was suitable for the efficient expression of the functional recombinant proteins GFP and PEP. The expression system was tightly regulated by the agmatine concentration and allowed high protein production without leakiness.

Analyses of Sox-B and Sox-E Family Genes in the Cephalopod Sepia officinalis: Revealing the Conserved and the Unusual

PubMed Central

Focareta, Laura; Cole, Alison G.

2016-01-01

Cephalopods provide an unprecedented opportunity for comparative studies of the developmental genetics of organ systems that are convergent with analogous vertebrate structures. The Sox-family of transcription factors is an important class of DNA-binding proteins that are known to be involved in many aspects of differentiation, but have been largely unstudied in lophotrochozoan systems. Using a degenerate primer strategy we have isolated coding sequence for three members of the Sox family of transcription factors from a cephalopod mollusk, the European cuttlefish Sepia officinalis: Sof-SoxE, Sof-SoxB1, and Sof-SoxB2. Analyses of their expression patterns during organogenesis reveals distinct spatial and temporal expression domains. Sof-SoxB1 shows early ectodermal expression throughout the developing epithelium, which is gradually restricted to presumptive sensory epithelia. Expression within the nervous system appears by mid-embryogenesis. Sof-SoxB2 expression is similar to Sof-SoxB1 within the developing epithelia in early embryogenesis, however appears in largely non-overlapping expression domains within the central nervous system and is not expressed in the maturing sensory epithelium. In contrast, Sof-SoxE is expressed throughout the presumptive mesodermal territories at the onset of organogenesis. As development proceeds, Sof-SoxE expression is elevated throughout the developing peripheral circulatory system. This expression disappears as the circulatory system matures, but expression is maintained within undifferentiated connective tissues throughout the animal, and appears within the nervous system near the end of embryogenesis. SoxB proteins are widely known for their role in neural specification in numerous phylogenetic lineages. Our data suggests that Sof-SoxB genes play similar roles in cephalopods. In contrast, Sof-SoxE appears to be involved in the early stages of vasculogenesis of the cephalopod closed circulatory system, a novel role for a member of this gene family. PMID:27331398

Venus Express Chemical Propulsion System - The Mars Express Legacy

NASA Astrophysics Data System (ADS)

Hunter, C. J.

2004-10-01

ESA's ambition of inter-planetary exploration using a fast-track low cost industrial programme was well achieved with Mars Express. Reusing the platform architecture for the service module and specifically the Propulsion system enabled Venus Express to benefit from several lessons learnt from the Mars Express experience. Using all existing components qualified for previous programmes, many of them commercial telecommunication spacecraft programmes with components available from stock, an industrial organisation familiar from Mars Express was able to compress the schedule to make the November 2005 launch window a realistic target. While initial inspection of the CPS schematic indicates a modified Eurostar type architecture, - a similar system using some Eurostar components - would be a fairer description. The use of many parts of the system on arrival at the destination (Mars or Venus in this case) is a departure from the usual mode of operation, where many components are used during the initial few weeks of GTO or GEO. The system modifications over the basic Eurostar system have catered for this in terms of reliability contingencies by replacing components, or providing different levels of test capability or isolation in flight. This paper aims to provide an introduction to the system, address the evolution from Eurostar, and provide an initial assessment of the success of these modifications using the Mars Express experience, and how measures have been adopted specifically for Venus Express.

The Challenges of Recombinant Endostatin in Clinical Application: Focus on the Different Expression Systems and Molecular Bioengineering

PubMed Central

Mohajeri, Abbas; Sanaei, Sarvin; Kiafar, Farhad; Fattahi, Amir; Khalili, Majid; Zarghami, Nosratollah

2017-01-01

Angiogenesis plays an essential role in rapid growing and metastasis of the tumors. Inhibition of angiogenesis is a putative strategy for cancer therapy. Endostatin (Es) is an attractive anti-angiogenesis protein with some clinical application challenges including; short half-life, instability in serum and requirement to high dosage. Therefore, production of recombinant endostatin (rEs) is necessary in large scale. The production of rEs is difficult because of its structural properties and is high-cost. Therefore, this review focused on the different expression systems that involved in rEs production including; mammalian, baculovirus, yeast, and Escherichia coli (E. coli) expression systems. The evaluating of the results of different expression systems declared that none of the mentioned systems can be considered to be generally superior to the other. Meanwhile with considering the advantages and disadvantage of E. coli expression system compared with other systems beside the molecular properties of Es, E. coli expression system can be a preferred expression system for expressing of the Es in large scale. Also, the molecular bioengineering and sustained release formulations that lead to improving of its stability and bioactivity will be discussed. Point mutation (P125A) of Es, addition of RGD moiety or an additional zinc biding site to N-terminal of Es , fusing of Es to anti-HER2 IgG or heavy-chain of IgG, and finally loading of the endostar by PLGA and PEG- PLGA nanoparticles and gold nano-shell particles are the effective bioengineering methods to overcome to clinical changes of endostatin. PMID:28507934

Expression of monellin in a food-grade delivery system in Saccharomyces cerevisiae.

PubMed

Liu, Jun; Yan, Da-zhong; Zhao, Sheng-jun

2015-10-01

Genetically modified (GM) foods have caused much controversy. Construction of a food-grade delivery system is a desirable technique with presumptive impact on industrial applications from the perspective of bio-safety. The aim of this study was to construct a food-grade delivery system for Saccharomyces cerevisiae and to study the expression of monellin from the berries of the West African forest plant Dioscoreophyllum cumminsii in this system. A food-grade system for S. cerevisiae was constructed based on ribosomal DNA (rDNA)-mediated homologous recombination to enable high-copy-number integration of the expression cassette inserted into the rDNA locus. A copper resistance gene (CUP1) was used as the selection marker for yeast transformation. Because variants of transformants containing different copy numbers at the CUP1 locus can be readily selected after growth in the presence of elevated copper levels, we suggest that this system would prove useful in the generation of tandemly iterated gene clusters. Using this food-grade system, a single-chain monellin gene was heterologously expressed. The yield of monellin reached a maximum of 675 mg L(-1) . This system harbors exclusively S. cerevisiae DNA with no antibiotic resistance genes, and it should therefore be appropriate for safe use in the food industry. Monellin was shown to be expressed in this food-grade delivery system. To our knowledge, this is the first report so far on expression of monellin in a food-grade expression system in S. cerevisiae. © 2014 Society of Chemical Industry.

Stable long-term indigo production by overexpression of dioxygenase genes using a chromosomal integrated cascade expression circuit.

PubMed

Royo, Jose Luis; Moreno-Ruiz, Emilia; Cebolla, Angel; Santero, Eduardo

2005-03-16

In our laboratory we have analyzed different factors to maximize the yield in heterologous protein expression for long-term cultivation, by combination of an efficient cascade expression system and stable integration in the bacterial chromosome. In this work, we have explored this system for the production of indigo dye as a model for biotechnological production, by expressing in Escherichia coli the thnA1A2A3A4 genes from Sphingomonas macrogolitabida strain TFA, which encode the components of a tetralin dioxygenase activity. We compared Ptac, and the Pm-based cascade expression circuit in a multicopy plasmid and stably integrated into the bacterial chromosome. Plasmid-based expression systems resulted in instability of indigo production when serially diluted batch experiments were performed without a selective pressure. This problem was solved by integrating the expression module in the chromosome. Despite the gene dosage reduction, the synergic effect of the cascade expression system produced comparable expression to the dioxygenase activity in the plasmid configuration but could be stably maintained for at least 5 days. Here, we show that the cascade amplification circuit integrated in the chromosome could be an excellent system for tight control and stable production of recombinant products.

Automatic decoding of facial movements reveals deceptive pain expressions

PubMed Central

Bartlett, Marian Stewart; Littlewort, Gwen C.; Frank, Mark G.; Lee, Kang

2014-01-01

Summary In highly social species such as humans, faces have evolved to convey rich information for social interaction, including expressions of emotions and pain [1–3]. Two motor pathways control facial movement [4–7]. A subcortical extrapyramidal motor system drives spontaneous facial expressions of felt emotions. A cortical pyramidal motor system controls voluntary facial expressions. The pyramidal system enables humans to simulate facial expressions of emotions not actually experienced. Their simulation is so successful that they can deceive most observers [8–11]. Machine vision may, however, be able to distinguish deceptive from genuine facial signals by identifying the subtle differences between pyramidally and extrapyramidally driven movements. Here we show that human observers could not discriminate real from faked expressions of pain better than chance, and after training, improved accuracy to a modest 55%. However a computer vision system that automatically measures facial movements and performs pattern recognition on those movements attained 85% accuracy. The machine system’s superiority is attributable to its ability to differentiate the dynamics of genuine from faked expressions. Thus by revealing the dynamics of facial action through machine vision systems, our approach has the potential to elucidate behavioral fingerprints of neural control systems involved in emotional signaling. PMID:24656830

What is adapted in face adaptation? The neural representations of expression in the human visual system.

PubMed

Fox, Christopher J; Barton, Jason J S

2007-01-05

The neural representation of facial expression within the human visual system is not well defined. Using an adaptation paradigm, we examined aftereffects on expression perception produced by various stimuli. Adapting to a face, which was used to create morphs between two expressions, substantially biased expression perception within the morphed faces away from the adapting expression. This adaptation was not based on low-level image properties, as a different image of the same person displaying that expression produced equally robust aftereffects. Smaller but significant aftereffects were generated by images of different individuals, irrespective of gender. Non-face visual, auditory, or verbal representations of emotion did not generate significant aftereffects. These results suggest that adaptation affects at least two neural representations of expression: one specific to the individual (not the image), and one that represents expression across different facial identities. The identity-independent aftereffect suggests the existence of a 'visual semantic' for facial expression in the human visual system.

Dynamics of Immune System Gene Expression upon Bacterial Challenge and Wounding in a Social Insect (Bombus terrestris)

PubMed Central

Erler, Silvio; Popp, Mario; Lattorff, H. Michael G.

2011-01-01

The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT). There is a lack of immune genes in social insects (e.g. honeybees) when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals). The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge. Antimicrobial peptides (AMP) (abaecin, defensin 1, hymenoptaecin) were strongly up-regulated by wounding and bacterial challenge, the latter showing a higher impact on the gene expression level. Sterile wounding down-regulated TEP A, an effector gene of the JAK/STAT pathway, and bacterial infection influenced genes of the Imd (relish) and JNK pathway (basket). Relish was up-regulated within the first hour after bacterial challenge, but decreased strongly afterwards. AMP expression following wounding and bacterial challenge correlates with the expression pattern of relish whereas correlated expression with dorsal was absent. Although expression of AMPs was high, continuous bacterial growth was observed throughout the experiment. Here we demonstrate for the first time the temporal dynamics of immune system gene expression in a social insect. Wounding and bacterial challenge affected the innate immune system significantly. Induction of AMP expression due to wounding might comprise a pre-adaptation to accompanying bacterial infections. Compared with solitary species this social insect exhibits reduced immune system efficiency, as bacterial growth could not be inhibited. A negative feedback loop regulating the Imd-pathway is suggested. AMPs, the end product of the Imd-pathway, inhibited the up-regulation of the transcription factor relish, which is necessary for effector gene expression. PMID:21479237

Role of endogenous cortistatin in the regulation of ghrelin system expression at pancreatic level under normal and obese conditions.

PubMed

Chanclón, Belén; Luque, Raúl M; Córdoba-Chacón, José; Gahete, Manuel D; Pozo-Salas, Ana I; Castaño, Justo P; Gracia-Navarro, Francisco; Martínez-Fuentes, Antonio J

2013-01-01

Ghrelin-system components [native ghrelin, In1-ghrelin, Ghrelin-O-acyltransferase enzyme (GOAT) and receptors (GHS-Rs)] are expressed in a wide variety of tissues, including the pancreas, where they exert different biological actions including regulation of neuroendocrine secretions, food intake and pancreatic function. The expression of ghrelin system is regulated by metabolic conditions (fasting/obesity) and is associated with the progression of obesity and insulin resistance. Cortistatin (CORT), a neuropeptide able to activate GHS-R, has emerged as an additional link in gut-brain interplay. Indeed, we recently reported that male CORT deficient mice (cort-/-) are insulin-resistant and present a clear dysregulation in the stomach ghrelin-system. The present work was focused at analyzing the expression pattern of ghrelin-system components at pancreas level in cort-/- mice and their control littermates (cort +/+) under low- or high-fat diet. Our data reveal that all the ghrelin-system components are expressed at the mouse pancreatic level, where, interestingly, In1-ghrelin was expressed at higher levels than native-ghrelin. Thus, GOAT mRNA levels were significantly lower in cort-/- mice compared with controls while native ghrelin, In1-ghrelin and GHS-R transcript levels remained unaltered under normal metabolic conditions. Moreover, under obese condition, a significant increase in pancreatic expression of native-ghrelin, In1-ghrelin and GHS-R was observed in obese cort+/+ but not in cort-/- mice. Interestingly, insulin expression and release was elevated in obese cort+/+, while these changes were not observed in obese cort-/- mice. Altogether, our results indicate that the ghrelin-system expression is clearly regulated in the pancreas of cort+/+ and cort -/- under normal and/or obesity conditions suggesting that this system may play relevant roles in the endocrine pancreas. Most importantly, our data demonstrate, for the first time, that endogenous CORT is essential for the obesity-induced changes in insulin expression/secretion observed in mice, suggesting that CORT is a key regulatory component of the pancreatic function.

Fungal Gene Expression on Demand: an Inducible, Tunable, and Metabolism-Independent Expression System for Aspergillus niger▿†

PubMed Central

Meyer, Vera; Wanka, Franziska; van Gent, Janneke; Arentshorst, Mark; van den Hondel, Cees A. M. J. J.; Ram, Arthur F. J.

2011-01-01

Filamentous fungi are the cause of serious human and plant diseases but are also exploited in biotechnology as production platforms. Comparative genomics has documented their genetic diversity, and functional genomics and systems biology approaches are under way to understand the functions and interaction of fungal genes and proteins. In these approaches, gene functions are usually inferred from deletion or overexpression mutants. However, studies at these extreme points give only limited information. Moreover, many overexpression studies use metabolism-dependent promoters, often causing pleiotropic effects and thus limitations in their significance. We therefore established and systematically evaluated a tunable expression system for Aspergillus niger that is independent of carbon and nitrogen metabolism and silent under noninduced conditions. The system consists of two expression modules jointly targeted to a defined genomic locus. One module ensures constitutive expression of the tetracycline-dependent transactivator rtTA2S-M2, and one module harbors the rtTA2S-M2-dependent promoter that controls expression of the gene of interest (the Tet-on system). We show here that the system is tight, responds within minutes after inducer addition, and allows fine-tuning based on the inducer concentration or gene copy number up to expression levels higher than the expression levels of the gpdA promoter. We also validate the Tet-on system for the generation of conditional overexpression mutants and demonstrate its power when combined with a gene deletion approach. Finally, we show that the system is especially suitable when the functions of essential genes must be examined. PMID:21378046

General introduction: recombinant protein production and purification of insoluble proteins.

PubMed

Ferrer-Miralles, Neus; Saccardo, Paolo; Corchero, José Luis; Xu, Zhikun; García-Fruitós, Elena

2015-01-01

Proteins are synthesized in heterologous systems because of the impossibility to obtain satisfactory yields from natural sources. The production of soluble and functional recombinant proteins is among the main goals in the biotechnological field. In this context, it is important to point out that under stress conditions, protein folding machinery is saturated and this promotes protein misfolding and, consequently, protein aggregation. Thus, the selection of the optimal expression organism and the most appropriate growth conditions to minimize the formation of insoluble proteins should be done according to the protein characteristics and downstream requirements. Escherichia coli is the most popular recombinant protein expression system despite the great development achieved so far by eukaryotic expression systems. Besides, other prokaryotic expression systems, such as lactic acid bacteria and psychrophilic bacteria, are gaining interest in this field. However, it is worth mentioning that prokaryotic expression system poses, in many cases, severe restrictions for a successful heterologous protein production. Thus, eukaryotic systems such as mammalian cells, insect cells, yeast, filamentous fungus, and microalgae are an interesting alternative for the production of these difficult-to-express proteins.

A novel regulation mechanism of the T7 RNA polymerase based expression system improves overproduction and folding of membrane proteins.

PubMed

Angius, Federica; Ilioaia, Oana; Amrani, Amira; Suisse, Annabelle; Rosset, Lindsay; Legrand, Amélie; Abou-Hamdan, Abbas; Uzan, Marc; Zito, Francesca; Miroux, Bruno

2018-06-05

Membrane protein (MP) overproduction is one of the major bottlenecks in structural genomics and biotechnology. Despite the emergence of eukaryotic expression systems, bacteria remain a cost effective and powerful tool for protein production. The T7 RNA polymerase (T7RNAP)-based expression system is a successful and efficient expression system, which achieves high-level production of proteins. However some foreign MPs require a fine-tuning of their expression to minimize the toxicity associated with their production. Here we report a novel regulation mechanism for the T7 expression system. We have isolated two bacterial hosts, namely C44(DE3) and C45(DE3), harboring a stop codon in the T7RNAP gene, whose translation is under the control of the basal nonsense suppressive activity of the BL21(DE3) host. Evaluation of hosts with superfolder green fluorescent protein (sfGFP) revealed an unprecedented tighter control of transgene expression with a marked accumulation of the recombinant protein during stationary phase. Analysis of a collection of twenty MP fused to GFP showed an improved production yield and quality of several bacterial MPs and of one human monotopic MP. These mutant hosts are complementary to the other existing T7 hosts and will increase the versatility of the T7 expression system.

Emotional Expression at Different Managerial Career Stages: Female Principals in Arab Schools in Israel

ERIC Educational Resources Information Center

Arar, Khalid

2017-01-01

This paper examines emotional expression experienced by female principals in the Arab school system in Israel over their managerial careers--role-related emotions that they choose to express or repress before others. I employed narrative methodology, interviewing nine female principals from the Arab school system to investigate expression of…

Construction of two Lactococcus lactis expression vectors combining the Gateway and the NIsin Controlled Expression systems.

PubMed

Douillard, François P; Mahony, Jennifer; Campanacci, Valérie; Cambillau, Christian; van Sinderen, Douwe

2011-09-01

Over the last 10 years, the NIsin Controlled Expression (NICE) system has been extensively used in the food-grade bacterium Lactococcus lactis subsp. cremoris to produce homologous and heterologous proteins for academic and biotechnological purposes. Although various L. lactis molecular tools have been developed, no expression vectors harboring the popular Gateway recombination system are currently available for this widely used cloning host. In this study, we constructed two expression vectors that combine the NICE and the Gateway recombination systems and we tested their applicability by recombining and over-expressing genes encoding structural proteins of lactococcal phages Tuc2009 and TP901-1. Over-expressed phage proteins were analyzed by immunoblotting and purified by His-tag affinity chromatography with protein productions yielding 2.8-3.7 mg/l of culture. This therefore is the first description of L. lactis NICE expression vectors which integrate the Gateway cloning technology and which are suitable for the production of sufficient amounts of proteins to facilitate subsequent structural and functional analyses. Copyright © 2011 Elsevier Inc. All rights reserved.

Simultaneous monitoring of independent gene expression patterns in two types of cocultured fibroblasts with different color-emitting luciferases

PubMed Central

Noguchi, Takako; Ikeda, Masaaki; Ohmiya, Yoshihiro; Nakajima, Yoshihiro

2008-01-01

Background Luciferase assay systems enable the real-time monitoring of gene expression in living cells. We have developed a dual-color luciferase assay system in which the expression of multiple genes can be tracked simultaneously using green- and red-emitting beetle luciferases. We have applied the system to monitoring independent gene expressions in two types of cocultured fibroblasts in real time. Results Two Rat-1 cell lines were established that stably express either green- or red-emitting luciferases under the control of the mBmal1 promoter, a canonical clock gene. We cocultured these cell lines, and gene expression profiles in both were monitored simultaneously. The circadian rhythms of these cell lines are independent, oscillating following their intrinsic circadian phases, even when cocultured. Furthermore, the independent rhythms were synchronized by medium change as an external stimulus. Conclusion Using this system, we successfully monitored independent gene expression patterns in two lines of cocultured fibroblasts. PMID:18416852

WP1: transgenic opto-animals

NASA Astrophysics Data System (ADS)

UŻarowska, E.; Czajkowski, Rafał; Konopka, W.

2014-11-01

We aim to create a set of genetic tools where permanent opsin expression (ChR or NpHR) is precisely limited to the population of neurons that express immediate early gene c-fos during a specific temporal window of behavioral training. Since the c-fos gene is only expressed in neurons that form experience-dependent ensemble, this approach will result in specific labeling of a small subset of cells that create memory trace for the learned behavior. To this end we employ two alternative inducible gene expression systems: Tet Expression System and Cre/lox System. In both cases, the temporal window for opsin induction is controlled pharmacologically, by doxycycline or tamoxifen, respectively. Both systems will be used for creating lines of transgenic animals.

EXPRESS Rack Mockup

NASA Technical Reports Server (NTRS)

2002-01-01

The EXPRESS Rack is a standardized payload rack system that transports, stores, and supports experiments aboard the International Space Station (ISS). EXPRESS stands for EXpedite the PRocessing of Experiments to the Space Station, reflecting the fact that this system was developed specifically to maximize the Station's research capabilities. The EXPRESS Rack system supports science payloads in several disciplines, including biology, chemistry, physics, ecology, and medicine. With the EXPRESS Rack, getting experiments to space has never been easier or more affordable. With its standardized hardware interfaces and streamlined approach, the EXPRESS Rack enables quick, simple integration of multiple payloads aboard the ISS. The system is comprised of elements that remain on the ISS, as well as elements that travel back and forth between the ISS and Earth via the Space Shuttle. The Racks stay on orbit continually, while experiments are exchanged in and out of the EXPRESS Racks as needed, remaining on the ISS for three months to several years, depending on the experiment's time requirements. A refrigerator-sized Rack can be divided into segments, as large as half of an entire rack or as small as a bread box. Payloads within EXPRESS Racks can operate independently of each other, allowing for differences in temperature, power levels, and schedules. Experiments contained within EXPRESS Racks may be controlled by the ISS crew or remotely by the Payload Rack Officer at the Payload Operations Center at the Marshall Space Flight Center (MSFC). The EXPRESS Rack system was developed by MSFC and built by the Boeing Co. in Huntsville, Alabama. Eight EXPRESS Racks are being built for use on the ISS.

BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data.

PubMed

Chae, Heejoon; Lee, Sangseon; Seo, Seokjun; Jung, Daekyoung; Chang, Hyeonsook; Nephew, Kenneth P; Kim, Sun

2016-12-01

Measuring gene expression, DNA sequence variation, and DNA methylation status is routinely done using high throughput sequencing technologies. To analyze such multi-omics data and explore relationships, reliable bioinformatics systems are much needed. Existing systems are either for exploring curated data or for processing omics data in the form of a library such as R. Thus scientists have much difficulty in investigating relationships among gene expression, DNA sequence variation, and DNA methylation using multi-omics data. In this study, we report a system called BioVLAB-mCpG-SNP-EXPRESS for the integrated analysis of DNA methylation, sequence variation (SNPs), and gene expression for distinguishing cellular phenotypes at the pairwise and multiple phenotype levels. The system can be deployed on either the Amazon cloud or a publicly available high-performance computing node, and the data analysis and exploration of the analysis result can be conveniently done using a web-based interface. In order to alleviate analysis complexity, all the process are fully automated, and graphical workflow system is integrated to represent real-time analysis progression. The BioVLAB-mCpG-SNP-EXPRESS system works in three stages. First, it processes and analyzes multi-omics data as input in the form of the raw data, i.e., FastQ files. Second, various integrated analyses such as methylation vs. gene expression and mutation vs. methylation are performed. Finally, the analysis result can be explored in a number of ways through a web interface for the multi-level, multi-perspective exploration. Multi-level interpretation can be done by either gene, gene set, pathway or network level and multi-perspective exploration can be explored from either gene expression, DNA methylation, sequence variation, or their relationship perspective. The utility of the system is demonstrated by performing analysis of phenotypically distinct 30 breast cancer cell line data set. BioVLAB-mCpG-SNP-EXPRESS is available at http://biohealth.snu.ac.kr/software/biovlab_mcpg_snp_express/. Copyright © 2016 Elsevier Inc. All rights reserved.

Systemic Sclerosis Patients Present Alterations in the Expression of Molecules Involved in B-Cell Regulation

PubMed Central

Soto, Lilian; Ferrier, Ashley; Aravena, Octavio; Fonseca, Elianet; Berendsen, Jorge; Biere, Andrea; Bueno, Daniel; Ramos, Verónica; Aguillón, Juan Carlos; Catalán, Diego

2015-01-01

The activation threshold of B cells is tightly regulated by an array of inhibitory and activator receptors in such a way that disturbances in their expression can lead to the appearance of autoimmunity. The aim of this study was to evaluate the expression of activating and inhibitory molecules involved in the modulation of B cell functions in transitional, naive, and memory B-cell subpopulations from systemic sclerosis patients. To achieve this, blood samples were drawn from 31 systemic sclerosis patients and 53 healthy individuals. Surface expression of CD86, MHC II, CD19, CD21, CD40, CD22, Siglec 10, CD35, and FcγRIIB was determined by flow cytometry. IL-10 production was evaluated by intracellular flow cytometry from isolated B cells. Soluble IL-6 and IL-10 levels were measured by ELISA from supernatants of stimulated B cells. Systemic sclerosis patients exhibit an increased frequency of transitional and naive B cells related to memory B cells compared with healthy controls. Transitional and naive B cells from patients express higher levels of CD86 and FcγRIIB than healthy donors. Also, B cells from patients show high expression of CD19 and CD40, whereas memory cells from systemic sclerosis patients show reduced expression of CD35. CD19 and CD35 expression levels associate with different autoantibody profiles. IL-10+ B cells and secreted levels of IL-10 were markedly reduced in patients. In conclusion, systemic sclerosis patients show alterations in the expression of molecules involved in B-cell regulation. These abnormalities may be determinant in the B-cell hyperactivation observed in systemic sclerosis. PMID:26483788

International Space Station (ISS)

NASA Image and Video Library

2001-05-14

Astronaut James S. Voss, Expedition Two flight engineer, works with a series of cables on the EXPRESS Rack in the United State's Destiny laboratory on the International Space Station (ISS). The EXPRESS Rack is a standardized payload rack system that transports, stores, and supports experiments aboard the ISS. EXPRESS stands for EXpedite the PRocessing of Experiments to the Space Station, reflecting the fact that this system was developed specifically to maximize the Station's research capabilities. The EXPRESS Rack system supports science payloads in several disciplines, including biology, chemistry, physics, ecology, and medicine. With the EXPRESS Rack, getting experiments to space has never been easier or more affordable. With its standardized hardware interfaces and streamlined approach, the EXPRESS Rack enables quick, simple integration of multiple payloads aboard the ISS. The system is comprised of elements that remain on the ISS, as well as elements that travel back and forth between the ISS and Earth via the Space Shuttle.

Versatile control of Plasmodium falciparum gene expression with an inducible protein-RNA interaction

PubMed Central

Goldfless, Stephen J.; Wagner, Jeffrey C.; Niles, Jacquin C.

2014-01-01

The available tools for conditional gene expression in Plasmodium falciparum are limited. Here, to enable reliable control of target gene expression, we build a system to efficiently modulate translation. We overcame several problems associated with other approaches for regulating gene expression in P. falciparum. Specifically, our system functions predictably across several native and engineered promoter contexts, and affords control over reporter and native parasite proteins irrespective of their subcellular compartmentalization. Induction and repression of gene expression are rapid, homogeneous, and stable over prolonged periods. To demonstrate practical application of our system, we used it to reveal direct links between antimalarial drugs and their native parasite molecular target. This is an important out come given the rapid spread of resistance, and intensified efforts to efficiently discover and optimize new antimalarial drugs. Overall, the studies presented highlight the utility of our system for broadly controlling gene expression and performing functional genetics in P. falciparum. PMID:25370483

Astronaut James S. Voss Performs Tasks in the Destiny Laboratory

NASA Technical Reports Server (NTRS)

2001-01-01

Astronaut James S. Voss, Expedition Two flight engineer, works with a series of cables on the EXPRESS Rack in the United State's Destiny laboratory on the International Space Station (ISS). The EXPRESS Rack is a standardized payload rack system that transports, stores, and supports experiments aboard the ISS. EXPRESS stands for EXpedite the PRocessing of Experiments to the Space Station, reflecting the fact that this system was developed specifically to maximize the Station's research capabilities. The EXPRESS Rack system supports science payloads in several disciplines, including biology, chemistry, physics, ecology, and medicine. With the EXPRESS Rack, getting experiments to space has never been easier or more affordable. With its standardized hardware interfaces and streamlined approach, the EXPRESS Rack enables quick, simple integration of multiple payloads aboard the ISS. The system is comprised of elements that remain on the ISS, as well as elements that travel back and forth between the ISS and Earth via the Space Shuttle.

A self-initiating eukaryotic transient gene expression system based on contransfection of bacteriophage T7 RNA polymerase and DNA vectors containing a T7 autogene.

PubMed Central

Chen, X; Li, Y; Xiong, K; Wagner, T E

1994-01-01

A novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter gene driven by another T7 promoter (T7T7/T7-gene construct). Once this DNA-enzyme complex is introduced into eukaryotic cells, the transcription of the T7 RNAP and the functional/reporter genes is initiated by the co-delivered T7 RNAP. The T7 RNAP, which is responsible for the initiation and maintenance of expression of both T7 and functional/reporter genes, is replenished by translation of newly synthesized T7 mRNA. This T7 system was designed in such a manner that the expression of the functional/reporter genes can occur in the cytoplasm and does not require any nuclear involvement. When transfected by either a pT7T7/T7Luc or a pT7T7/T7hGH plasmids with the cointroduced T7 RNAP, mouse L cells were found to express high levels of luciferase immediately after transfection, apparently due to the cytoplasmic gene expression; the expression of human growth hormone (hGH) could be sustained for at least 6 days. Both T7 and hGH mRNA were expressed by the cells transfected with pT7T7/T7hGH. These results suggest that this cytoplasmic expression system may be used for certain targets of somatic gene therapy. Images PMID:8029020

Bacterial cell-free expression technology to in vitro systems engineering and optimization.

PubMed

Caschera, Filippo

2017-06-01

Cell-free expression system is a technology for the synthesis of proteins in vitro . The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.

Using heterologous expression systems to characterize potassium and sodium transport activities.

PubMed

Rodríguez, Alonso; Benito, Begoña; Cagnac, Olivier

2012-01-01

The expression of plant transporters in simple well-characterized cell systems is an irreplaceable technique for gaining insights into the kinetic and energetic features of plant transporters. Among all the available expression systems, yeast cells offer the highest simplicity and have the capacity to mimic the in vivo properties of plant transporters. Here, we describe the use of yeast mutants to express K(+) and Na(+) plant transporters and discuss some experimental problems that can produce misleading results.

Initiating New Science Partnerships in Rural Education (INSPIRE): Enhancing Scientific Communication by Bringing STEM Research into the Classroom

NASA Astrophysics Data System (ADS)

Pierce, D.; Radencic, S.; Funderburk, W. K.; Walker, R. M.; Jackson, B. S.; Dawkins, K. S.; Schmitz, D.; Bruce, L. M.; McNeal, K.

2014-12-01

INSPIRE, a five-year partnership between Mississippi State University and three local school districts, is designed to strengthen the communication skills of graduate Fellows in geosciences, physics, astronomy, chemistry, and engineering as they incorporate their research into inquiry-based lessons in 7th - 12th grade science and math classrooms. All lesson plans designed and taught by the graduate Fellows must include one or more connections to their research, and these connections must be demonstrated to the students during the lessons. International research partnerships with Australia, the Bahamas, England, and Poland provide valuable opportunities for graduate Fellows to conduct field work abroad and allow our partner teachers to have authentic research experiences that they can bring back to their classrooms. Program effectiveness has been examined using pre- and post-year attitudinal surveys, formal lesson plan documents, Fellow and teacher journals, focus group meetings with a project evaluator, and direct observation of Fellow-led classroom activities. Analyses of data gathered during the past four years of the partnership will be presented that examine the diversity in approaches taken by Fellows to communicate big ideas, changes in the ability of Fellows to find connections between their research and classroom lessons while keeping them aligned with state and national standards, and the quality of the mentorship provided to the Fellows by our partner teachers. INSPIRE is funded by the Graduate K-12 (GK-12) STEM Fellowship Program of the National Science Foundation (Award No. DGE-0947419).

To flap or not to flap: a discussion between a fish and a jellyfish

NASA Astrophysics Data System (ADS)

Martin, Nathan; Roh, Chris; Idrees, Suhail; Gharib, Morteza

2016-11-01

Fish and jellyfish are known to swim by flapping and by periodically contracting respectively, but which is the more effective propulsion mechanism? In an attempt to answer this question, an experimental comparison is made between simplified versions of these motions to determine which generates the greatest thrust for the least power. The flapping motion is approximated by pitching plates while periodic contractions are approximated by clapping plates. A machine is constructed to operate in either a flapping or a clapping mode between Reynolds numbers 1,880 and 11,260 based on the average plate tip velocity and span. The effect of the total sweep angle, total sweep time, plate flexibility, and duty cycle are investigated. The average thrust generated and power required per cycle are compared between the two modes when their total sweep angle and total sweep time are identical. In general, operating in the clapping mode required significantly more power to generate a similar thrust compared to the flapping mode. However, modifying the duty cycle for clapping caused the effectiveness to approach that of flapping with an unmodified duty cycle. These results suggest that flapping is the more effective propulsion mechanism within the range of Reynolds numbers tested. This work was supported by the Charyk Bio-inspired Laboratory at the California Institute of Technology, the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1144469, and the Summer Undergraduate Research Fellowships program.

To flap or not to flap: continued discussion with particle image velocimetry of the near wake

NASA Astrophysics Data System (ADS)

Martin, Nathan; Roh, Chris; Idrees, Suhail; Gharib, Morteza

2017-11-01

We continue the discussion of which underwater propulsion mechanism is more effective: flapping used by fish or periodic contractions used by jellyfish. The two propulsion mechanisms are simplified into flapping and clapping plate motions, respectively, to allow for a direct comparison. A device is designed to operate in either mode of propulsion between Reynolds numbers 1,880 and 11,260, based on the average tip velocity and the span of the plate. The stroke angle, stroke time, flexibility, and duty cycle are varied to determine their impact on the generated thrust and the required torque. Overall, the clapping mode tends to require significantly more power to generate a similar thrust compared to that from the flapping mode. The performance of the clapping mode is increased by modifying the duty cycle such that the closing motion is faster than the opening motion causing a greater thrust and a similar efficiency to that from the flapping mode. Interestingly, when using rigid plates, the average thrust generated per cycle is similar between the two modes when the overall kinematics are equivalent. Investigation of the near wake of both modes through digital particle image velocimetry provides insight into the cause of this similar thrust. This work was supported by the Charyk Bio-inspired Laboratory at the California Institute of Technology, the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1144469, and the Summer Undergraduate Research Fellowships program.

Utah Southwest Regional Geothermal Development Operations Research Project. Appendix 10 of regional operations research program for development of geothermal energy in the Southeast United States. Final technical report, June 1977--August 1978

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

Green, Stanley; Wagstaff, Lyle W.

1979-01-01

The Southwest Regional Geothermal Operations/Research project was initiated to investigate geothermal development in the five states within the region: Arizona, Colorado, Nevada, New Mexico, and Utah. Although the region changed during the first year to include Idaho, Montana, North Dakota, South Dakota, and Wyoming, the project objectives and procedures remained unchanged. The project was funded by the DOE/DGE and the Four Corners Regional Commission with participation by the New Mexico Energy Resources Board. The study was coordinated by the New Mexico Energy Institute at New Mexico State University, acting through a 'Core Team'. A 'state' team, assigned by the states,more » conducted the project within each state. This report details most of the findings of the first year's efforts by the Utah Operations/Research team. It is a conscientious effort to report the findings and activities of the Utah team, either explicitly or by reference. The results are neither comprehensive nor final, and should be regarded as preliminary efforts to much of what the Operations/Research project was envisioned to accomplish. In some cases the report is probably too detailed, in other cases too vague; hopefully, however, the material in the report, combined with the Appendices, will be able to serve as source material for others interested in geothermal development in Utah.« less

S-Nitrosylation Proteome Profile of Peripheral Blood Mononuclear Cells in Human Heart Failure

PubMed Central

Spratt, Heidi M.; Gupta, Shivali; Petersen, John R.; Kuyumcu-Martinez, Muge N.

2016-01-01

Nitric oxide (NO) protects the heart against ischemic injury; however, NO- and superoxide-dependent S-nitrosylation (S-NO) of cysteines can affect function of target proteins and play a role in disease outcome. We employed 2D-GE with thiol-labeling FL-maleimide dye and MALDI-TOF MS/MS to capture the quantitative changes in abundance and S-NO proteome of HF patients (versus healthy controls, n = 30/group). We identified 93 differentially abundant (59-increased/34-decreased) and 111 S-NO-modified (63-increased/48-decreased) protein spots, respectively, in HF subjects (versus controls, fold-change | ≥1.5|, p ≤ 0.05). Ingenuity pathway analysis of proteome datasets suggested that the pathways involved in phagocytes' migration, free radical production, and cell death were activated and fatty acid metabolism was decreased in HF subjects. Multivariate adaptive regression splines modeling of datasets identified a panel of proteins that will provide >90% prediction success in classifying HF subjects. Proteomic profiling identified ATP-synthase, thrombospondin-1 (THBS1), and vinculin (VCL) as top differentially abundant and S-NO-modified proteins, and these proteins were verified by Western blotting and ELISA in different set of HF subjects. We conclude that differential abundance and S-NO modification of proteins serve as a mechanism in regulating cell viability and free radical production, and THBS1 and VCL evaluation will potentially be useful in the prediction of heart failure. PMID:27635260

How Accurately Can We Measure Galaxy Environment at High Redshift Using Only Photometric Redshifts?

NASA Astrophysics Data System (ADS)

Florez, Jonathan; Jogee, Shardha; Sherman, Sydney; Papovich, Casey J.; Finkelstein, Steven L.; Stevans, Matthew L.; Kawinwanichakij, Lalitwadee; Ciardullo, Robin; Gronwall, Caryl; SHELA/HETDEX

2017-06-01

We use a powerful synergy of six deep photometric surveys (Herschel SPIRE, Spitzer IRAC, NEWFIRM K-band, DECam ugriz, and XMM X-ray) and a future optical spectroscopic survey (HETDEX) in the Stripe 82 field to study galaxy evolution during the 1.9 < z < 3.5 epoch when cosmic star formation and black hole activity peaked, and protoclusters began to collapse. With an area of 24 sq. degrees, a sample size of ~ 0.8 million galaxies complete in stellar mass above M* ~ 10^10 solar masses, and a comoving volume of ~ 0.45 Gpc^3, our study will allow us to make significant advancements in understanding the connection between galaxies and their respective dark matter components. In this poster, we characterize how robustly we can measure environment using only our photometric redshifts. We compare both local and large-scale measures of environment (e.g., projected two-point correlation function, projected nearest neighbor densities, and galaxy counts within some projected aperture) at different photometric redshifts to cosmological simulations in order to quantify the uncertainty in our estimates of environment. We also explore how robustly one can recover the variation of galaxy properties with environment, when using only photometric redshifts. In the era of large photometric surveys, this work has broad implications for studies addressing the impact of environment on galaxy evolution at early cosmic epochs. We acknowledge support from NSF grants AST-1614798, AST-1413652 and NSF GRFP grant DGE-1610403.

Induction of indolamine 2,3-dioxygenase and kynurenine 3-monooxygenase in rat brain following a systemic inflammatory challenge: a role for IFN-gamma?

PubMed

Connor, Thomas J; Starr, Neasa; O'Sullivan, Joan B; Harkin, Andrew

2008-08-15

Inflammation-mediated dysregulation of the kynurenine pathway has been implicated as a contributor to a number of major brain disorders. Consequently, we examined the impact of a systemic inflammatory challenge on kynurenine pathway enzyme expression in rat brain. Indoleamine 2,3-dioxygenase (IDO) expression was induced in cortex and hippocampus following systemic lipopolysaccharide (LPS) administration. Whilst IDO expression was paralleled by increased circulating interferon (IFN)-gamma concentrations, IFN-gamma expression in the brain was only modestly altered following LPS administration. In contrast, induction of IDO was associated with increased central tumour necrosis factor (TNF)-alpha and interleukin (IL)-6 expression. Similarly, in cultured glial cells LPS-induced IDO expression was accompanied by increased TNF-alpha and IL-6 expression, whereas IFN-gamma was not detectable. These findings indicate that IFN-gamma is not required for LPS-induced IDO expression in brain. A robust increase in kynurenine-3-monooxygenase (KMO) expression was observed in rat brain 24h post LPS, without any change in kynurenine aminotransferase II (KAT II) expression. In addition, we report that constitutive expression of KAT II is approximately 8-fold higher than KMO in cortex and 20-fold higher in hippocampus. Similarly, in glial cells constitutive expression of KAT II was approximately 16-fold higher than KMO, and expression of KMO but not KAT II was induced by LPS. These data are the first to demonstrate that a systemic inflammatory challenge stimulates KMO expression in brain; a situation that is likely to favour kynurenine metabolism in a neurotoxic direction. However, our observation that expression of KAT II is much higher than KMO in rat brain is likely to counteract potential neurotoxicity that could arise from KMO induction following an acute inflammation.

Integration of multiple stimuli-sensing systems to regulate HrpS and type III secretion system in Erwinia amylovora.

PubMed

Lee, Jae Hoon; Zhao, Youfu

2018-02-01

The bacterial enhancer binding protein (bEBP) HrpS is essential for Erwinia amylovora virulence by activating the type III secretion system (T3SS). However, how the hrpS gene is regulated remains poorly understood in E. amylovora. In this study, 5' rapid amplification of cDNA ends and promoter deletion analyses showed that the hrpS gene contains two promoters driven by HrpX/HrpY and the Rcs phosphorelay system, respectively. Electrophoretic mobility shift and gene expression assays demonstrated that integration host factor IHF positively regulates hrpS expression through directly binding the hrpX promoter and positively regulating hrpX/hrpY expression. Moreover, hrpX expression was down-regulated in the relA/spoT ((p)ppGpp-deficient) mutant and the dksA mutant, but up-regulated when the wild-type strain was treated with serine hydroxamate, which induced (p)ppGpp-mediated stringent response. Furthermore, the csrA mutant showed significantly reduced transcripts of major hrpS activators, including the hrpX/hrpY, rcsA and rcsB genes, indicating that CsrA is required for full hrpS expression. On the other hand, the csrB mutant exhibited up-regulation of the rcsA and rcsB genes, and hrpS expression was largely diminished in the csrB/rcsB mutant, indicating that the Rcs system is mainly responsible for the increased hrpS expression in the csrB mutant. These findings suggest that E. amylovora recruits multiple stimuli-sensing systems, including HrpX/HrpY, the Rcs phosphorelay system and the Gac-Csr system, to regulate hrpS and T3SS gene expression.

Serotonin systems upregulate the expression of hypothalamic NUCB2 via 5-HT2C receptors and induce anorexia via a leptin-independent pathway in mice.

PubMed

Nonogaki, Katsunori; Ohba, Yukie; Sumii, Makiko; Oka, Yoshitomo

2008-07-18

NEFA/nucleobindin2 (NUCB2), a novel satiety molecule, is associated with leptin-independent melanocortin signaling in the central nervous system. Here, we show that systemic administration of m-chlorophenylpiperazine (mCPP), a serotonin 5-HT1B/2C receptor agonist, significantly increased the expression of hypothalamic NUCB2 in wild-type mice. The increases in hypothalamic NUCB2 expression induced by mCPP were attenuated in 5-HT2C receptor mutant mice. Systemic administration of mCPP suppressed food intake in db/db mice with leptin receptor mutation as well as lean control mice. On the other hand, the expression of hypothalamic NUCB2 and proopiomelanocortin (POMC) was significantly decreased in hyperphagic and non-obese 5-HT2C receptor mutants compared with age-matched wild-type mice. Interestingly, despite increased expression of hypothalamic POMC, hypothalamic NUCB2 expression was decreased in 5-HT2C receptor mutant mice with heterozygous mutation of beta-endorphin gene. These findings suggest that 5-HT systems upregulate the expression of hypothalamic NUCB2 via 5-HT2C receptors, and induce anorexia via a leptin-independent pathway in mice.

[Facial expressions of negative emotions in clinical interviews: The development, reliability and validity of a categorical system for the attribution of functions to facial expressions of negative emotions].

PubMed

Bock, Astrid; Huber, Eva; Peham, Doris; Benecke, Cord

2015-01-01

The development (Study 1) and validation (Study 2) of a categorical system for the attribution of facial expressions of negative emotions to specific functions. The facial expressions observed inOPDinterviews (OPD-Task-Force 2009) are coded according to the Facial Action Coding System (FACS; Ekman et al. 2002) and attributed to categories of basic emotional displays using EmFACS (Friesen & Ekman 1984). In Study 1 we analyze a partial sample of 20 interviews and postulate 10 categories of functions that can be arranged into three main categories (interactive, self and object). In Study 2 we rate the facial expressions (n=2320) from the OPD interviews (10 minutes each interview) of 80 female subjects (16 healthy, 64 with DSM-IV diagnosis; age: 18-57 years) according to the categorical system and correlate them with problematic relationship experiences (measured with IIP,Horowitz et al. 2000). Functions of negative facial expressions can be attributed reliably and validly with the RFE-Coding System. The attribution of interactive, self-related and object-related functions allows for a deeper understanding of the emotional facial expressions of patients with mental disorders.

Time-varying sodium absorption in the Type Ia supernova 2013gh

DOE PAGES

Ferretti, Raphael; Amanullah, R.; Goobar, A.; ...

2016-07-18

Context. Temporal variability of narrow absorption lines in high-resolution spectra of Type Ia supernovae (SNe Ia) is studied to search for circumstellar matter. Time series which resolve the profiles of absorption lines such as Na I D or Ca II H&K are expected to reveal variations due to photoionisation and subsequent recombination of the gases. The presence, composition, and geometry of circumstellar matter may hint at the elusive progenitor system of SNe Ia and could also affect the observed reddening law. Aims. To date, there are few known cases of time-varying Na I D absorption in SNe Ia, all ofmore » which occurred during relatively late phases of the supernova (SN) evolution. Photoionisation, however, is predicted to occur during the early phases of SNe Ia, when the supernovae peak in the ultraviolet. We attempt, therefore, to observe early-time absorption-line variations by obtaining high-resolution spectra of SNe before maximum light. Methods. In this paper, we have obtained photometry and high-resolution spectroscopy of SNe Ia 2013gh and iPTF 13dge, to search for absorption-line variations. Furthermore, we study interstellar absorption features in relation to the observed photometric colours of the SNe. Results. Both SNe display deep Na I D and Ca II H&K absorption features. Furthermore, small but significant variations are detected in a feature of the Na I D profile of SN 2013gh. The variations are consistent with either geometric effects of rapidly moving or patchy gas clouds or photoionisation of Na I gas at R ≈ 10 19 cm from the explosion. Conclusions. Our analysis indicates that it is necessary to focus on early phases to detect photoionisation effects of gases in the circumstellar medium of SNe Ia. Different absorbers such as Na I and Ca II can be used to probe for matter at different distances from the SNe. Finally, the nondetection of variations during early phases makes it possible to put limits on the abundance of the species at those distances.« less

A gene expression system offering multiple levels of regulation: the Dual Drug Control (DDC) system.

PubMed

Sudomoina, Marina; Latypova, Ekaterina; Favorova, Olga O; Golemis, Erica A; Serebriiskii, Ilya G

2004-04-29

Whether for cell culture studies of protein function, construction of mouse models to enable in vivo analysis of disease epidemiology, or ultimately gene therapy of human diseases, a critical enabling step is the ability to achieve finely controlled regulation of gene expression. Previous efforts to achieve this goal have explored inducible drug regulation of gene expression, and construction of synthetic promoters based on two-hybrid paradigms, among others. In this report, we describe the combination of dimerizer-regulated two-hybrid and tetracycline regulatory elements in an ordered cascade, placing expression of endpoint reporters under the control of two distinct drugs. In this Dual Drug Control (DDC) system, a first plasmid expresses fusion proteins to DBD and AD, which interact only in the presence of a small molecule dimerizer; a second plasmid encodes a cassette transcriptionally responsive to the first DBD, directing expression of the Tet-OFF protein; and a third plasmid encodes a reporter gene transcriptionally responsive to binding by Tet-OFF. We evaluate the dynamic range and specificity of this system in comparison to other available systems. This study demonstrates the feasibility of combining two discrete drug-regulated expression systems in a temporally sequential cascade, without loss of dynamic range of signal induction. The efficient layering of control levels allowed by this combination of elements provides the potential for the generation of complex control circuitry that may advance ability to regulate gene expression in vivo.

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Part 11; Express/T-160E Project Express A2 and A3 Data Agreement Document

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.; Dunning, John (Technical Monitor)

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80deg E. and 11deg W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3-99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Part 12; Express/T-160 Project Express A2 and A3 Sensors Operations Procedures Document

NASA Technical Reports Server (NTRS)

Dunning, John (Technical Monitor); Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 deg. E. and 11 deg. W respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

The LIKE system, a novel protein expression toolbox for Bacillus subtilis based on the liaI promoter

PubMed Central

2012-01-01

Background Bacillus subtilis is a very important Gram-positive model organism of high biotechnological relevance, which is widely used as a host for the production of both secreted and cytoplasmic proteins. We developed a novel and efficient expression system, based on the liaI promoter (PliaI) from B. subtilis, which is under control of the LiaRS antibiotic-inducible two-component system. In the absence of a stimulus, this promoter is kept tightly inactive. Upon induction by cell wall antibiotics, it shows an over 100-fold increase in activity within 10 min. Results Based on these traits of PliaI, we developed a novel LiaRS-controlled gene expression system for B. subtilis (the “LIKE" system). Two expression vectors, the integrative pLIKE-int and the replicative pLIKE-rep, were constructed. To enhance the performance of the PliaI-derived system, site-directed mutagenesis was employed to optimize the ribosome binding site and alter its spacing to the initiation codon used for the translational fusion. The impact of these genetic modifications on protein production yield was measured using GFP as a model protein. Moreover, a number of tailored B. subtilis expression strains containing different markerless chromosomal deletions of the liaIH region were constructed to circumvent undesired protein production, enhance the positive autoregulation of the LiaRS system and thereby increase target gene expression strength from the PliaI promoter. Conclusions The LIKE protein expression system is a novel protein expression system, which offers a number of advantages over existing systems. Its major advantages are (i) a tightly switched-off promoter during exponential growth in the absence of a stimulus, (ii) a concentration-dependent activation of PliaI in the presence of suitable inducers, (iii) a very fast but transient response with a very high dynamic range of over 100-fold (up to 1,000-fold) induction, (iv) a choice from a range of well-defined, commercially available, and affordable inducers and (v) the convenient conversion of LIKE-derived inducible expression strains into strong constitutive protein production factories. PMID:23110498

Extrinsic factors regulate partial agonist efficacy of strychnine-sensitive glycine receptors

PubMed Central

Farroni, Jeffrey S; McCool, Brian A

2004-01-01

Background Strychnine-sensitive glycine receptors in many adult forebrain regions consist of alpha2 + beta heteromeric channels. This subunit composition is distinct from the alpha1 + beta channels found throughout the adult spinal cord. Unfortunately, the pharmacology of forebrain alpha2beta receptors are poorly defined compared to 'neonatal' alpha2 homomeric channels or 'spinal' alpha1beta heteromers. In addition, the pharmacologic properties of native alpha2beta glycine receptors have been generally distinct from receptors produced by heterologous expression. To identify subtype-specific pharmacologic tools for the forebrain alpha2beta receptors, it is important to identify a heterologous expression system that closely resembles these native glycine-gated chloride channels. Results While exploring pharmacological properties of alpha2beta glycine receptors compared to alpha2-homomers, we found that distinct heterologous expression systems appeared to differentially influence partial agonist pharmacology. The β-amino acid taurine possessed 30–50% efficacy for alpha2-containing receptor isoforms when expressed in HEK 293 cells. However, taurine efficacy was dramatically reduced in L-cell fibroblasts. Similar results were obtained for β-alanine. The efficacy of these partial agonists was also strongly reduced by the beta subunit. There were no significant differences in apparent strychnine affinity values calculated from concentration-response data between expression systems or subunit combinations. Nor did relative levels of expression correlate with partial agonist efficacy when compared within or between several different expression systems. Finally, disruption of the tubulin cytoskeleton reduced the efficacy of partial agonists in a subunit-dependent, but system-independent, fashion. Conclusions Our results suggest that different heterologous expression systems can dramatically influence the agonist pharmacology of strychnine-sensitive glycine receptors. In the systems examine here, these effects are independent of both absolute expression level and any system-related alterations in the agonist binding site. We conclude that complex interactions between receptor composition and extrinsic factors may play a significant role in determining strychnine-sensitive glycine receptor partial agonist pharmacology. PMID:15301692

Extrinsic factors regulate partial agonist efficacy of strychnine-sensitive glycine receptors.

PubMed

Farroni, Jeffrey S; McCool, Brian A

2004-08-09

Strychnine-sensitive glycine receptors in many adult forebrain regions consist of alpha2 + beta heteromeric channels. This subunit composition is distinct from the alpha1 + beta channels found throughout the adult spinal cord. Unfortunately, the pharmacology of forebrain alpha2beta receptors are poorly defined compared to 'neonatal' alpha2 homomeric channels or 'spinal' alpha1beta heteromers. In addition, the pharmacologic properties of native alpha2beta glycine receptors have been generally distinct from receptors produced by heterologous expression. To identify subtype-specific pharmacologic tools for the forebrain alpha2beta receptors, it is important to identify a heterologous expression system that closely resembles these native glycine-gated chloride channels. While exploring pharmacological properties of alpha2beta glycine receptors compared to alpha2-homomers, we found that distinct heterologous expression systems appeared to differentially influence partial agonist pharmacology. The beta-amino acid taurine possessed 30-50% efficacy for alpha2-containing receptor isoforms when expressed in HEK 293 cells. However, taurine efficacy was dramatically reduced in L-cell fibroblasts. Similar results were obtained for beta-alanine. The efficacy of these partial agonists was also strongly reduced by the beta subunit. There were no significant differences in apparent strychnine affinity values calculated from concentration-response data between expression systems or subunit combinations. Nor did relative levels of expression correlate with partial agonist efficacy when compared within or between several different expression systems. Finally, disruption of the tubulin cytoskeleton reduced the efficacy of partial agonists in a subunit-dependent, but system-independent, fashion. Our results suggest that different heterologous expression systems can dramatically influence the agonist pharmacology of strychnine-sensitive glycine receptors. In the systems examine here, these effects are independent of both absolute expression level and any system-related alterations in the agonist binding site. We conclude that complex interactions between receptor composition and extrinsic factors may play a significant role in determining strychnine-sensitive glycine receptor partial agonist pharmacology.

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

PubMed Central

Farasat, Iman; Kushwaha, Manish; Collens, Jason; Easterbrook, Michael; Guido, Matthew; Salis, Howard M

2014-01-01

Developing predictive models of multi-protein genetic systems to understand and optimize their behavior remains a combinatorial challenge, particularly when measurement throughput is limited. We developed a computational approach to build predictive models and identify optimal sequences and expression levels, while circumventing combinatorial explosion. Maximally informative genetic system variants were first designed by the RBS Library Calculator, an algorithm to design sequences for efficiently searching a multi-protein expression space across a > 10,000-fold range with tailored search parameters and well-predicted translation rates. We validated the algorithm's predictions by characterizing 646 genetic system variants, encoded in plasmids and genomes, expressed in six gram-positive and gram-negative bacterial hosts. We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. Using model predictions, we designed and characterized 47 additional pathway variants to navigate its activity space, find optimal expression regions with desired activity response curves, and relieve rate-limiting steps in metabolism. Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs. PMID:24952589

21 CFR 862.1163 - Cardiac allograft gene expression profiling test system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1163 Cardiac allograft gene expression profiling test system. (a...

21 CFR 862.1163 - Cardiac allograft gene expression profiling test system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1163 Cardiac allograft gene expression profiling test system. (a...

21 CFR 862.1163 - Cardiac allograft gene expression profiling test system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1163 Cardiac allograft gene expression profiling test system. (a...

21 CFR 862.1163 - Cardiac allograft gene expression profiling test system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1163 Cardiac allograft gene expression profiling test system. (a...

Engineering of a green-light inducible gene expression system in Synechocystis sp. PCC6803.

PubMed

Abe, Koichi; Miyake, Kotone; Nakamura, Mayumi; Kojima, Katsuhiro; Ferri, Stefano; Ikebukuro, Kazunori; Sode, Koji

2014-03-01

In order to construct a green-light-regulated gene expression system for cyanobacteria, we characterized a green-light sensing system derived from Synechocystis sp. PCC6803, consisting of the green-light sensing histidine kinase CcaS, the cognate response regulator CcaR, and the promoter of cpcG2 (PcpcG 2 ). CcaS and CcaR act as a genetic controller and activate gene expression from PcpcG 2 with green-light illumination. The green-light induction level of the native PcpcG 2 was investigated using GFPuv as a reporter gene inserted in a broad-host-range vector. A clear induction of protein expression from native PcpcG 2 under green-light illumination was observed; however, the expression level was very low compared with Ptrc , which was reported to act as a constitutive promoter in cyanobacteria. Therefore, a Shine-Dalgarno-like sequence derived from the cpcB gene was inserted in the 5' untranslated region of the cpcG2 gene, and the expression level of CcaR was increased. Thus, constructed engineered green-light sensing system resulted in about 40-fold higher protein expression than with the wild-type promoter with a high ON/OFF ratio under green-light illumination. The engineered green-light gene expression system would be a useful genetic tool for controlling gene expression in the emergent cyanobacterial bioprocesses. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Stability of Lentiviral Vector-Mediated Transgene Expression in the Brain in the Presence of Systemic Antivector Immune Responses

PubMed Central

ABORDO-ADESIDA, EVELYN; FOLLENZI, ANTONIA; BARCIA, CARLOS; SCIASCIA, SANDRA; CASTRO, MARIA G.; NALDINI, LUIGI; LOWENSTEIN, PEDRO R.

2009-01-01

Lentiviral vectors are promising tools for gene therapy in the CNS. It is therefore important to characterize their interactions with the immune system in the CNS. This work characterizes transgene expression and brain inflammation in the presence or absence of immune responses generated after systemic immunization with lentiviral vectors. We characterized transduction with SIN-LV vectors in the CNS. A dose—response curve using SIN-LV-GFP demonstrated detectable transgene expression in the striatum at a dose of 102, and maximum expression at 106, transducing units of lentiviral vector, with minimal increase in inflammatory markers between the lowest and highest dose of vector injected. Our studies demonstrate that injection of a lentiviral vector into the CNS did not cause a measurable inflammatory response. Systemic immunization after CNS injection, with the lentiviral vector expressing the same transgene as a vector injected into the CNS, caused a decrease in transgene expression in the CNS, concomitantly with an infiltration of inflammatory cells into the CNS parenchyma at the injection site. However, peripheral immunization with a lentiviral vector carrying a different transgene did not diminish transgene expression, or cause CNS inflammation. Systemic immunization preceding injection of lentiviral vectors into the CNS determined that preexisting antilentiviral immunity, regardless of the transgene, did not affect transgene expression. Furthermore, we showed that the transgene, but not the virion or vector components, is responsible for providing antigenic epitopes to the activated immune system, on systemic immunization with lentivirus. Low immunogenicity and prolonged transgene expression in the presence of preexisting lentiviral immunity are encouraging data for the future use of lentiviral vectors in CNS gene therapy. In summary, the lentiviral vectors tested induced undetectable activation of innate immune responses, and stimulation of adaptive immune responses against lentiviral vectors was effective in causing a decrease in transgene expression only if the immune response was directed against the transgene. A systemic immune response against vector components alone did not cause brain inflammation, possibly because vector-derived epitopes were not being presented in the CNS. PMID:15960605

Efficient expression systems for cysteine proteases of malaria parasites

PubMed Central

Sarduy, Emir Salas; de los A. Chávez Planes, María

2013-01-01

Papain-like cysteine proteases of malaria parasites are considered important chemotherapeutic targets or valuable models for the evaluation of drug candidates. Consequently, many of these enzymes have been cloned and expressed in Escherichia coli for their biochemical characterization. However, their expression has been problematic, showing low yield and leading to the formation of insoluble aggregates. Given that highly-productive expression systems are required for the high-throughput evaluation of inhibitors, we analyzed the existing expression systems to identify the causes of such apparent issues. We found that significant divergences in codon and nucleotide composition from host genes are the most probable cause of expression failure, and propose several strategies to overcome these limitations. Finally we predict that yeast hosts Saccharomyces cerevisiae and Pichia pastoris may be better suited than E. coli for the efficient expression of plasmodial genes, presumably leading to soluble and active products reproducing structural and functional characteristics of the natural enzymes. PMID:23018863

Formal Specifications for an Electrical Power Grid System Stability and Reliability

DTIC Science & Technology

2015-09-01

expressed in this thesis are those of the author and do not reflect the official policy or position of the Department of Defense or the U.S. Government. IRB...analyze the power grid system requirements and express the critical runtime behavior using first-order logic. First, we identify observable...Verification System, and Type systems to name a few [5]. Theorem proving’s specification dimension is dependent on the expressive power of the formal

Transient expression and cellular localization of recombinant proteins in cultured insect cells

USDA-ARS?s Scientific Manuscript database

Heterologous protein expression systems are used for production of recombinant proteins, interpretation of cellular trafficking/localization, and for the determination of biochemical function of proteins at the sub-organismal level. Although baculovirus expression systems are increasingly used for ...

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Part 7; Acquire Express-A3 SPT-100 Based Propulsion Subsystem and Other Subsystem Flight Operation TM-Data, Task 32

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 E. and 11 W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Development and application of a T7 RNA polymerase-dependent expression system for antibiotic production improvement in Streptomyces.

PubMed

Wei, Junhong; Tian, Jinjin; Pan, Guoqing; Xie, Jie; Bao, Jialing; Zhou, Zeyang

2017-06-01

To develop a reliable and easy to use expression system for antibiotic production improvement of Streptomyces. A two-compound T7 RNA polymerase-dependent gene expression system was developed to fulfill this demand. In this system, the T7 RNA polymerase coding sequence was optimized based on the codon usage of Streptomyces coelicolor. To evaluate the functionality of this system, we constructed an activator gene overexpression strain for enhancement of actinorhodin production. By overexpression of the positive regulator actII-ORF4 with this system, the maximum actinorhodin yield of engineered strain was 15-fold higher and the fermentation time was decreased by 48 h. The modified two-compound T7 expression system improves both antibiotic production and accelerates the fermentation process in Streptomyces. This provides a general and useful strategy for strain improvement of important antibiotic producing Streptomyces strains.

Double promoter expression systems for recombinant protein production by industrial microorganisms.

PubMed

Öztürk, Sibel; Ergün, Burcu Gündüz; Çalık, Pınar

2017-10-01

Using double promoter expression systems is a promising approach to increase heterologous protein production. In this review, current double promoter expression systems for the production of recombinant proteins (r-proteins) by industrially important bacteria, Bacillus subtilis and Escherichia coli; and yeasts, Saccharomyces cerevisiae and Pichia pastoris, are discussed by assessing their potentials and drawbacks. Double promoter expression systems need to be designed to maintain a higher specific product formation rate within the production domain. While bacterial double promoter systems have been constructed as chimeric tandem promoters, yeast dual promoter systems have been developed as separate expression cassettes. To increase production and productivity, the optimal transcriptional activity should be justified either by simultaneously satisfying the requirements of both promoters, or by consecutively stimulating the changeover from one to another in a biphasic process or via successive-iterations. Thus, considering the dynamics of a fermentation process, double promoters can be classified according to their operational mechanisms, as: i) consecutively operating double promoter systems, and ii) simultaneously operating double promoter systems. Among these metabolic design strategies, extending the expression period with two promoters activated under different conditions, or enhancing the transcriptional activity with two promoters activated under similar conditions within the production domain, can be applied independently from the host. Novel studies with new insights, which aim a rational systematic design and construction of dual promoter expression vectors with tailored transcriptional activity, will empower r-protein production with enhanced production and productivity. Finally, the current state-of-the-art review emphasizes the advantages of double promoter systems along with the necessity for discovering new promoters for the development of more effective and adaptive processes to meet the increasing demand of r-protein industry.

Computer transformation of partial differential equations into any coordinate system

NASA Technical Reports Server (NTRS)

Sullivan, R. D.

1977-01-01

The use of tensors to provide a compact way of writing partial differential equations in a form valid in all coordinate systems is discussed. In order to find solutions to the equations with their boundary conditions they must be expressed in terms of the coordinate system under consideration. The process of arriving at these expressions from the tensor formulation was automated by a software system, TENSR. An allied system that analyzes the resulting expressions term by term and drops those that are negligible is also described.

Analytical expressions for the nonlinear interference in dispersion managed transmission coherent optical systems

NASA Astrophysics Data System (ADS)

Qiao, Yaojun; Li, Ming; Yang, Qiuhong; Xu, Yanfei; Ji, Yuefeng

2015-01-01

Closed-form expressions of nonlinear interference of dense wavelength-division-multiplexed (WDM) systems with dispersion managed transmission (DMT) are derived. We carry out a simulative validation by addressing an ample and significant set of the Nyquist-WDM systems based on polarization multiplexed quadrature phase-shift keying (PM-QPSK) subcarriers at a baud rate of 32 Gbaud per channel. Simulation results show the simple closed-form analytical expressions can provide an effective tool for the quick and accurate prediction of system performance in DMT coherent optical systems.

MultiSite Gateway-Compatible Cell Type-Specific Gene-Inducible System for Plants1[OPEN

PubMed Central

Siligato, Riccardo; Wang, Xin; Yadav, Shri Ram; Lehesranta, Satu; Ma, Guojie; Ursache, Robertas; Sevilem, Iris; Zhang, Jing; Gorte, Maartje; Prasad, Kalika; Heidstra, Renze

2016-01-01

A powerful method to study gene function is expression or overexpression in an inducible, cell type-specific system followed by observation of consequent phenotypic changes and visualization of linked reporters in the target tissue. Multiple inducible gene overexpression systems have been developed for plants, but very few of these combine plant selection markers, control of expression domains, access to multiple promoters and protein fusion reporters, chemical induction, and high-throughput cloning capabilities. Here, we introduce a MultiSite Gateway-compatible inducible system for Arabidopsis (Arabidopsis thaliana) plants that provides the capability to generate such constructs in a single cloning step. The system is based on the tightly controlled, estrogen-inducible XVE system. We demonstrate that the transformants generated with this system exhibit the expected cell type-specific expression, similar to what is observed with constitutively expressed native promoters. With this new system, cloning of inducible constructs is no longer limited to a few special cases but can be used as a standard approach when gene function is studied. In addition, we present a set of entry clones consisting of histochemical and fluorescent reporter variants designed for gene and promoter expression studies. PMID:26644504

2014 Salish Kootenai College Equipment Grant

DTIC Science & Technology

2016-09-14

using an appropriate purification machine. With this appropriate equipment, protein has been purified from a yeast expression system to explore the...purification machine. With this appropriate equipment, protein has been purified from a yeast expression system to explore the effects of that protein on...Scientific Progress We have successfully purified human YKL39 chilectin protein from a yeast expression system. We are currently working on purification

Effect of the feeding system on the fatty acid composition, expression of the Δ9-desaturase, Peroxisome Proliferator-Activated Receptor Alpha, Gamma, and Sterol Regulatory Element Binding Protein 1 genes in the semitendinous muscle of light lambs of the Rasa Aragonesa breed

PubMed Central

2010-01-01

Background Conjugated linoleic acids (CLAs) are receiving increasing attention because of their beneficial effects on human health, with milk and meat products derived from ruminants as important sources of CLA in the human diet. SCD gene is responsible for some of the variation in CLA concentration in adipose tissues, and PPARγ, PPARα and SREBP1 genes are regulator of SCD gene. The aim of this work was to evaluate the effect of the feeding system on fatty acid composition, CLA content and relative gene expression of Δ9-desaturase (SCD), Peroxisome Proliferator-Activated Receptor Gamma (PPARγ), Peroxisome Proliferator-Activated Receptor Alpha, (PPARα) and Sterol Regulatory Element Binding Protein (SREBP1) in Rasa Aragonesa light lambs in semitendinous muscle. Forty-four single-born male lambs were used to evaluate the effect of the feeding system, varying on an intensity gradient according to the use of concentrates: 1. grazing alfalfa, 2. grazing alfalfa with a supplement for lambs, 3. indoor lambs with grazing ewes and 4. drylot. Results Both grazing systems resulted in a higher concentration of vaccenic acid (VA), CLA, CLA/VA acid ratio, and a lower oleic content, oleic acid (C18:1)/stearic acid (C18:0) ratio, PUFA n-6/n-3 ratio and SCD expression compared to other diets. In addition feeding system affected the fatty acid composition and SCD expression, possibly due to CLA concentration or the PUFA n-6/n-3 ratio. Both expression of the SCD gene and the feeding system were important factors affecting CLA concentration in the animal's semitendinous muscle. PPARγ, PPARα and SREBP1 expression seemed to be unaffected by the feeding system. Although no significant results were found, PPARγ, PPARα and SREBP1 showed similar expression pattern as SCD. Moreover, the correlation results between SCD expression and PPARγ (p < 0.01), as well as SREBP1 (p < 0.01) expression, may suggest that these genes were affecting SCD expression in a different way. Conclusions The data indicated that the feeding system is the main factor affecting the fatty acid composition and SCD gene expression, which is also affected by CLA and possibly by n-6/n-3 PUFAs. PMID:20649987

Transient, Inducible, Placenta-Specific Gene Expression in Mice

PubMed Central

Fan, Xiujun; Petitt, Matthew; Gamboa, Matthew; Huang, Mei; Dhal, Sabita; Druzin, Maurice L.; Wu, Joseph C.

2012-01-01

Molecular understanding of placental functions and pregnancy disorders is limited by the absence of methods for placenta-specific gene manipulation. Although persistent placenta-specific gene expression has been achieved by lentivirus-based gene delivery methods, developmentally and physiologically important placental genes have highly stage-specific functions, requiring controllable, transient expression systems for functional analysis. Here, we describe an inducible, placenta-specific gene expression system that enables high-level, transient transgene expression and monitoring of gene expression by live bioluminescence imaging in mouse placenta at different stages of pregnancy. We used the third generation tetracycline-responsive tranactivator protein Tet-On 3G, with 10- to 100-fold increased sensitivity to doxycycline (Dox) compared with previous versions, enabling unusually sensitive on-off control of gene expression in vivo. Transgenic mice expressing Tet-On 3G were created using a new integrase-based, site-specific approach, yielding high-level transgene expression driven by a ubiquitous promoter. Blastocysts from these mice were transduced with the Tet-On 3G-response element promoter-driving firefly luciferase using lentivirus-mediated placenta-specific gene delivery and transferred into wild-type pseudopregnant recipients for placenta-specific, Dox-inducible gene expression. Systemic Dox administration at various time points during pregnancy led to transient, placenta-specific firefly luciferase expression as early as d 5 of pregnancy in a Dox dose-dependent manner. This system enables, for the first time, reliable pregnancy stage-specific induction of gene expression in the placenta and live monitoring of gene expression during pregnancy. It will be widely applicable to studies of both placental development and pregnancy, and the site-specific Tet-On G3 mouse will be valuable for studies in a broad range of tissues. PMID:23011919

Microbial expression of alkaloid biosynthetic enzymes for characterization of their properties.

PubMed

Minami, Hiromichi; Ikezawa, Nobuhiro; Sato, Fumihiko

2010-01-01

A wide variety of secondary metabolites are produced in higher plants. These metabolites are synthesized in specific organs/cells at certain developmental stages and/or under specific environmental conditions. Since these biosynthetic activities are rather restricted and difficult to detect, the biochemical characterization of biosynthetic enzymes involved in secondary metabolism has been limited compared to those involved in primary metabolism. Recently, however, progress in tissue culture and molecular biology has made it easier to study biosynthetic enzymes. Here we describe protocols for expressing some biosynthetic enzymes in Escherichia coli expression systems, since this system is both efficient and cost-effective. First, we describe a standard system for expressing biosynthetic enzymes as a soluble protein under the T7 promoter of the pET expression system in E. coli. In addition, the successful expression of cytochrome P450 in E. coli in an active soluble form with N-terminal modification is discussed, since P450 is the critical enzyme in secondary metabolite biosynthesis.

Evaluation of the Pichia pastoris expression system for the production of GPCRs for structural analysis

PubMed Central

2011-01-01

Background Various protein expression systems, such as Escherichia coli (E. coli), Saccharomyces cerevisiae (S. cerevisiae), Pichia pastoris (P. pastoris), insect cells and mammalian cell lines, have been developed for the synthesis of G protein-coupled receptors (GPCRs) for structural studies. Recently, the crystal structures of four recombinant human GPCRs, namely β2 adrenergic receptor, adenosine A2a receptor, CXCR4 and dopamine D3 receptor, were successfully determined using an insect cell expression system. GPCRs expressed in insect cells are believed to undergo mammalian-like posttranscriptional modifications and have similar functional properties than in mammals. Crystal structures of GPCRs have not yet been solved using yeast expression systems. In the present study, P. pastoris and insect cell expression systems for the human muscarinic acetylcholine receptor M2 subtype (CHRM2) were developed and the quantity and quality of CHRM2 synthesized by both expression systems were compared for the application in structural studies. Results The ideal conditions for the expression of CHRM2 in P. pastoris were 60 hr at 20°C in a buffer of pH 7.0. The specific activity of the expressed CHRM2 was 28.9 pmol/mg of membrane protein as determined by binding assays using [3H]-quinuclidinyl benzilate (QNB). Although the specific activity of the protein produced by P. pastoris was lower than that of Sf9 insect cells, CHRM2 yield in P. pastoris was 2-fold higher than in Sf9 insect cells because P. pastoris was cultured at high cell density. The dissociation constant (Kd) for QNB in P. pastoris was 101.14 ± 15.07 pM, which was similar to that in Sf9 insect cells (86.23 ± 8.57 pM). There were no differences in the binding affinity of CHRM2 for QNB between P. pastoris and Sf9 insect cells. Conclusion Compared to insect cells, P. pastoris is easier to handle, can be grown at lower cost, and can be expressed quicker at a large scale. Yeast, P. pastoris, and insect cells are all effective expression systems for GPCRs. The results of the present study strongly suggested that protein expression in P. pastoris can be applied to the structural and biochemical studies of GPCRs. PMID:21513509

Reconstructing dynamic mental models of facial expressions in prosopagnosia reveals distinct representations for identity and expression.

PubMed

Richoz, Anne-Raphaëlle; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Caldara, Roberto

2015-04-01

The human face transmits a wealth of signals that readily provide crucial information for social interactions, such as facial identity and emotional expression. Yet, a fundamental question remains unresolved: does the face information for identity and emotional expression categorization tap into common or distinct representational systems? To address this question we tested PS, a pure case of acquired prosopagnosia with bilateral occipitotemporal lesions anatomically sparing the regions that are assumed to contribute to facial expression (de)coding (i.e., the amygdala, the insula and the posterior superior temporal sulcus--pSTS). We previously demonstrated that PS does not use information from the eye region to identify faces, but relies on the suboptimal mouth region. PS's abnormal information use for identity, coupled with her neural dissociation, provides a unique opportunity to probe the existence of a dichotomy in the face representational system. To reconstruct the mental models of the six basic facial expressions of emotion in PS and age-matched healthy observers, we used a novel reverse correlation technique tracking information use on dynamic faces. PS was comparable to controls, using all facial features to (de)code facial expressions with the exception of fear. PS's normal (de)coding of dynamic facial expressions suggests that the face system relies either on distinct representational systems for identity and expression, or dissociable cortical pathways to access them. Interestingly, PS showed a selective impairment for categorizing many static facial expressions, which could be accounted for by her lesion in the right inferior occipital gyrus. PS's advantage for dynamic facial expressions might instead relate to a functionally distinct and sufficient cortical pathway directly connecting the early visual cortex to the spared pSTS. Altogether, our data provide critical insights on the healthy and impaired face systems, question evidence of deficits obtained from patients by using static images of facial expressions, and offer novel routes for patient rehabilitation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Prognostic impact of MYC protein expression in central nervous system diffuse large B-cell lymphoma: comparison with MYC rearrangement and MYC mRNA expression.

PubMed

Son, Seung-Myoung; Ha, Sang-Yun; Yoo, Hae-Yong; Oh, Dongryul; Kim, Seok-Jin; Kim, Won-Seog; Ko, Young-Hyeh

2017-01-01

The prognostic role of MYC has been well documented in non-central nervous system diffuse large B-cell lymphoma; however, it remains controversial in central nervous system diffuse large B-cell lymphoma. To investigate the prognostic value of MYC, we analyzed the MYC protein expression by immunohistochemistry, mRNA expression by RNA in situ hybridization, and gene status by fluorescence in situ hybridization in 74 cases of central nervous system diffuse large B-cell lymphoma. Moreover, we examined the correlation between MYC translocation, mRNA expression, and protein expression. The mean percentage of MYC immunopositive cells was 49%. Using a 44% cutoff value, 49 (66%) cases showed MYC protein overexpression. The result of mRNA in situ hybridization using the RNA scope technology was obtained using the H-scoring system; the median value was 34.2. Using the cutoff value of 63.5, 16 (22%) cases showed MYC mRNA overexpression. MYC gene rearrangement was detected in five out of 68 (7%) cases. MYC translocation showed no statistically significant correlation with mRNA expression; however, all MYC translocation-positive cases showed MYC protein overexpression, with a higher mean percentage of MYC protein expression than that of translocation-negative cases (78 vs 48%, P=0.001). The level of MYC mRNA expression was moderately correlated with the level of MYC protein expression (P<0.001). The mean percentage of MYC protein expression in the high MYC mRNA group was higher than that in the low MYC mRNA group (70 vs 47%, P<0.001). A univariate analysis showed that age over 60 years, Eastern Cooperative Oncology Group (ECOG) performance status ≥2 and MYC protein overexpression were significantly associated with an increased risk of death. MYC translocation and MYC mRNA expression had no prognostic significance. On multivariate analysis, MYC protein overexpression and ECOG score retained prognostic significance.

A wearable device for emotional recognition using facial expression and physiological response.

PubMed

Jangho Kwon; Da-Hye Kim; Wanjoo Park; Laehyun Kim

2016-08-01

This paper introduces a glasses-typed wearable system to detect user's emotions using facial expression and physiological responses. The system is designed to acquire facial expression through a built-in camera and physiological responses such as photoplethysmogram (PPG) and electrodermal activity (EDA) in unobtrusive way. We used video clips for induced emotions to test the system suitability in the experiment. The results showed a few meaningful properties that associate emotions with facial expressions and physiological responses captured by the developed wearable device. We expect that this wearable system with a built-in camera and physiological sensors may be a good solution to monitor user's emotional state in daily life.

Performance benchmarking of four cell-free protein expression systems.

PubMed

Gagoski, Dejan; Polinkovsky, Mark E; Mureev, Sergey; Kunert, Anne; Johnston, Wayne; Gambin, Yann; Alexandrov, Kirill

2016-02-01

Over the last half century, a range of cell-free protein expression systems based on pro- and eukaryotic organisms have been developed and have found a range of applications, from structural biology to directed protein evolution. While it is generally accepted that significant differences in performance among systems exist, there is a paucity of systematic experimental studies supporting this notion. Here, we took advantage of the species-independent translation initiation sequence to express and characterize 87 N-terminally GFP-tagged human cytosolic proteins of different sizes in E. coli, wheat germ (WGE), HeLa, and Leishmania-based (LTE) cell-free systems. Using a combination of single-molecule fluorescence spectroscopy, SDS-PAGE, and Western blot analysis, we assessed the expression yields, the fraction of full-length translation product, and aggregation propensity for each of these systems. Our results demonstrate that the E. coli system has the highest expression yields. However, we observe that high expression levels are accompanied by production of truncated species-particularly pronounced in the case of proteins larger than 70 kDa. Furthermore, proteins produced in the E. coli system display high aggregation propensity, with only 10% of tested proteins being produced in predominantly monodispersed form. The WGE system was the most productive among eukaryotic systems tested. Finally, HeLa and LTE show comparable protein yields that are considerably lower than the ones achieved in the E. coli and WGE systems. The protein products produced in the HeLa system display slightly higher integrity, whereas the LTE-produced proteins have the lowest aggregation propensity among the systems analyzed. The high quality of HeLa- and LTE-produced proteins enable their analysis without purification and make them suitable for analysis of multi-domain eukaryotic proteins. © 2015 Wiley Periodicals, Inc.

Engrailed negatively regulates the expression of cell adhesion molecules connectin and neuroglian in embryonic Drosophila nervous system.

PubMed

Siegler, M V; Jia, X X

1999-02-01

Engrailed is expressed in subsets of interneurons that do not express Connectin or appreciable Neuroglian, whereas other neurons that are Engrailed negative strongly express these adhesion molecules. Connectin and Neuroglian expression are virtually eliminated in interneurons when engrailed expression is driven ubiquitously in neurons, and greatly increased when engrailed genes are lacking in mutant embryos. The data suggest that Engrailed is normally a negative regulator of Connectin and neuroglian. These are the first two "effector" genes identified in the nervous system of Drosophila as regulatory targets for Engrailed. We argue that differential Engrailed expression is crucial in determining the pattern of expression of cell adhesion molecules and thus constitutes an important determinant of neuronal shape and perhaps connectivity.

Facial Expression Recognition using Multiclass Ensemble Least-Square Support Vector Machine

NASA Astrophysics Data System (ADS)

Lawi, Armin; Sya'Rani Machrizzandi, M.

2018-03-01

Facial expression is one of behavior characteristics of human-being. The use of biometrics technology system with facial expression characteristics makes it possible to recognize a person’s mood or emotion. The basic components of facial expression analysis system are face detection, face image extraction, facial classification and facial expressions recognition. This paper uses Principal Component Analysis (PCA) algorithm to extract facial features with expression parameters, i.e., happy, sad, neutral, angry, fear, and disgusted. Then Multiclass Ensemble Least-Squares Support Vector Machine (MELS-SVM) is used for the classification process of facial expression. The result of MELS-SVM model obtained from our 185 different expression images of 10 persons showed high accuracy level of 99.998% using RBF kernel.

Systems, methods and computer-readable media to model kinetic performance of rechargeable electrochemical devices

DOEpatents

Gering, Kevin L.

2013-01-01

A system includes an electrochemical cell, monitoring hardware, and a computing system. The monitoring hardware samples performance characteristics of the electrochemical cell. The computing system determines cell information from the performance characteristics. The computing system also analyzes the cell information of the electrochemical cell with a Butler-Volmer (BV) expression modified to determine exchange current density of the electrochemical cell by including kinetic performance information related to pulse-time dependence, electrode surface availability, or a combination thereof. A set of sigmoid-based expressions may be included with the modified-BV expression to determine kinetic performance as a function of pulse time. The determined exchange current density may be used with the modified-BV expression, with or without the sigmoid expressions, to analyze other characteristics of the electrochemical cell. Model parameters can be defined in terms of cell aging, making the overall kinetics model amenable to predictive estimates of cell kinetic performance along the aging timeline.

The GDNF System Is Altered in Diverticular Disease – Implications for Pathogenesis

PubMed Central

Böttner, Martina; Barrenschee, Martina; Hellwig, Ines; Harde, Jonas; Egberts, Jan-Hendrik; Becker, Thomas; Zorenkov, Dimitri; Schäfer, Karl-Herbert; Wedel, Thilo

2013-01-01

Background & Aims Absence of glial cell line-derived neurotrophic factor (GDNF) leads to intestinal aganglionosis. We recently demonstrated that patients with diverticular disease (DD) exhibit hypoganglionosis suggesting neurotrophic factor deprivation. Thus, we screened mRNA expression pattern of the GDNF system in DD and examined the effects of GDNF on cultured enteric neurons. Methods Colonic specimens obtained from patients with DD (n = 21) and controls (n = 20) were assessed for mRNA expression levels of the GDNF system (GDNF, GDNF receptors GFRα1 and RET). To identify the tissue source of GDNF and its receptors, laser-microdissected (LMD) samples of human myenteric ganglia and intestinal muscle layers were analyzed separately by qPCR. Furthermore, the effects of GDNF treatment on cultured enteric neurons (receptor expression, neuronal differentiation and plasticity) were monitored. Results mRNA expression of GDNF and its receptors was significantly down-regulated in the muscularis propria of patients with DD. LMD samples revealed high expression of GDNF in circular and longitudinal muscle layers, whereas GDNF receptors were also expressed in myenteric ganglia. GDNF treatment of cultured enteric neurons increased mRNA expression of its receptors and promoted neuronal differentiation and plasticity revealed by synaptophysin mRNA and protein expression. Conclusions Our results suggest that the GDNF system is compromised in DD. In vitro studies demonstrate that GDNF enhances expression of its receptors and promotes enteric neuronal differentiation and plasticity. Since patients with DD exhibit hypoganglionosis, we propose that the observed enteric neuronal loss in DD may be due to lacking neurotrophic support mediated by the GDNF system. PMID:23805210

Effects of prebiotics on immune system and cytokine expression.

PubMed

Shokryazdan, Parisa; Faseleh Jahromi, Mohammad; Navidshad, Bahman; Liang, Juan Boo

2017-02-01

Nowadays, use of prebiotics as feed and food additives has received increasing interest because of the beneficial effects of prebiotics on the health of animals and humans. One of the beneficial effects of prebiotics is stimulation of immune system, which can be direct or indirect through increasing population of beneficial microbes or probiotics, especially lactic acid bacteria and bifidobacteria, in the gut. An important mechanism of action of probiotics and prebiotics, by which they can affect the immune system, is changing the expression of cytokines. The present review tried to summarize the findings of studies that investigated the effects of prebiotics on immune system with focusing on their effects on cytokine expression. Generally, most of reviewed studies indicated beneficial effects for prebiotics in terms of improving immune system, by increasing the expression of anti-inflammatory cytokines, while reducing the expressions of proinflammatory cytokines. However, most of studies mainly considered the indirect effects of prebiotics on the immune system (through changing the composition and population of gut microbiota), and their direct effects still need to be further studied using prebiotics with different degree of polymerization in different hosts.

Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants

DOE PAGES

Liang, Yan; Richardson, Sarah; Yan, Jingwei; ...

2017-01-17

Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. In meeting these challenges we will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression–repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repressmore » transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Here, we identified 54 orthologous systems from various bacteria, using a bioinformatics approach and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.« less

Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants

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

Liang, Yan; Richardson, Sarah; Yan, Jingwei

Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. In meeting these challenges we will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression–repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repressmore » transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Here, we identified 54 orthologous systems from various bacteria, using a bioinformatics approach and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.« less

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 E. and 11 W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Mifepristone-inducible transgene expression in neural progenitor cells in vitro and in vivo

PubMed Central

Hjelm, BE; Grunseich, C; Gowing, G; Avalos, P; Tian, J; Shelley, BC; Mooney, M; Narwani, K; Shi, Y; Svendsen, CN; Wolfe, JH; Fischbeck, KH; Pierson, TM

2016-01-01

Numerous gene and cell therapy strategies are being developed for the treatment of neurodegenerative disorders. Many of these strategies use constitutive expression of therapeutic transgenic proteins, and although functional in animal models of disease, this method is less likely to provide adequate flexibility for delivering therapy to humans. Ligand-inducible gene expression systems may be more appropriate for these conditions, especially within the central nervous system (CNS). Mifepristone’s ability to cross the blood–brain barrier makes it an especially attractive ligand for this purpose. We describe the production of a mifepristone-inducible vector system for regulated expression of transgenes within the CNS. Our inducible system used a lentivirus-based vector platform for the ex vivo production of mifepristone-inducible murine neural progenitor cells that express our transgenes of interest. These cells were processed through a series of selection steps to ensure that the cells exhibited appropriate transgene expression in a dose-dependent and temporally controlled manner with minimal background activity. Inducible cells were then transplanted into the brains of rodents, where they exhibited appropriate mifepristone-inducible expression. These studies detail a strategy for regulated expression in the CNS for use in the development of safe and efficient gene therapy for neurological disorders. PMID:26863047

Functional evaluation of candidate ice structuring proteins using cell-free expression systems.

PubMed

Brödel, A K; Raymond, J A; Duman, J G; Bier, F F; Kubick, S

2013-02-10

Ice structuring proteins (ISPs) protect organisms from damage or death by freezing. They depress the non-equilibrium freezing point of water and prevent recrystallization, probably by binding to the surface of ice crystals. Many ISPs have been described and it is likely that many more exist in nature that have not yet been identified. ISPs come in many forms and thus cannot be reliably identified by their structure or consensus ice-binding motifs. Recombinant protein expression is the gold standard for proving the activity of a candidate ISP. Among existing expression systems, cell-free protein expression is the simplest and gives the fastest access to the protein of interest, but selection of the appropriate cell-free expression system is crucial for functionality. Here we describe cell-free expression methods for three ISPs that differ widely in structure and glycosylation status from three organisms: a fish (Macrozoarces americanus), an insect (Dendroides canadensis) and an alga (Chlamydomonas sp. CCMP681). We use both prokaryotic and eukaryotic expression systems for the production of ISPs. An ice recrystallization inhibition assay is used to test functionality. The techniques described here should improve the success of cell-free expression of ISPs in future applications. Copyright © 2012 Elsevier B.V. All rights reserved.

33 CFR 161.18 - Reporting requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... call. H HOTEL Date, time and point of entry system Entry time expressed as in (B) and into the entry... KILO Date, time and point of exit from system Exit time expressed as in (B) and exit position expressed....; for a dredge or floating plant: configuration of pipeline, mooring configuration, number of assist...

Positive Bioluminescence Imaging of MicroRNA Expression in Small Animal Models Using an Engineered Genetic-Switch Expression System, RILES.

PubMed

Baril, Patrick; Pichon, Chantal

2016-01-01

MicroRNAs (miRNAs) are a class of small, noncoding RNAs which regulate gene expression by directing their target mRNA for degradation or translational repression. Since their discovery in the early 1990s, miRNAs have emerged as key components in the posttranscriptional regulation of gene networks, shaping many biological processes from development, morphogenesis, differentiation, proliferation and apoptosis. Although understanding of the molecular basis of miRNA biology is improving, methods to monitor the dynamic and the spatiotemporal aspects of miRNA expression under physiopathological conditions are required. However, monitoring of miRNAs is difficult due to their small size, low abundance, high degree of sequence similarity, and their dynamic expression pattern which is subjected to tight transcriptional and post-transcriptional controls. Recently, we developed a miRNA monitoring system called RILES, standing for RNAi-inducible expression system, which relies on an engineered regulatable expression system, to switch on the expression of the luciferase gene when the targeted miRNA is expressed in cells. We demonstrated that RILES is a specific, sensitive, and robust method to determine the fine-tuning of miRNA expression during the development of an experimental pathological process in mice. Because RILES offers the possibility for longitudinal studies on individual subjects, sharper insights into miRNA regulation can be generated, with applications in physiology, pathophysiology and development of RNAi-based therapies. This chapter describes methods and protocols to monitor the expression of myomiR-206, -1, and -133 in the tibialis anterior muscle of mice. These protocols can be used and adapted to monitor the expression of other miRNAs in other biological processes.

Cross-Layer Design for Space-Time coded MIMO Systems over Rice Fading Channel

NASA Astrophysics Data System (ADS)

Yu, Xiangbin; Zhou, Tingting; Liu, Xiaoshuai; Yin, Xin

A cross-layer design (CLD) scheme for space-time coded MIMO systems over Rice fading channel is presented by combining adaptive modulation and automatic repeat request, and the corresponding system performance is investigated well. The fading gain switching thresholds subject to a target packet error rate (PER) and fixed power constraint are derived. According to these results, and using the generalized Marcum Q-function, the calculation formulae of the average spectrum efficiency (SE) and PER of the system with CLD are derived. As a result, closed-form expressions for average SE and PER are obtained. These expressions include some existing expressions in Rayleigh channel as special cases. With these expressions, the system performance in Rice fading channel is evaluated effectively. Numerical results verify the validity of the theoretical analysis. The results show that the system performance in Rice channel is effectively improved as Rice factor increases, and outperforms that in Rayleigh channel.

Analytical expressions for the evolution of many-body quantum systems quenched far from equilibrium

NASA Astrophysics Data System (ADS)

Santos, Lea F.; Torres-Herrera, E. Jonathan

2017-12-01

Possible strategies to describe analytically the dynamics of many-body quantum systems out of equilibrium include the use of solvable models and of full random matrices. None of the two approaches represent actual realistic systems, but they serve as references for the studies of these ones. We take the second path and obtain analytical expressions for the survival probability, density imbalance, and out-of-time-ordered correlator. Using these findings, we then propose an approximate expression that matches very well numerical results for the evolution of realistic finite quantum systems that are strongly chaotic and quenched far from equilibrium. In the case of the survival probability, the expression proposed covers all different time scales, from the moment the system is taken out of equilibrium to the moment it reaches a new equilibrium. The realistic systems considered are described by one-dimensional spin-1/2 models.

Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system

PubMed Central

Fujiwara, Kei; Katayama, Tsutomu; Nomura, Shin-ichiro M.

2013-01-01

Replication of all living cells relies on the multirounds flow of the central dogma. Especially, expression of DNA replication proteins is a key step to circulate the processes of the central dogma. Here we achieved the entire sequential transcription–translation–replication process by autonomous expression of chromosomal DNA replication machineries from a reconstituted transcription–translation system (PURE system). We found that low temperature is essential to express a complex protein, DNA polymerase III, in a single tube using the PURE system. Addition of the 13 genes, encoding initiator, DNA helicase, helicase loader, RNA primase and DNA polymerase III to the PURE system gave rise to a DNA replication system by a coupling manner. An artificial genetic circuit demonstrated that the DNA produced as a result of the replication is able to provide genetic information for proteins, indicating the in vitro central dogma can sequentially undergo two rounds. PMID:23737447

A high-level prokaryotic expression system: synthesis of human interleukin 1 alpha and its receptor antagonist.

PubMed

Birikh, K R; Lebedenko, E N; Boni, I V; Berlin, Y A

1995-10-27

Synthetic intronless genes, coding for human interleukin 1 alpha (IL 1 alpha) and interleukin 1 receptor antagonist (IL1ra), have been expressed efficiently in a specially designed prokaryotic vector, pGMCE (a pGEM1 derivative), where the target gene forms the second part of a two-cistron system. The first part of the system is a translation enhancer-containing mini-cistron, whose termination codon overlaps the start codon of the target gene. In the case of the IL1 alpha gene, the high expression level is largely due to the direct efficient translation initiation at the second cistron, whereas with the IL1ra gene in the same system, the proximal translation initiation region (TIR) provides a high level of coupled expression of the target gene. Thus, pGMCE is a potentially versatile vector for direct prokaryotic expression.

Direct multiplexed measurement of gene expression with color-coded probe pairs.

PubMed

Geiss, Gary K; Bumgarner, Roger E; Birditt, Brian; Dahl, Timothy; Dowidar, Naeem; Dunaway, Dwayne L; Fell, H Perry; Ferree, Sean; George, Renee D; Grogan, Tammy; James, Jeffrey J; Maysuria, Malini; Mitton, Jeffrey D; Oliveri, Paola; Osborn, Jennifer L; Peng, Tao; Ratcliffe, Amber L; Webster, Philippa J; Davidson, Eric H; Hood, Leroy; Dimitrov, Krassen

2008-03-01

We describe a technology, the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 fM and 0.5 fM, and a linear dynamic range of over 500-fold. Comparison of the NanoString nCounter gene expression system with microarrays and TaqMan PCR demonstrated that the nCounter system is more sensitive than microarrays and similar in sensitivity to real-time PCR. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels.

The role of ZAP70 kinase in acute lymphoblastic leukemia infiltration into the central nervous system.

PubMed

Alsadeq, Ameera; Fedders, Henning; Vokuhl, Christian; Belau, Nele M; Zimmermann, Martin; Wirbelauer, Tim; Spielberg, Steffi; Vossen-Gajcy, Michaela; Cario, Gunnar; Schrappe, Martin; Schewe, Denis M

2017-02-01

Central nervous system infiltration and relapse are poorly understood in childhood acute lymphoblastic leukemia. We examined the role of zeta-chain-associated protein kinase 70 in preclinical models of central nervous system leukemia and performed correlative studies in patients. Zeta-chain-associated protein kinase 70 expression in acute lymphoblastic leukemia cells was modulated using short hairpin ribonucleic acid-mediated knockdown or ectopic expression. We show that zeta-chain-associated protein kinase 70 regulates CCR7/CXCR4 via activation of extracellular signal-regulated kinases. High expression of zeta-chain-associated protein kinase 70 in acute lymphoblastic leukemia cells resulted in a higher proportion of central nervous system leukemia in xenografts as compared to zeta-chain-associated protein kinase 70 low expressing counterparts. High zeta-chain-associated protein kinase 70 also enhanced the migration potential towards CCL19/CXCL12 gradients in vitro CCR7 blockade almost abrogated homing of acute lymphoblastic leukemia cells to the central nervous system in xenografts. In 130 B-cell precursor acute lymphoblastic leukemia and 117 T-cell acute lymphoblastic leukemia patients, zeta-chain-associated protein kinase 70 and CCR7/CXCR4 expression levels were significantly correlated. Zeta-chain-associated protein kinase 70 expression correlated with central nervous system disease in B-cell precursor acute lymphoblastic leukemia, and CCR7/CXCR4 correlated with central nervous system involvement in T-cell acute lymphoblastic leukemia patients. In multivariate analysis, zeta-chain-associated protein kinase 70 expression levels in the upper third and fourth quartiles were associated with central nervous system involvement in B-cell precursor acute lymphoblastic leukemia (odds ratio=7.48, 95% confidence interval, 2.06-27.17; odds ratio=6.86, 95% confidence interval, 1.86-25.26, respectively). CCR7 expression in the upper fourth quartile correlated with central nervous system positivity in T-cell acute lymphoblastic leukemia (odds ratio=11.00, 95% confidence interval, 2.00-60.62). We propose zeta-chain-associated protein kinase 70, CCR7 and CXCR4 as markers of central nervous system infiltration in acute lymphoblastic leukemia warranting prospective investigation. Copyright© Ferrata Storti Foundation.

A Modular Lentiviral and Retroviral Construction System to Rapidly Generate Vectors for Gene Expression and Gene Knockdown In Vitro and In Vivo

PubMed Central

Geiling, Benjamin; Vandal, Guillaume; Posner, Ada R.; de Bruyns, Angeline; Dutchak, Kendall L.; Garnett, Samantha; Dankort, David

2013-01-01

The ability to express exogenous cDNAs while suppressing endogenous genes via RNAi represents an extremely powerful research tool with the most efficient non-transient approach being accomplished through stable viral vector integration. Unfortunately, since traditional restriction enzyme based methods for constructing such vectors are sequence dependent, their construction is often difficult and not amenable to mass production. Here we describe a non-sequence dependent Gateway recombination cloning system for the rapid production of novel lentiviral (pLEG) and retroviral (pREG) vectors. Using this system to recombine 3 or 4 modular plasmid components it is possible to generate viral vectors expressing cDNAs with or without inhibitory RNAs (shRNAmirs). In addition, we demonstrate a method to rapidly produce and triage novel shRNAmirs for use with this system. Once strong candidate shRNAmirs have been identified they may be linked together in tandem to knockdown expression of multiple targets simultaneously or to improve the knockdown of a single target. Here we demonstrate that these recombinant vectors are able to express cDNA and effectively knockdown protein expression using both cell culture and animal model systems. PMID:24146852

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Part 2; Acquire TM Date for Type B Sensors for "Express-A" Number 2 Satellite for the Period of March 12, 2000 to and Including June 15, 2000, Task 25

NASA Technical Reports Server (NTRS)

Dunning, John (Technical Monitor); Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 E. and 11 W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Hall Effect Thruster Interactions Data from the Russian Express-A2 and Express-A3 Satellites. Part 4; Acquire TM-Data for Type A and Type B Sensors for "Express-A" Number 3 Satellite, Task 27A

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80deg E., and 11deg W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3-99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Acquire Express-A2 SPT-100 Based Propulsion Subsystem and Other Subsystem Flight Operation TM-Data for the Period of March 12, 2000 to and Including June 15, 2000, Task 29

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 E. and 11 W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney s Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Hall Effect Thruster Interactions Data from the Russian Express-A2 and Express-A3 Satellites. Part 5; Acquire Express-A3 SPT?100 Based Propulsion Subsystem and Other Subsystem Flight Operation TM-Data, Task 31

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80deg E. and 11deg W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3-99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Acquire Express-A3 SPT 100 Based Propulsion Subsystem and Other Subsystem Flight Operation TM-Data, Task 33

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 deg E and 11 deg W, respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3-99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Facial expression system on video using widrow hoff

NASA Astrophysics Data System (ADS)

Jannah, M.; Zarlis, M.; Mawengkang, H.

2018-03-01

Facial expressions recognition is one of interesting research. This research contains human feeling to computer application Such as the interaction between human and computer, data compression, facial animation and facial detection from the video. The purpose of this research is to create facial expression system that captures image from the video camera. The system in this research uses Widrow-Hoff learning method in training and testing image with Adaptive Linear Neuron (ADALINE) approach. The system performance is evaluated by two parameters, detection rate and false positive rate. The system accuracy depends on good technique and face position that trained and tested.

Drug-loaded nanoparticles induce gene expression in human pluripotent stem cell derivatives

NASA Astrophysics Data System (ADS)

Gajbhiye, Virendra; Escalante, Leah; Chen, Guojun; Laperle, Alex; Zheng, Qifeng; Steyer, Benjamin; Gong, Shaoqin; Saha, Krishanu

2013-12-01

Tissue engineering and advanced manufacturing of human stem cells requires a suite of tools to control gene expression spatiotemporally in culture. Inducible gene expression systems offer cell-extrinsic control, typically through addition of small molecules, but small molecule inducers typically contain few functional groups for further chemical modification. Doxycycline (DXC), a potent small molecule inducer of tetracycline (Tet) transgene systems, was conjugated to a hyperbranched dendritic polymer (Boltorn H40) and subsequently reacted with polyethylene glycol (PEG). The resulting PEG-H40-DXC nanoparticle exhibited pH-sensitive drug release behavior and successfully controlled gene expression in stem-cell-derived fibroblasts with a Tet-On system. While free DXC inhibited fibroblast proliferation and matrix metalloproteinase (MMP) activity, PEG-H40-DXC nanoparticles maintained higher fibroblast proliferation levels and MMP activity. The results demonstrate that the PEG-H40-DXC nanoparticle system provides an effective tool to controlling gene expression in human stem cell derivatives.Tissue engineering and advanced manufacturing of human stem cells requires a suite of tools to control gene expression spatiotemporally in culture. Inducible gene expression systems offer cell-extrinsic control, typically through addition of small molecules, but small molecule inducers typically contain few functional groups for further chemical modification. Doxycycline (DXC), a potent small molecule inducer of tetracycline (Tet) transgene systems, was conjugated to a hyperbranched dendritic polymer (Boltorn H40) and subsequently reacted with polyethylene glycol (PEG). The resulting PEG-H40-DXC nanoparticle exhibited pH-sensitive drug release behavior and successfully controlled gene expression in stem-cell-derived fibroblasts with a Tet-On system. While free DXC inhibited fibroblast proliferation and matrix metalloproteinase (MMP) activity, PEG-H40-DXC nanoparticles maintained higher fibroblast proliferation levels and MMP activity. The results demonstrate that the PEG-H40-DXC nanoparticle system provides an effective tool to controlling gene expression in human stem cell derivatives. Electronic supplementary information (ESI) available: ESI containing 1H NMR spectra and additional fibroblast characterization data. See DOI: 10.1039/c3nr04794f

Expression of a Dianthus flavonoid glucosyltransferase in Saccharomyces cerevisiae for whole-cell biocatalysis.

PubMed

Werner, Sean R; Morgan, John A

2009-07-15

Glycosyltransferases are promising biocatalysts for the synthesis of small molecule glycosides. In this study, Saccharomyces cerevisiae expressing a flavonoid glucosyltransferase (GT) from Dianthus caryophyllus (carnation) was investigated as a whole-cell biocatalyst. Two yeast expression systems were compared using the flavonoid naringenin as a model substrate. Under in vitro conditions, naringenin-7-O-glucoside was formed and a higher specific glucosyl transfer activity was found using a galactose inducible expression system compared to a constitutive expression system. However, S. cerevisiae expressing the GT constitutively was significantly more productive than the galactose inducible system under in vivo conditions. Interestingly, the glycosides were recovered directly from the culture broth and did not accumulate intracellularly. A previously uncharacterized naringenin glycoside formed using the D. caryophyllus GT was identified as naringenin-4'-O-glucoside. It was found that S. cerevisiae cells hydrolyze naringenin-7-O-glucoside during whole-cell biocatalysis, resulting in a low final glycoside titer. When phloretin was added as a substrate to the yeast strain expressing the GT constitutively, the natural product phlorizin was formed. This study demonstrates S. cerevisiae is a promising whole-cell biocatalyst host for the production of valuable glycosides.

Magnetic field-controlled gene expression in encapsulated cells

PubMed Central

Ortner, Viktoria; Kaspar, Cornelius; Halter, Christian; Töllner, Lars; Mykhaylyk, Olga; Walzer, Johann; Günzburg, Walter H.; Dangerfield, John A.; Hohenadl, Christine; Czerny, Thomas

2012-01-01

Cell and gene therapies have an enormous range of potential applications, but as for most other therapies, dosing is a critical issue, which makes regulated gene expression a prerequisite for advanced strategies. Several inducible expression systems have been established, which mainly rely on small molecules as inducers, such as hormones or antibiotics. The application of these inducers is difficult to control and the effects on gene regulation are slow. Here we describe a novel system for induction of gene expression in encapsulated cells. This involves the modification of cells to express potential therapeutic genes under the control of a heat inducible promoter and the co-encapsulation of these cells with magnetic nanoparticles. These nanoparticles produce heat when subjected to an alternating magnetic field; the elevated temperatures in the capsules then induce gene expression. In the present study we define the parameters of such systems and provide proof-of-principle using reporter gene constructs. The fine-tuned heating of nanoparticles in the magnetic field allows regulation of gene expression from the outside over a broad range and within short time. Such a system has great potential for advancement of cell and gene therapy approaches. PMID:22197778

iFER: facial expression recognition using automatically selected geometric eye and eyebrow features

NASA Astrophysics Data System (ADS)

Oztel, Ismail; Yolcu, Gozde; Oz, Cemil; Kazan, Serap; Bunyak, Filiz

2018-03-01

Facial expressions have an important role in interpersonal communications and estimation of emotional states or intentions. Automatic recognition of facial expressions has led to many practical applications and became one of the important topics in computer vision. We present a facial expression recognition system that relies on geometry-based features extracted from eye and eyebrow regions of the face. The proposed system detects keypoints on frontal face images and forms a feature set using geometric relationships among groups of detected keypoints. Obtained feature set is refined and reduced using the sequential forward selection (SFS) algorithm and fed to a support vector machine classifier to recognize five facial expression classes. The proposed system, iFER (eye-eyebrow only facial expression recognition), is robust to lower face occlusions that may be caused by beards, mustaches, scarves, etc. and lower face motion during speech production. Preliminary experiments on benchmark datasets produced promising results outperforming previous facial expression recognition studies using partial face features, and comparable results to studies using whole face information, only slightly lower by ˜ 2.5 % compared to the best whole face facial recognition system while using only ˜ 1 / 3 of the facial region.

Fasting modulates GH/IGF-I axis and its regulatory systems in the mammary gland of female mice: Influence of endogenous cortistatin.

PubMed

Villa-Osaba, Alicia; Gahete, Manuel D; Cordoba-Chacon, José; de Lecea, Luis; Castaño, Justo P; Luque, Raúl M

2016-10-15

Growth hormone (GH) and insulin-like growth factor-I (IGF-I) are essential factors in mammary-gland (MG) development and are altered during fasting. However, no studies have investigated the alterations in the expression of GH/IGF-I and its regulatory systems (somatostatin/cortistatin and ghrelin) in MG during fasting. Therefore, this study was aimed at characterizing the regulation of GH/IGF-I/somatostatin/cortistatin/ghrelin-systems expression in MG of fasted female-mice (compared to fed-controls) and the influence of endogenous-cortistatin (using cortistatin-knockouts). Fasting decreased IGF-I while increased IGF-I/Insulin-receptors expression in MGs. Fasting provoked an increase in GH expression that might be associated to enhanced ghrelin-variants/ghrelin-O-acyl-transferase enzyme expression, while an upregulation of somatostatin-receptors was observed. However, cortistatin-knockouts mice showed a decrease in GH and somatostatin receptor-subtypes expression. Altogether, we demonstrate that GH/IGF-I, somatostatin/cortistatin and ghrelin systems expression is altered in MG during fasting, suggesting a relevant role in coordinating its response to metabolic stress, wherein endogenous cortistatin might be essential for an appropriate response. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Construction of new synthetic biology tools for the control of gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002.

PubMed

Zess, Erin K; Begemann, Matthew B; Pfleger, Brian F

2016-02-01

Predictive control of gene expression is an essential tool for developing synthetic biological systems. The current toolbox for controlling gene expression in cyanobacteria is a barrier to more in-depth genetic analysis and manipulation. Towards relieving this bottleneck, this work describes the use of synthetic biology to construct an anhydrotetracycline-based induction system and adapt a trans-acting small RNA (sRNA) system for use in the cyanobacterium Synechococcus sp. strain PCC 7002. An anhydrotetracycline-inducible promoter was developed to maximize intrinsic strength and dynamic range. The resulting construct, PEZtet , exhibited tight repression and a maximum 32-fold induction upon addition of anhydrotetracycline. Additionally, a sRNA system based on the Escherichia coli IS10 RNA-IN/OUT regulator was adapted for use in Synechococcus sp. strain PCC 7002. This system exhibited 70% attenuation of target gene expression, providing a demonstration of the use of sRNAs for differential gene expression in cyanobacteria. These systems were combined to produce an inducible sRNA system, which demonstrated 59% attenuation of target gene expression. Lastly, the role of Hfq, a critical component of sRNA systems in E. coli, was investigated. Genetic studies showed that the Hfq homolog in Synechococcus sp. strain PCC 7002 did not impact repression by the engineered sRNA system. In summary, this work describes new synthetic biology tools that can be applied to physiological studies, metabolic engineering, or sRNA platforms in Synechococcus sp. strain PCC 7002. © 2015 Wiley Periodicals, Inc.

Expression and functional characterisation of System L amino acid transporters in the human term placenta.

PubMed

Gaccioli, Francesca; Aye, Irving L M H; Roos, Sara; Lager, Susanne; Ramirez, Vanessa I; Kanai, Yoshikatsu; Powell, Theresa L; Jansson, Thomas

2015-06-09

System L transporters LAT1 (SLC7A5) and LAT2 (SLC7A8) mediate the uptake of large, neutral amino acids in the human placenta. Many System L substrates are essential amino acids, thus representing crucial nutrients for the growing fetus. Both LAT isoforms are expressed in the human placenta, but the relative contribution of LAT1 and LAT2 to placental System L transport and their subcellular localisation are not well established. Moreover, the influence of maternal body mass index (BMI) on placental System L amino acid transport is poorly understood. Therefore the aims of this study were to determine: i) the relative contribution of the LAT isoforms to System L transport activity in primary human trophoblast (PHT) cells isolated from term placenta; ii) the subcellular localisation of LAT transporters in human placenta; and iii) placental expression and activity of System L transporters in response to maternal overweight/obesity. System L mediated leucine uptake was measured in PHT cells after treatment with si-RNA targeting LAT1 and/or LAT2. The localisation of LAT isoforms was studied in isolated microvillous plasma membranes (MVM) and basal membranes (BM) by Western blot analysis. Results were confirmed by immunohistochemistry in sections of human term placenta. Expression and activity System L transporters was measured in isolated MVM from women with varying pre-pregnancy BMI. Both LAT1 and LAT2 isoforms contribute to System L transport activity in primary trophoblast cells from human term placenta. LAT1 and LAT2 transporters are highly expressed in the MVM of the syncytiotrophoblast layer at term. LAT2 is also localised in the basal membrane and in endothelial cells lining the fetal capillaries. Measurements in isolated MVM vesicles indicate that System L transporter expression and activity is not influenced by maternal BMI. LAT1 and LAT2 are present and functional in the syncytiotrophoblast MVM, whereas LAT2 is also expressed in the BM and in the fetal capillary endothelium. In contrast to placental System A and beta amino acid transporters, MVM System L activity is unaffected by maternal overweight/obesity.

Screening Fusion Tags for Improved Recombinant Protein Expression in E. coli with the Expresso® Solubility and Expression Screening System.

PubMed

Steinmetz, Eric J; Auldridge, Michele E

2017-11-01

The simplicity, speed, and low cost of bacterial culture make E. coli the system of choice for most initial trials of recombinant protein expression. However, many heterologous proteins are either poorly expressed in bacteria, or are produced as incorrectly folded, insoluble aggregates that lack the activity of the native protein. In many cases, fusion to a partner protein can allow for improved expression and/or solubility of a difficult target protein. Although several different fusion partners have gained favor, none are universally effective, and identifying the one that best improves soluble expression of a given target protein is an empirical process. This unit presents a strategy for parallel screening of fusion partners for enhanced expression or solubility. The Expresso® Solubility and Expression Screening System includes a panel of seven distinct fusion partners and utilizes an extremely simple cloning strategy to enable rapid screening and identification of the most effective fusion partner. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts.

PubMed

Wang, Weishan; Yang, Tongjian; Li, Yihong; Li, Shanshan; Yin, Shouliang; Styles, Kathryn; Corre, Christophe; Yang, Keqian

2016-07-15

Precise control of gene expression using exogenous factors is of great significance. To develop ideal inducible expression systems for streptomycetes, new genetic parts, oxytetracycline responsive repressor OtrR, operator otrO, and promoter otrBp from Streptomyces rimosus, were selected de novo and characterized in vivo and in vitro. OtrR showed strong affinity to otrO (KD = 1.7 × 10(-10) M) and oxytetracycline induced dissociation of the OtrR/DNA complex in a concentration-dependent manner. On the basis of these genetic parts, a synthetic inducible expression system Potr* was optimized. Induction of Potr* with 0.01-4 μM of oxytetracycline triggered a wide-range expression level of gfp reporter gene in different Streptomyces species. Benchmarking Potr* against the widely used constitutive promoters ermE* and kasOp* revealed greatly enhanced levels of expression when Potr* was fully induced. Finally, Potr* was used as a tool to activate and optimize the expression of the silent jadomycin biosynthetic gene cluster in Streptomyces venezuelae. Altogether, the synthetic Potr* presents a new versatile tool for fine-tuning gene expression in streptomycetes.

The cAMP signaling system inhibits the repair of {gamma}-ray-induced DNA damage by promoting Epac1-mediated proteasomal degradation of XRCC1 protein in human lung cancer cells

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

Cho, Eun-Ah; Juhnn, Yong-Sung, E-mail: juhnn@snu.ac.kr

2012-06-01

Highlights: Black-Right-Pointing-Pointer cAMP signaling system inhibits repair of {gamma}-ray-induced DNA damage. Black-Right-Pointing-Pointer cAMP signaling system inhibits DNA damage repair by decreasing XRCC1 expression. Black-Right-Pointing-Pointer cAMP signaling system decreases XRCC1 expression by promoting its proteasomal degradation. Black-Right-Pointing-Pointer The promotion of XRCC1 degradation by cAMP signaling system is mediated by Epac1. -- Abstract: Cyclic AMP is involved in the regulation of metabolism, gene expression, cellular growth and proliferation. Recently, the cAMP signaling system was found to modulate DNA-damaging agent-induced apoptosis by regulating the expression of Bcl-2 family proteins and inhibitors of apoptosis. Thus, we hypothesized that the cAMP signaling may modulate DNAmore » repair activity, and we investigated the effects of the cAMP signaling system on {gamma}-ray-induced DNA damage repair in lung cancer cells. Transient expression of a constitutively active mutant of stimulatory G protein (G{alpha}sQL) or treatment with forskolin, an adenylyl cyclase activator, augmented radiation-induced DNA damage and inhibited repair of the damage in H1299 lung cancer cells. Expression of G{alpha}sQL or treatment with forskolin or isoproterenol inhibited the radiation-induced expression of the XRCC1 protein, and exogenous expression of XRCC1 abolished the DNA repair-inhibiting effect of forskolin. Forskolin treatment promoted the ubiquitin and proteasome-dependent degradation of the XRCC1 protein, resulting in a significant decrease in the half-life of the protein after {gamma}-ray irradiation. The effect of forskolin on XRCC1 expression was not inhibited by PKA inhibitor, but 8-pCPT-2 Prime -O-Me-cAMP, an Epac-selective cAMP analog, increased ubiquitination of XRCC1 protein and decreased XRCC1 expression. Knockdown of Epac1 abolished the effect of 8-pCPT-2 Prime -O-Me-cAMP and restored XRCC1 protein level following {gamma}-ray irradiation. From these results, we conclude that the cAMP signaling system inhibits the repair of {gamma}-ray-induced DNA damage by promoting the ubiquitin-proteasome dependent degradation of XRCC1 in an Epac-dependent pathway in lung cancer cells.« less

Delay in polling systems in heavy traffic

NASA Astrophysics Data System (ADS)

van der Mei, Robert D.

1998-10-01

We study the delay in asymmetric cyclic polling systems with general mixtures of gated and exhaustive service, with generally distributed service times and switch-over times, in heavy traffic. We obtain closed-form expressions for all moments of the delay incurred at each of the queues. The expressions are strikingly simple and can even be expressed as finite products of known factors. The results provide new insights into the heavy-traffic behavior of polling systems.

Prognostic and predictive values of PD-L1 expression in patients with digestive system cancer: a meta-analysis.

PubMed

Dai, Cong; Wang, Meng; Lu, Jun; Dai, Zhiming; Lin, Shuai; Yang, Pengtao; Tian, Tian; Liu, Xinghan; Min, Weili; Dai, Zhijun

2017-01-01

PD-L1 has been reported to be expressed in diverse human malignancies. However, the prognostic value of PD-L1 in digestive system cancers remains inconclusive. Therefore, we conducted this meta-analysis to evaluate the prognostic impact of PD-L1 expression in digestive system cancers. We searched the PubMed, Embase, and the Chinese National Knowledge Infrastructure for publications concerning PD-L1 expression in digestive system cancers. Correlations of PD-L1 expression level with overall survival (OS), disease-free survival (DFS), and recurrence-free survival (RFS) were analyzed. Finally, 32 studies with 7,308 patients were included. Our results show that PD-L1 expression was significantly associated with poorer OS (hazard ratio [HR] =1.44, 95% confidence interval [CI] =1.18-1.76, P <0.001), but not DFS (HR =0.91, 95% CI =0.61-1.37, P =0.657) or RFS (HR =1.27, 95% CI =0.75-2.14, P =0.368). Moreover, in the subgroup analysis, significant associations between PD-L1 expression and OS were found in Asians (HR =1.50, 95% CI =1.19-1.89, P =0.001), gastric cancer (HR =1.43, 95% CI =1.05-1.94, P =0.021), and pancreatic carcinoma (HR =2.64, 95% CI =1.78-3.93, P <0.001). These results suggest that the expression of PD-L1 is associated with worse OS in digestive system cancers, especially in gastric cancer and pancreatic cancer. In addition, PD-L1 may act as a new parameter for predicting poor prognosis and a promising target for anticancer therapy in digestive system cancers.

Bovine papillomavirus type 4 L1 gene transfection in a Drosophila S2 cell expression system: absence of L1 protein expression

PubMed Central

Góes, Luiz Gustavo Bentim; de Freitas, Antonio Carlos; Ferraz, Oilita Pereira; Rieger, Tania Tassinari; dos Santos, José Ferreira; Pereira, Alexandre; Beçak, Willy; Lindsey, Charles J.; de Cassia Stocco, Rita

2008-01-01

The development of a bovine papillomavirus (BPV) vaccine is an outstanding challenge. BPV protein L1 gene transfection in the Drosophila melanogaster S2 cell expression system failed to produce L1 protein notwithstanding correct L1 gene insertion. Severe genetic inbalance in the host cell line, including cytogenetic alterations, may account for the lack of protein expression. PMID:24031166

Real-time Avatar Animation from a Single Image.

PubMed

Saragih, Jason M; Lucey, Simon; Cohn, Jeffrey F

2011-01-01

A real time facial puppetry system is presented. Compared with existing systems, the proposed method requires no special hardware, runs in real time (23 frames-per-second), and requires only a single image of the avatar and user. The user's facial expression is captured through a real-time 3D non-rigid tracking system. Expression transfer is achieved by combining a generic expression model with synthetically generated examples that better capture person specific characteristics. Performance of the system is evaluated on avatars of real people as well as masks and cartoon characters.

Real-time Avatar Animation from a Single Image

PubMed Central

Saragih, Jason M.; Lucey, Simon; Cohn, Jeffrey F.

2014-01-01

A real time facial puppetry system is presented. Compared with existing systems, the proposed method requires no special hardware, runs in real time (23 frames-per-second), and requires only a single image of the avatar and user. The user’s facial expression is captured through a real-time 3D non-rigid tracking system. Expression transfer is achieved by combining a generic expression model with synthetically generated examples that better capture person specific characteristics. Performance of the system is evaluated on avatars of real people as well as masks and cartoon characters. PMID:24598812

ClinData Express – A Metadata Driven Clinical Research Data Management System for Secondary Use of Clinical Data

PubMed Central

Li, Zuofeng; Wen, Jingran; Zhang, Xiaoyan; Wu, Chunxiao; Li, Zuogao; Liu, Lei

2012-01-01

Aim to ease the secondary use of clinical data in clinical research, we introduce a metadata driven web-based clinical data management system named ClinData Express. ClinData Express is made up of two parts: 1) m-designer, a standalone software for metadata definition; 2) a web based data warehouse system for data management. With ClinData Express, what the researchers need to do is to define the metadata and data model in the m-designer. The web interface for data collection and specific database for data storage will be automatically generated. The standards used in the system and the data export modular make sure of the data reuse. The system has been tested on seven disease-data collection in Chinese and one form from dbGap. The flexibility of system makes its great potential usage in clinical research. The system is available at http://code.google.com/p/clindataexpress. PMID:23304327

On the use of the T-REx tetracycline-inducible gene expression system in vivo.

PubMed

Dobrovolsky, Vasily N; Heflich, Robert H

2007-10-15

Components of the commercially available T-REx system were used to create two types of transgenic mice. The first contained the tetracycline-repressor transgene under the control of the CMV promoter/enhancer; the second type contained a green fluorescent protein (GFP) reporter transgene under the control of the CMV promoter/enhancer with a tetracycline repressor operator sequence. Transgene expression was unpredictable in animals containing the individual transgenes. Animals with the reporter transgene expressed GFP in only some tissues (e.g., pancreas, kidney), and one line of reporter transgenic animals developed kidney disease, presumably due to expression of the transgene. The two types of transgenic animals were crossbred to produce double-transgenic animals with the object of regulating the expression of the reporter in vivo. When a similar double-transgenic system was constructed in cultured cells, the repressor protein suppressed the transcription of the reporter transgene. The presence of the repressor in double-transgenic animals had no effect on the expression of the reporter; double transgenic animals developed the same kidney disease that was seen in singly transgenic mice with the reporter. Our results indicate that transgenes under the control of the CMV promoter in the T-REx system express somewhat unpredictably and in only a limited number of tissues, making the use of this system for the development of in vivo models problematical. Copyright 2007 Wiley Periodicals, Inc.

The Facial Expression Coding System (FACES): Development, Validation, and Utility

ERIC Educational Resources Information Center

Kring, Ann M.; Sloan, Denise M.

2007-01-01

This article presents information on the development and validation of the Facial Expression Coding System (FACES; A. M. Kring & D. Sloan, 1991). Grounded in a dimensional model of emotion, FACES provides information on the valence (positive, negative) of facial expressive behavior. In 5 studies, reliability and validity data from 13 diverse…

Optimized Assembly of a Multifunctional RNA-Protein Nanostructure in a Cell-Free Gene Expression System.

PubMed

Schwarz-Schilling, Matthaeus; Dupin, Aurore; Chizzolini, Fabio; Krishnan, Swati; Mansy, Sheref S; Simmel, Friedrich C

2018-04-11

Molecular complexes composed of RNA molecules and proteins are promising multifunctional nanostructures for a wide variety of applications in biological cells or in artificial cellular systems. In this study, we systematically address some of the challenges associated with the expression and assembly of such hybrid structures using cell-free gene expression systems. As a model structure, we investigated a pRNA-derived RNA scaffold functionalized with four distinct aptamers, three of which bind to proteins, streptavidin and two fluorescent proteins, while one binds the small molecule dye malachite green (MG). Using MG fluorescence and Förster resonance energy transfer (FRET) between the RNA-scaffolded proteins, we assess critical assembly parameters such as chemical stability, binding efficiency, and also resource sharing effects within the reaction compartment. We then optimize simultaneous expression and coassembly of the RNA-protein nanostructure within a single-compartment cell-free gene expression system. We demonstrate expression and assembly of the multicomponent nanostructures inside of emulsion droplets and their aptamer-mediated localization onto streptavidin-coated substrates, plus the successful assembly of the hybrid structures inside of bacterial cells.

Expression of PD-1 and PD-L1 in poorly differentiated neuroendocrine carcinomas of the digestive system: a potential target for anti-PD-1/PD-L1 therapy.

PubMed

Roberts, Jordan A; Gonzalez, Raul S; Das, Satya; Berlin, Jordan; Shi, Chanjuan

2017-12-01

Poorly differentiated neuroendocrine carcinoma of the digestive system has a dismal prognosis with limited treatment options. This study aimed to investigate expression of the PD-1/PD-L1 pathway in these tumors. Thirty-seven patients with a poorly differentiated neuroendocrine carcinoma of the digestive system were identified. Their electronic medical records, pathology reports, and pathology slides were reviewed for demographics, clinical history, and pathologic features. Tumor sections were immunohistochemically labeled for PD-1 and PD-L1, and expression of PD-1 and PD-L1 on tumor and tumor-associated immune cells was analyzed and compared between small cell and large cell neuroendocrine carcinomas. The mean age of patients was 61 years old with 18 men and 19 women. The colorectum (n=20) was the most common primary site; other primary sites included the pancreaticobiliary system, esophagus, stomach, duodenum, and ampulla. Expression of PD-1 was detected on tumor cells (n=6, 16%) as well as on tumor-associated immune cells (n=23, 63%). The 6 cases with PD-1 expression on tumor cells also had the expression on immune cells. Expression of PD-L1 was visualized on tumor cells in 5 cases (14%) and on tumor-associated immune cells in 10 cases (27%). There was no difference in PD-1 and PD-L1 expression between small cell and large cell neuroendocrine carcinomas. In conclusion, PD-1/PD-L1 expression is a frequent occurrence in poorly differentiated neuroendocrine carcinomas of the digestive system. Checkpoint blockade targeting the PD-1/PD-L1 pathway may have a potential role in treating patients with this disease. Copyright © 2017 Elsevier Inc. All rights reserved.

A Green-Light-Responsive System for the Control of Transgene Expression in Mammalian and Plant Cells.

PubMed

Chatelle, Claire; Ochoa-Fernandez, Rocio; Engesser, Raphael; Schneider, Nils; Beyer, Hannes M; Jones, Alex R; Timmer, Jens; Zurbriggen, Matias D; Weber, Wilfried

2018-05-18

The ever-increasing complexity of synthetic gene networks and applications of synthetic biology requires precise and orthogonal gene expression systems. Of particular interest are systems responsive to light as they enable the control of gene expression dynamics with unprecedented resolution in space and time. While broadly used in mammalian backgrounds, however, optogenetic approaches in plant cells are still limited due to interference of the activating light with endogenous photoreceptors. Here, we describe the development of the first synthetic light-responsive system for the targeted control of gene expression in mammalian and plant cells that responds to the green range of the light spectrum in which plant photoreceptors have minimal activity. We first engineered a system based on the light-sensitive bacterial transcription factor CarH and its cognate DNA operator sequence CarO from Thermus thermophilus to control gene expression in mammalian cells. The system was functional in various mammalian cell lines, showing high induction (up to 350-fold) along with low leakiness, as well as high reversibility. We quantitatively described the systems characteristics by the development and experimental validation of a mathematical model. Finally, we transferred the system into A. thaliana protoplasts and demonstrated gene repression in response to green light. We expect that this system will provide new opportunities in applications based on synthetic gene networks and will open up perspectives for optogenetic studies in mammalian and plant cells.

Directed chromosomal integration and expression of porcine rotavirus outer capsid protein VP4 in Lactobacillus casei ATCC393.

PubMed

Yin, Ji-Yuan; Guo, Chao-Qun; Wang, Zi; Yu, Mei-Ling; Gao, Shuai; Bukhari, Syed M; Tang, Li-Jie; Xu, Yi-Gang; Li, Yi-Jing

2016-11-01

Using two-step plasmid integration in the presence of 5-fluorouracil (5-FU), we developed a stable and markerless Lactobacillus casei strain for vaccine antigen expression. The upp of L. casei, which encodes uracil phosphoribosyltransferase (UPRTase), was used as a counterselection marker. We employed the Δupp isogenic mutant, which is resistant to 5-FU, as host and a temperature-sensitive suicide plasmid bearing upp expression cassette as counterselectable integration vector. Extrachromosomal expression of UPRTase complemented the mutated chromosomal upp allele and restored sensitivity to 5-FU. The resultant genotype can either be wild type or recombinant. The efficacy of the system was demonstrated by insertion and expression of porcine rotavirus (PRV) VP4. To improve VP4 expression, we analyzed L. casei transcriptional profiles and selected the constitutive highly expressed enolase gene (eno). The VP4 inserted after the eno termination codon were screened in the presence of 5-FU. Using genomic PCR amplification, we confirmed that VP4 was successfully integrated and stably inherited for at least 50 generations. Western blot demonstrated that VP4 was steadily expressed in medium with different carbohydrates. RT-qPCR and ELISA analysis showed that VP4 expression from the chromosomal location was similar to that achieved by a plasmid expression system. Applying the recombinant strain to immunize BALB/c mice via oral administration revealed that the VP4-expressing L. casei could induce both specific local and systemic humoral immune responses in mice. Overall, the improved gene replacement system represents an efficient method for chromosome recombination in L. casei and provides a safe tool for vaccine production.

Systems Reconsolidation Reveals a Selective Role for the Anterior Cingulate Cortex in Generalized Contextual Fear Memory Expression

PubMed Central

Einarsson, Einar Ö; Pors, Jennifer; Nader, Karim

2015-01-01

After acquisition, hippocampus-dependent memories undergo a systems consolidation process, during which they become independent of the hippocampus and dependent on the anterior cingulate cortex (ACC) for memory expression. However, consolidated remote memories can become transiently hippocampus-dependent again following memory reactivation. How this systems reconsolidation affects the role of the ACC in remote memory expression is not known. Using contextual fear conditioning, we show that the expression of 30-day-old remote memory can transiently be supported by either the ACC or the dorsal hippocampus following memory reactivation, and that the ACC specifically mediates expression of remote generalized contextual fear memory. We found that suppression of neural activity in the ACC with the AMPA/kainate receptor antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) impaired the expression of remote, but not recent, contextual fear memory. Fear expression was not affected by this treatment if preceded by memory reactivation 6 h earlier, nor was it affected by suppression of neural activity in the dorsal hippocampus with the GABA-receptor agonist muscimol. However, simultaneous targeting of both the ACC and the dorsal hippocampus 6 h after memory reactivation disrupted contextual fear memory expression. Second, we observed that expression of a 30-day-old generalized contextual fear memory in a novel context was not affected by memory reactivation 6 h earlier. However, intra-ACC CNQX infusion before testing impaired contextual fear expression in the novel context, but not the original training context. Together, these data suggest that although the dorsal hippocampus may be recruited during systems reconsolidation, the ACC remains necessary for the expression of generalized contextual fear memory. PMID:25091528

Systems reconsolidation reveals a selective role for the anterior cingulate cortex in generalized contextual fear memory expression.

PubMed

Einarsson, Einar Ö; Pors, Jennifer; Nader, Karim

2015-01-01

After acquisition, hippocampus-dependent memories undergo a systems consolidation process, during which they become independent of the hippocampus and dependent on the anterior cingulate cortex (ACC) for memory expression. However, consolidated remote memories can become transiently hippocampus-dependent again following memory reactivation. How this systems reconsolidation affects the role of the ACC in remote memory expression is not known. Using contextual fear conditioning, we show that the expression of 30-day-old remote memory can transiently be supported by either the ACC or the dorsal hippocampus following memory reactivation, and that the ACC specifically mediates expression of remote generalized contextual fear memory. We found that suppression of neural activity in the ACC with the AMPA/kainate receptor antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) impaired the expression of remote, but not recent, contextual fear memory. Fear expression was not affected by this treatment if preceded by memory reactivation 6 h earlier, nor was it affected by suppression of neural activity in the dorsal hippocampus with the GABA-receptor agonist muscimol. However, simultaneous targeting of both the ACC and the dorsal hippocampus 6 h after memory reactivation disrupted contextual fear memory expression. Second, we observed that expression of a 30-day-old generalized contextual fear memory in a novel context was not affected by memory reactivation 6 h earlier. However, intra-ACC CNQX infusion before testing impaired contextual fear expression in the novel context, but not the original training context. Together, these data suggest that although the dorsal hippocampus may be recruited during systems reconsolidation, the ACC remains necessary for the expression of generalized contextual fear memory.

Construction of doxycycline-mediated BMP-2 transgene combining with APA microcapsules for bone repair.

PubMed

Qian, Dongyang; Bai, Bo; Yan, Guangbin; Zhang, Shujiang; Liu, Qi; Chen, Yi; Tan, Xiaobo; Zeng, Yanjun

2016-01-01

The repairing of large segmental bone defects is difficult for clinical orthopedists at present. Gene therapy is regarded as a promising method for bone defects repair. The present study aimed to construct an effective and controllable Tet-On expression system for transferring hBMP-2 gene into bone marrow mesenchymal progenitor cells (BMSCs). Meanwhile, with combination of alginate-poly-L-lysine-alginate (APA) microencapsulation technology, we attempted to reduce the influence of immunologic rejection and examine the effect of the Tet-On expression system on osteogenesis of BMSCs. The adenovirus encoding hBMP-2 (ADV-hBMP2) was constructed using the means of molecular cloning. The ADV-hBMP2 and Adeno-X Tet-On virus was respectively transfected to the HEK293 for amplification and afterward BMSCs were co-infected with the virus of ADV-hBMP2 and the Adeno-X Tet-On. The expression of hBMP-2 was measured with induction by doxycycline (DOX) at different concentration by means of RT-PCR and ELISA. Combining Tet-On expression system and APA microcapsules with the use of the pulsed high-voltage electrostatic microcapsule instrument, we examined the expression level of hBMP-2 in APA microcapsules by ELISA as well as the osteogenesis by alizarin red S staining. An effective Tet-On expression system for transferring hBMP-2 gene into BMSCs was constructed successfully. Also, the expression of hBMP-2 could be regulated by concentration of DOX. The data exhibited that BMSCs in APA microcapsules maintained the capability of proliferation and differentiation. The combination of Tet-On expression system and APA microcapsules could promote the osteogenesis of BMSCs. According to the results, microencapsulated Tet-On expression system showed the effective characteristics of secreting hBMP-2 and enhancing osteogenesis, which would provide a promising way for bone repair.

Development of a tightly regulated and highly responsive copper-inducible gene expression system and its application to control of flowering time.

PubMed

Saijo, Takanori; Nagasawa, Akitsu

2014-01-01

A newly developed copper-inducible gene expression system overcame the mixed results reported earlier, worked well both in cultured cells and a whole plant, and enabled to control flowering timing. Copper is one of the essential microelements and is readily taken up by plants. However, to date, it has rarely been used to control the expression of genes of interest, probably due to the inefficiency of the gene expression systems. In this study, we successfully developed a copper-inducible gene expression system that is based on the regulation of the yeast metallothionein gene. This system can be applied in the field and regulated at approximately one-hundredth of the rate used for registered copper-based fungicides. In the presence of copper, a translational fusion of the ACE1 transcription factor with the VP16 activation domain (VP16AD) of herpes simplex virus strongly activated transcription of the GFP gene in transgenic Arabidopsis. Interestingly, insertion of the To71 sequence, a 5'-untranslated region of the 130k/180k gene of tomato mosaic virus, upstream of the GFP gene reduced the basal expression of GFP in the absence of copper to almost negligible levels, even in soil-grown plants that were supplemented with ordinary liquid nutrients. Exposure of plants to 100 μM copper resulted in an over 1,000-fold induction ratio at the transcriptional level of GFP. This induction was copper-specific and dose-dependent with rapid and reversible responses. Using this expression system, we also succeeded in regulating floral transition by copper treatment. These results indicate that our newly developed copper-inducible system can accelerate gene functional analysis in model plants and can be used to generate novel agronomic traits in crop species.

A real-time control system of gene expression using ligand-bound nucleic acid aptamer for metabolic engineering.

PubMed

Wang, Jing; Cui, Xun; Yang, Le; Zhang, Zhe; Lv, Liping; Wang, Haoyuan; Zhao, Zhenmin; Guan, Ningzi; Dong, Lichun; Chen, Rachel

2017-07-01

Artificial control of bio-functions through regulating gene expression is one of the most important and attractive technologies to build novel living systems that are useful in the areas of chemical synthesis, nanotechnology, pharmacology, cell biology. Here, we present a novel real-time control system of gene regulation that includes an enhancement element by introducing duplex DNA aptamers upstream promoter and a repression element by introducing a RNA aptamer upstream ribosome binding site. With the presence of ligands corresponding to the DNA aptamers, the expression of the target gene can be potentially enhanced at the transcriptional level by strengthening the recognition capability of RNAP to the recognition region and speeding up the separation efficiency of the unwinding region due to the induced DNA bubble around the thrombin-bound aptamers; while with the presence of RNA aptamer ligand, the gene expression can be repressed at the translational level by weakening the recognition capability of ribosome to RBS due to the shielding of RBS by the formed aptamer-ligand complex upstream RBS. The effectiveness and potential utility of the developed gene regulation system were demonstrated by regulating the expression of ecaA gene in the cell-free systems. The realistic metabolic engineering application of the system has also tested by regulating the expression of mgtC gene and thrombin cDNA in Escherichia coli JD1021 for controlling metabolic flux and improving thrombin production, verifying that the real-time control system of gene regulation is able to realize the dynamic regulation of gene expression with potential applications in bacterial physiology studies and metabolic engineering. Copyright © 2017. Published by Elsevier Inc.

Molecular cloning, sequence characterization and recombinant expression of Nanog gene in goat fibroblast cells using lentiviral based expression system.

PubMed

Singhal, Dinesh K; Singhal, Raxita; Malik, Hruda N; Kumar, Surender; Kumar, Sudarshan; Mohanty, Ashok K; Kaushik, Jai K; Malakar, Dhruba

2014-01-01

Nanog is a homeodomain containing protein which plays important roles in regulation of signaling pathways for maintenance and induction of pluripotency in stem cells. Because of its unique expression in stem cells it is also regarded as pluripotency marker. In this study goat Nanog (gNanog) gene has been amplified, cloned and characterized at sequence level with successful over-expression in CHO-K1 cell line using a lentiviral based system. gNanog ORF is 903 bp long which codes for Nanog protein of size 300 amino acids (aas). Complete nucleotide sequence shows some evolutionary mutation in goat in comparision to other species. Protein sequence of goat is highly similar to other species. Overall, gNanog nucleotide sequence and predicted protein sequence showed high similarity and minimum divergence with cattle (96 % identity/4 % divergence) and buffalo (94/5 %) while low similarity and high divergence with pig (84/15 %), human (81/23 %) and mouse (69/40 %) indicating evolutionary closeness of gNanog to cattle and buffalo. gNanog lentiviral expression construct was prepared for over-expression of Nanog gene in adult goat fibroblast cells. Lentiviral expression construct of Nanog enabled continuous protein expression for induction and maintenance of pluripotency. Western blotting revealed the expression of Nanog gene at protein level which supported that the lentiviral expression system is highly promising for Nanog protein expression in differentiated goat cell.

Brain selective transgene expression in zebrafish using an NRSE derived motif

PubMed Central

Bergeron, Sadie A.; Hannan, Markus C.; Codore, Hiba; Fero, Kandice; Li, Grace H.; Moak, Zachary; Yokogawa, Tohei; Burgess, Harold A.

2012-01-01

Transgenic technologies enable the manipulation and observation of circuits controlling behavior by permitting expression of genetically encoded reporter genes in neurons. Frequently though, neuronal expression is accompanied by transgene expression in non-neuronal tissues, which may preclude key experimental manipulations, including assessment of the contribution of neurons to behavior by ablation. To better restrict transgene expression to the nervous system in zebrafish larvae, we have used DNA sequences derived from the neuron-restrictive silencing element (NRSE). We find that one such sequence, REx2, when used in conjunction with several basal promoters, robustly suppresses transgene expression in non-neuronal tissues. Both in transient transgenic experiments and in stable enhancer trap lines, suppression is achieved without compromising expression within the nervous system. Furthermore, in REx2 enhancer trap lines non-neuronal expression can be de-repressed by knocking down expression of the NRSE binding protein RE1-silencing transcription factor (Rest). In one line, we show that the resulting pattern of reporter gene expression coincides with that of the adjacent endogenous gene, hapln3. We demonstrate that three common basal promoters are susceptible to the effects of the REx2 element, suggesting that this method may be useful for confining expression from many other promoters to the nervous system. This technique enables neural specific targeting of reporter genes and thus will facilitate the use of transgenic methods to manipulate circuit function in freely behaving larvae. PMID:23293587

Expression of eukaryotic polypeptides in chloroplasts

DOEpatents

Mayfield, Stephen P.

2013-06-04

The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

[Pichia pastoris as an expression system for recombinant protein production].

PubMed

Ciarkowska, Anna; Jakubowska, Anna

2013-01-01

Pichia pastoris has become increasingly popular as a host for recombinant protein production in recent years. P. pastoris is more cost effective and allows achieving higher expression levels than insect and mammalian cells. It also offers some significant advantages over E. coli expression systems, such as avoiding problems with proper protein folding. Also, P. pastoris as an eukaryotic organism can carry out posttranslational modifications of produced proteins. Additionally, P. pastoris can produce high levels of recombinant proteins in extracellular medium which simplifies protein purification. Having many advantages over other expression systems makes P. pastoris an organism of choice for industrial protein production.

Dendrimer-driven neurotrophin expression differs in temporal patterns between rodent and human stem cells.

PubMed

Shakhbazau, Antos; Shcharbin, Dzmitry; Seviaryn, Ihar; Goncharova, Natalya; Kosmacheva, Svetlana; Potapnev, Mihail; Bryszewska, Maria; Kumar, Ranjan; Biernaskie, Jeffrey; Midha, Rajiv

2012-05-07

This study reports the use of a nonviral expression system based on polyamidoamine dendrimers for time-restricted neurotrophin overproduction in mesenchymal stem cells and skin precursor-derived Schwann cells. The dendrimers were used to deliver plasmids for brain-derived neurotrophic factor (BDNF) or neurotrophin-3 (NT-3) expression in both rodent and human stem cells, and the timelines of expression were studied. We have found that, despite the fact that transfection efficiencies and protein expression levels were comparable, dendrimer-driven expression in human mesenchymal stem cells was characterized by a more rapid decline compared to rodent cells. Transient expression systems can be beneficial for some neurotrophins, which were earlier reported to cause unwanted side effects in virus-based long-term expression models. Nonviral neurotrophin expression is a biologically safe and accessible alternative to increase the therapeutic potential of autologous adult stem cells and stem cell-derived functional differentiated cells.

A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection.

PubMed

Schwessinger, Benjamin; Li, Xiang; Ellinghaus, Thomas L; Chan, Leanne Jade G; Wei, Tong; Joe, Anna; Thomas, Nicholas; Pruitt, Rory; Adams, Paul D; Chern, Maw Sheng; Petzold, Christopher J; Liu, Chang C; Ronald, Pamela C

2016-04-18

Posttranslational modification (PTM) of proteins and peptides is important for diverse biological processes in plants and animals. The paucity of heterologous expression systems for PTMs and the technical challenges associated with chemical synthesis of these modified proteins has limited detailed molecular characterization and therapeutic applications. Here we describe an optimized system for expression of tyrosine-sulfated proteins in Escherichia coli and its application in a bio-based crop protection strategy in rice.

A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection

DOE PAGES

Schwessinger, Benjamin; Li, Xiang; Ellinghaus, Thomas L.; ...

2015-11-27

Posttranslational modification (PTM) of proteins and peptides is important for diverse biological processes in plants and animals. The paucity of heterologous expression systems for PTMs and the technical challenges associated with chemical synthesis of these modified proteins has limited detailed molecular characterization and therapeutic applications. Here we describe an optimized system for expression of tyrosine-sulfated proteins in Escherichia coli and its application in a bio-based crop protection strategy in rice.

Expression, purification and characterization of inactive and active forms of ERK2 from insect expression system.

PubMed

Yan, Kelly; Merritt, Hanne; Crawford, Kenneth; Pardee, Gwynn; Cheng, Jan Marie; Widger, Stephania; Hekmat-Nejad, Mohammad; Zaror, Isabel; Sim, Janet

2015-06-01

Extracellular signal-regulated kinase 2 (ERK2) is a serine/threonine protein kinase involved in many cellular programs, such as cell proliferation, differentiation, motility and programed cell-death. It is therefore considered an important target in the treatment of cancer. In an effort to support biochemical screening and small molecule drug discovery, we established a robust system to generate both inactive and active forms of ERK2 using insect expression system. We report here, for the first time, that inactive ERK2 can be expressed and purified with 100% homogeneity in the unphosphorylated form using insect system. This resulted in a significant 20-fold yield improvement compared to that previously reported using bacterial expression system. We also report a newly developed system to generate active ERK2 in insect cells through in vivo co-expression with a constitutively active MEK1 (S218D S222D). Isolated active ERK2 was confirmed to be doubly phosphorylated at the correct sites, T185 and Y187, in the activation loop of ERK2. Both ERK2 forms, inactive and active, were well characterized by biochemical activity assay for their kinase function. Inactive and active ERK2 were the two key reagents that enabled successful high through-put biochemical assay screen and structural drug discovery studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Three-dimensional culture system can induce expression of casein in immortalized bovine mammary epithelial cells.

PubMed

Zhan, Kang; Lin, Miao; Liu, MingMei; Sui, YangNan; Babekir, Haitham Mohammed; Zhao, GuoQi

2017-05-01

Primary bovine mammary epithelial cells (BMECs) are not ideal models for long-term studies of lactation mechanisms because these cells in a monolayer culture system cannot be polarized to simulate the physiological functions in vitro. We investigate the effects of different culture models and karyotypes on casein expression in a three-dimensional (3D) culture system. The immortalized cells' karyotypes were analyzed at passages 10, 20, 30 and 40 to detect the effects of chromosome stability. Western blotting examined that whether or not the immortalized cells at passages 5, 10, 20, 30, 40 and 50 could induce expression of casein in a 3D culture system. The proper polarization of the acinar structures was monitored. BMECs were successfully immortalized. The cell karyotype at passage 30 remained at 60 chromosomes and the average value was 57.1 ± 0.40 after passage 40. The polarized protein's levels were up-regulated in 3D culture compared to 2D culture. Expression of αs1, β and κ-casein could be detectable in a passage range in 3D culture. Expression of αs2-casein was undetectable in all experimental groups. However, all casein expressions were barely detectable in traditional 2D culture system. Therefore, 3D culture system is an important tool for the long-term study of lactation mechanisms in vitro. © 2016 Japanese Society of Animal Science.

Systemic and local regulation of phosphate and nitrogen transporter genes by arbuscular mycorrhizal fungi in roots of winter wheat (Triticum aestivum L.).

PubMed

Duan, Jianfeng; Tian, Hui; Drijber, Rhae A; Gao, Yajun

2015-11-01

Previous studies have reported that the expression of phosphate (Pi) or nitrogen (N) transporter genes in roots of plants could be regulated by arbuscular mycorrhizal (AM) fungi, but little is known whether the regulation is systemic or not. The present study investigated the systemic and local regulation of multiple phosphate and nitrogen transporter genes by four AM fungal species belonging to four genera in the roots of winter wheat. A split-root culture system with AM inoculated (MR) and non-inoculated root compartments (NR) was used to investigate the systemic or local responses of phosphate and nitrogen transporter genes to colonization by four AM fungi in the roots of wheat. The expression of four Pi transporter, five nitrate transporter, and three ammonium transporter genes was quantified using real-time PCR. Of the four AM fungi tested, all locally increased expression of the AM-inducible Pi transporter genes, and most locally decreased expression of a Pi-starvation inducible Pi transporter gene. The addition of N in soil increased the expression of either Pi starvation inducible Pi transporters or AM inducible Pi transporters. Inoculation with AM fungi either had no effect, or could locally or systemically down-regulate expression of nitrogen transporter genes depending on gene type and AM fungal species. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Increasing the yield of middle silk gland expression system through transgenic knock-down of endogenous sericin-1.

PubMed

Ma, Sanyuan; Xia, Xiaojuan; Li, Yufeng; Sun, Le; Liu, Yue; Liu, Yuanyuan; Wang, Xiaogang; Shi, Run; Chang, Jiasong; Zhao, Ping; Xia, Qingyou

2017-08-01

Various genetically modified bioreactor systems have been developed to meet the increasing demands of recombinant proteins. Silk gland of Bombyx mori holds great potential to be a cost-effective bioreactor for commercial-scale production of recombinant proteins. However, the actual yields of proteins obtained from the current silk gland expression systems are too low for the proteins to be dissolved and purified in a large scale. Here, we proposed a strategy that reducing endogenous sericin proteins would increase the expression yield of foreign proteins. Using transgenic RNA interference, we successfully reduced the expression of BmSer1 to 50%. A total 26 transgenic lines expressing Discosoma sp. red fluorescent protein (DsRed) in the middle silk gland (MSG) under the control of BmSer1 promoter were established to analyze the expression of recombinant. qRT-PCR and western blotting showed that in BmSer1 knock-down lines, the expression of DsRed had significantly increased both at mRNA and protein levels. We did an additional analysis of DsRed/BmSer1 distribution in cocoon and effect of DsRed protein accumulation on the silk fiber formation process. This study describes not only a novel method to enhance recombinant protein expression in MSG bioreactor, but also a strategy to optimize other bioreactor systems.

Configurations of a two-tiered amplified gene expression system in adenoviral vectors designed to improve the specificity of in vivo prostate cancer imaging

PubMed Central

Sato, M; Figueiredo, ML; Burton, JB; Johnson, M; Chen, M; Powell, R; Gambhir, SS; Carey, M; Wu, L

2009-01-01

Effective treatment for recurrent, disseminated prostate cancer is notably limited. We have developed adenoviral vectors with a prostate-specific two-step transcriptional amplification (TSTA) system that would express therapeutic genes at a robust level to target metastatic disease. The TSTA system employs the prostate-specific antigen (PSA) promoter/enhancer to drive a potent synthetic activator, which in turn activates the expression of the therapeutic gene. In this study, we explored different configurations of this bipartite system and discovered that physical separation of the two TSTA components into E1 and E3 regions of adenovirus was able to enhance androgen regulation and cell-discriminatory expression. The TSTA vectors that express imaging reporter genes were assessed by noninvasive imaging technologies in animal models. The improved selectivity of the E1E3 configured vector was reflected in silenced ectopic expression in the lung. Significantly, the enhanced specificity of the E1E3 vector enabled the detection of lung metastasis of prostate cancer. An E1E3 TSTA vector that expresses the herpes simplex virus thymidine kinase gene can effectively direct positron emission tomography (PET) imaging of the tumor. The prostate-targeted gene delivery vectors with robust and cell-specific expression capability will advance the development of safe and effective imaging guided therapy for recurrent metastatic stages of prostate cancer. PMID:18305574

Central Nervous System and Vertebrae Development in Horses: a Chronological Study with Differential Temporal Expression of Nestin and GFAP.

PubMed

Rigoglio, Nathia N; Barreto, Rodrigo S N; Favaron, Phelipe O; Jacob, Júlio C F; Smith, Lawrence C; Gastal, Melba O; Gastal, Eduardo L; Miglino, Maria Angélica

2017-01-01

The neural system is one of the earliest systems to develop and the last to be fully developed after birth. This study presents a detailed description of organogenesis of the central nervous system (CNS) at equine embryonic/fetal development between 19 and 115 days of pregnancy. The expression of two important biomarkers in the main structure of the nervous system responsible for neurogenesis in the adult individual, and in the choroid plexus, was demonstrated by Nestin and glial fibrillary acid protein (GFAP) co-labeling. In the 29th day of pregnancy in the undifferentiated lateral ventricle wall, the presence of many cells expressing Nestin and few expressing GFAP was observed. After the differentiation of the lateral ventricle wall zones at 60 days of pregnancy, the subventricular zone, which initially had greater number of Nestin + cells, began to show higher numbers of GFAP + cells at 90 days of pregnancy. A similar pattern was observed for Nestin + and GFAP + cells during development of the choroid plexus. This study demonstrates, for the first time, detailed chronological aspects of the equine central nervous system organogenesis associated with downregulation of Nestin and upregulation of GFAP expression.

Transient Expression of Lumbrokinase (PI239) in Tobacco (Nicotiana tabacum) Using a Geminivirus-Based Single Replicon System Dissolves Fibrin and Blood Clots.

PubMed

Dickey, Alexia; Wang, Nan; Cooper, Edwin; Tull, Lauren; Breedlove, Drew; Mason, Hugh; Liu, Dehu; Wang, Kevin Yueju

2017-01-01

Lumbrokinases, a group of fibrinolytic enzymes extracted from earthworm, have been widely used to prevent and treat various cardiovascular diseases. They specifically target fibrin to effectively degrade thrombi without major side effects. Plant expression systems are becoming potential alternative expression platforms for producing pharmaceutical proteins. In this work, a lumbrokinase (PI239) was produced from a plant system. Both wild-type (WT) and plant codon-optimized (OP) PI239 gene sequences were synthesized and cloned into a geminivirus-based single-vector DNA replicon system. Both vectors were independently expressed in tobacco (Nicotiana tabacum) leaves transiently by agroinfiltration. Overexpressed PI239 resulted in sudden tissue necrosis 3 days after infiltration. Remaining proteins were purified through His-tag affinity chromatography and analyzed with SDS-PAGE and Western blot methods. Purified PI239 successfully degraded artificial fibrin with relative activity of 13,400 U/mg when compared with commercial lumbrokinase product. In vitro tests demonstrated that plant-derived PI239 dissolved human blood clots and that the plant expression system is capable of producing functional PI239.

Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Part 3; Acquire Express-A3 SPT-100 Based Propulsion Subsystem and Other Subsystem Flight Operation TM-Data for the Period of June 24, 2000 to and Including September 30, 2000, Task 30

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 E. and 11 W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Hall Effect Thruster Interactions Data from the Russian Express-A2 and Express-A3 Satellites. Part 8; Acquire TM-Data for Type A and Type B Sensors for "Express A" Number 3 Satellite for the Period of January 1, 2001 to and Including March 31, 2001, Task 27C

NASA Technical Reports Server (NTRS)

Dunning, John (Technical Monitor); Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80deg E. and 11deg W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.