Helicoidal Organization of Chitin in the Cuticle of the Migratory Locust Requires the Function of the Chitin Deacetylase2 Enzyme (LmCDA2)*

PubMed Central

Yu, Rongrong; Liu, Weimin; Li, Daqi; Zhao, Xiaoming; Ding, Guowei; Zhang, Min; Ma, Enbo; Zhu, KunYan; Li, Sheng; Moussian, Bernard; Zhang, Jianzhen

2016-01-01

In the three-dimensional extracellular matrix of the insect cuticle, horizontally aligned microfibrils composed of the polysaccharide chitin and associated proteins are stacked either parallel to each other or helicoidally. The underlying molecular mechanisms that implement differential chitin organization are largely unknown. To learn more about cuticle organization, we sought to study the role of chitin deacetylases (CDA) in this process. In the body cuticle of nymphs of the migratory locust Locusta migratoria, helicoidal chitin organization is changed to an organization with unidirectional microfibril orientation when LmCDA2 expression is knocked down by RNA interference. In addition, the LmCDA2-deficient cuticle is less compact suggesting that LmCDA2 is needed for chitin packaging. Animals with reduced LmCDA2 activity die at molting, underlining that correct chitin organization is essential for survival. Interestingly, we find that LmCDA2 localizes only to the initially produced chitin microfibrils that constitute the apical site of the chitin stack. Based on our data, we hypothesize that LmCDA2-mediated chitin deacetylation at the beginning of chitin production is a decisive reaction that triggers helicoidal arrangement of subsequently assembled chitin-protein microfibrils. PMID:27637332

Helicoidal Organization of Chitin in the Cuticle of the Migratory Locust Requires the Function of the Chitin Deacetylase2 Enzyme (LmCDA2).

PubMed

Yu, Rongrong; Liu, Weimin; Li, Daqi; Zhao, Xiaoming; Ding, Guowei; Zhang, Min; Ma, Enbo; Zhu, KunYan; Li, Sheng; Moussian, Bernard; Zhang, Jianzhen

2016-11-18

In the three-dimensional extracellular matrix of the insect cuticle, horizontally aligned microfibrils composed of the polysaccharide chitin and associated proteins are stacked either parallel to each other or helicoidally. The underlying molecular mechanisms that implement differential chitin organization are largely unknown. To learn more about cuticle organization, we sought to study the role of chitin deacetylases (CDA) in this process. In the body cuticle of nymphs of the migratory locust Locusta migratoria, helicoidal chitin organization is changed to an organization with unidirectional microfibril orientation when LmCDA2 expression is knocked down by RNA interference. In addition, the LmCDA2-deficient cuticle is less compact suggesting that LmCDA2 is needed for chitin packaging. Animals with reduced LmCDA2 activity die at molting, underlining that correct chitin organization is essential for survival. Interestingly, we find that LmCDA2 localizes only to the initially produced chitin microfibrils that constitute the apical site of the chitin stack. Based on our data, we hypothesize that LmCDA2-mediated chitin deacetylation at the beginning of chitin production is a decisive reaction that triggers helicoidal arrangement of subsequently assembled chitin-protein microfibrils. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Role of tyrosine 33 residue for the stabilization of the tetrameric structure of human cytidine deaminase.

PubMed

Micozzi, Daniela; Pucciarelli, Stefania; Carpi, Francesco M; Costanzi, Stefano; De Sanctis, Giampiero; Polzonetti, Valeria; Natalini, Paolo; Santarelli, Ivano F; Vita, Alberto; Vincenzetti, Silvia

2010-11-01

In the present work the effect of a mutation on tyrosine 33 residue (Y33G) of human cytidine deaminase (CDA) was investigated with regard to protein solubility and specific activity. Osmolytes and CDA ligands were used to increase the yield and the specific activity of the protein. The mutant enzyme was purified and subjected to a kinetic characterization and to stability studies. These investigations reinforced the hypothesis that in human CDA the side chain of Y33 is involved in intersubunit interactions with four glutamate residues (E108) forming a double latch that connects each of the two pairs of monomers of the tetrameric CDA. Copyright © 2010 Elsevier B.V. All rights reserved.

Visual Search Elicits the Electrophysiological Marker of Visual Working Memory

PubMed Central

Emrich, Stephen M.; Al-Aidroos, Naseem; Pratt, Jay; Ferber, Susanne

2009-01-01

Background Although limited in capacity, visual working memory (VWM) plays an important role in many aspects of visually-guided behavior. Recent experiments have demonstrated an electrophysiological marker of VWM encoding and maintenance, the contralateral delay activity (CDA), which has been shown in multiple tasks that have both explicit and implicit memory demands. Here, we investigate whether the CDA is evident during visual search, a thoroughly-researched task that is a hallmark of visual attention but has no explicit memory requirements. Methodology/Principal Findings The results demonstrate that the CDA is present during a lateralized search task, and that it is similar in amplitude to the CDA observed in a change-detection task, but peaks slightly later. The changes in CDA amplitude during search were strongly correlated with VWM capacity, as well as with search efficiency. These results were paralleled by behavioral findings showing a strong correlation between VWM capacity and search efficiency. Conclusions/Significance We conclude that the activity observed during visual search was generated by the same neural resources that subserve VWM, and that this activity reflects the maintenance of previously searched distractors. PMID:19956663

Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique

PubMed Central

Rahmani-Badi, Azadeh; Sepehr, Shayesteh; Fallahi, Hossein; Heidari-Keshel, Saeed

2015-01-01

Many bacterial pathogens use quorum-sensing (QS) signaling to regulate the expression of factors contributing to virulence and persistence. Bacteria produce signals of different chemical classes. The signal molecule, known as diffusible signal factor (DSF), is a cis-unsaturated fatty acid that was first described in the plant pathogen Xanthomonas campestris. Previous works have shown that human pathogen, Pseudomonas aeruginosa, also synthesizes a structurally related molecule, characterized as cis-2-decenoic acid (C10: Δ2, CDA) that induces biofilm dispersal by multiple types of bacteria. Furthermore, CDA has been shown to be involved in inter-kingdom signaling that modulates fungal behavior. Therefore, an understanding of its signaling mechanism could suggest strategies for interference, with consequences for disease control. To identify the components of CDA signaling pathway in this pathogen, a comparative transcritpome analysis was conducted, in the presence and absence of CDA. A protein-protein interaction (PPI) network for differentially expressed (DE) genes with known function was then constructed by STRING and Cytoscape. In addition, the effects of CDA in combination with antimicrobial agents on the biofilm surface area and bacteria viability were evaluated using fluorescence microscopy and digital image analysis. Microarray analysis identified 666 differentially expressed genes in the presence of CDA and gene ontology (GO) analysis revealed that in P. aeruginosa, CDA mediates dispersion of biofilms through signaling pathways, including enhanced motility, metabolic activity, virulence as well as persistence at different temperatures. PPI data suggested that a cluster of five genes (PA4978, PA4979, PA4980, PA4982, PA4983) is involved in the CDA synthesis and perception. Combined treatments using both CDA and antimicrobial agents showed that following exposure of the biofilms to CDA, remaining cells on the surface were easily removed and killed by antimicrobials. PMID:25972860

Combined treatment, based on lysomustine administration with mesenchymal stem cells expressing cytosine deaminase therapy, leads to pronounced murine Lewis lung carcinoma growth inhibition.

PubMed

Krassikova, Lyudmila S; Karshieva, Saida S; Cheglakov, Ivan B; Belyavsky, Alexander V

2016-09-01

The combination of stem cell-based gene therapy with chemotherapy comprises an advantageous strategy that results in a reduction of system toxicity effects and an improvement in the general efficacy of treatment. In the present study, we estimated the efficacy of adipose tissue-derived mesenchymal stem cells (AT-MSCs) expressing cytosine deaminase (CDA) combined with lysomustine chemotherapy in mice bearing late stage Lewis lung carcinoma (LLC). Adipose tissue-derived mesenchymal stem cells were transfected with non-insert plasmid construct transiently expressing fused cytosine deaminase-uracil phosphoribosyltransferase protein (CDA/UPRT) or the same construct fused with Herpes Simplex Virus Type1 tegument protein VP22 (CDA/UPRT/VP22). Systemic administration of 5-fluorocytosine (5FC) and lysomustine was implemented after a single intratumoral injection of transfected AT-MSCs. We demonstrated that direct intratumoral transplantation of AT-MSCs expressing CDA/UPRT or CDA/UPRT/VP22 followed by systemic administration of 5FC resulted in a significant tumor growth inhibition. There was a 56% reduction in tumor volume in mice treated by AT-MSCs-CDA/UPRT + 5FC or with AT-MSCs-CDA/UPRT/VP22 + 5FC compared to control animals grafted with lung carcinoma alone. Transplantation of AT-MSCs-CDA/UPRT + 5FC and AT-MSCs-CDA/UPRT/VP22 + 5FC prolonged the life span of mice bearing LLC by 27% and 31%, respectively. Co-administration of lysomustine and AT-MSCs-CDA/UPRT + 5FC led to tumor growth inhibition (by 86%) and life span extension (by 60%) compared to the control group. Our data indicate that a combination CDA/UPRT-expressing AT-MSCs with lysomustine has a superior antitumor effect in the murine lung carcinoma model compared to monotherapies with transfected AT-MSCs or lysomustine alone, possibly because of a synergistic effect of the combination therapy. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Chronic Cladribine Administration Increases Amyloid Beta Peptide Generation and Plaque Burden in Mice

PubMed Central

Hayes, Crystal D.; Dey, Debleena; Palavicini, Juan Pablo; Wang, Hongjie; Araki, Wataru; Lakshmana, Madepalli K.

2012-01-01

Background The clinical uses of 2-chloro-2′-deoxyadenosine (2-CDA) or cladribine which was initially prescribed to patients with hematological and lymphoid cancers is now extended to treat patients with multiple sclerosis (MS). Previous data has shown that 2-CDA has high affinity to the brain and readily passes through the blood brain barrier reaching CSF concentrations 25% of that found in plasma. However, whether long-term administration of 2-CDA can lead to any adverse effects in patients or animal models is not yet clearly known. Methodology Here we show that exposure of 2-CDA to CHO cells stably expressing wild-type APP751 increased generation and secretion of amyloid β peptide (Aβ) in to the conditioned medium. Interestingly, increased Aβ levels were noticed even at non-toxic concentrations of 2-CDA. Remarkably, chronic treatment of APdE9 mice, a model of Alzheimer's disease with 2-CDA for 60 days increased amyloid plaque burden by more than 1-fold. Increased Aβ generation appears to result from increased turnover of APP as revealed by cycloheximide-chase experiments. Additionally, surface labeling of APP with biotin and immunoprecipitation of surface labeled proteins with anti-biotin antibody also indicated increased APP at the cell surface in 2-CDA treated cells compared to controls. Increased turnover of APP by 2-CDA in turn might be a consequence of decreased protein levels of PIN 1, which is known to regulate cis-trans isomerization and phosphorylation of APP. Most importantly, like many other oncology drugs, 2-CDA administration led to significant delay in acquiring a reward-based learning task in a T maze paradigm. Conclusions Taken together, these data provide compelling evidence for the first time that chronic 2-CDA administration can increase amyloidogenic processing of APP leading to robustly increased plaque burden which may be responsible for the observed deficits in learning skills. Thus chronic treatment of mice with 2-CDA can have deleterious effects in vivo. PMID:23056220

Structural and functional analyses of Mycobacterium tuberculosis Rv3315c-encoded metal-dependent homotetrameric cytidine deaminase.

PubMed

Sánchez-Quitian, Zilpa A; Schneider, Cristopher Z; Ducati, Rodrigo G; de Azevedo, Walter F; Bloch, Carlos; Basso, Luiz A; Santos, Diógenes S

2010-03-01

The emergence of drug-resistant strains of Mycobacterium tuberculosis, the causative agent of tuberculosis, has exacerbated the treatment and control of this disease. Cytidine deaminase (CDA) is a pyrimidine salvage pathway enzyme that recycles cytidine and 2'-deoxycytidine for uridine and 2'-deoxyuridine synthesis, respectively. A probable M. tuberculosis CDA-coding sequence (cdd, Rv3315c) was cloned, sequenced, expressed in Escherichia coli BL21(DE3), and purified to homogeneity. Mass spectrometry, N-terminal amino acid sequencing, gel filtration chromatography, and metal analysis of M. tuberculosis CDA (MtCDA) were carried out. These results and multiple sequence alignment demonstrate that MtCDA is a homotetrameric Zn(2+)-dependent metalloenzyme. Steady-state kinetic measurements yielded the following parameters: K(m)=1004 microM and k(cat)=4.8s(-1) for cytidine, and K(m)=1059 microM and k(cat)=3.5s(-1) for 2'-deoxycytidine. The pH dependence of k(cat) and k(cat)/K(M) for cytidine indicate that protonation of a single ionizable group with apparent pK(a) value of 4.3 abolishes activity, and protonation of a group with pK(a) value of 4.7 reduces binding. MtCDA was crystallized and crystal diffracted at 2.0 A resolution. Analysis of the crystallographic structure indicated the presence of a Zn(2+) coordinated by three conserved cysteines and the structure exhibits the canonical cytidine deaminase fold. (c) 2009 Elsevier Inc. All rights reserved.

Coarse-to-fine construction for high-resolution representation in visual working memory.

PubMed

Gao, Zaifeng; Ding, Xiaowei; Yang, Tong; Liang, Junying; Shui, Rende

2013-01-01

This study explored whether the high-resolution representations created by visual working memory (VWM) are constructed in a coarse-to-fine or all-or-none manner. The coarse-to-fine hypothesis suggests that coarse information precedes detailed information in entering VWM and that its resolution increases along with the processing time of the memory array, whereas the all-or-none hypothesis claims that either both enter into VWM simultaneously, or neither does. We tested the two hypotheses by asking participants to remember two or four complex objects. An ERP component, contralateral delay activity (CDA), was used as the neural marker. CDA is higher for four objects than for two objects when coarse information is primarily extracted; yet, this CDA difference vanishes when detailed information is encoded. Experiment 1 manipulated the comparison difficulty of the task under a 500-ms exposure time to determine a condition in which the detailed information was maintained. No CDA difference was found between two and four objects, even in an easy-comparison condition. Thus, Experiment 2 manipulated the memory array's exposure time under the easy-comparison condition and found a significant CDA difference at 100 ms while replicating Experiment 1's results at 500 ms. In Experiment 3, the 500-ms memory array was blurred to block the detailed information; this manipulation reestablished a significant CDA difference. These findings suggest that the creation of high-resolution representations in VWM is a coarse-to-fine process.

Identification and characterization of a chitin deacetylase from a metagenomic library of deep-sea sediments of the Arctic Ocean.

PubMed

Liu, Jinlin; Jia, Zhijuan; Li, Sha; Li, Yan; You, Qiang; Zhang, Chunyan; Zheng, Xiaotong; Xiong, Guomei; Zhao, Jin; Qi, Chao; Yang, Jihong

2016-09-15

The chemical and biological compositions of deep-sea sediments are interesting because of the underexplored diversity when it comes to bioprospecting. The special geographical location and climates make Arctic Ocean a unique ocean area containing an abundance of microbial resources. A metagenomic library was constructed based on the deep-sea sediments of Arctic Ocean. Part of insertion fragments of this library were sequenced. A chitin deacetylase gene, cdaYJ, was identified and characterized. A metagenomic library with 2750 clones was obtained and ten clones were sequenced. Results revealed several interesting genes, including a chitin deacetylase coding sequence, cdaYJ. The CdaYJ is homologous to some known chitin deacetylases and contains conserved chitin deacetylase active sites. CdaYJ protein exhibits a long N-terminal and a relative short C-terminal. Phylogenetic analysis revealed that CdaYJ showed highest homology to CDAs from Alphaproteobacteria. The cdaYJ gene was subcloned into the pET-28a vector and the recombinant CdaYJ (rCdaYJ) was expressed in Escherichia coli BL21 (DE3). rCdaYJ showed a molecular weight of 43kDa, and exhibited deacetylation activity by using p-nitroacetanilide as substrate. The optimal pH and temperature of rCdaYJ were tested as pH7.4 and 28°C, respectively. The construction of metagenomic library of the Arctic deep-sea sediments provides us an opportunity to look into the microbial communities and exploiting valuable gene resources. A chitin deacetylase CdaYJ was identified from the library. It showed highest deacetylation activity under slight alkaline and low temperature conditions. CdaYJ might be a candidate chitin deacetylase that possesses industrial and pharmaceutical potentials. Copyright © 2016 Elsevier B.V. All rights reserved.

Vaccination with Recombinant Cryptococcus Proteins in Glucan Particles Protects Mice against Cryptococcosis in a Manner Dependent upon Mouse Strain and Cryptococcal Species

PubMed Central

Lee, Chrono K.; Huang, Haibin; Hester, Maureen M.; Liu, Jianhua; Luckie, Bridget A.; Torres Santana, Melanie A.; Mirza, Zeynep; Khoshkenar, Payam; Abraham, Ambily; Shen, Zu T.; Lodge, Jennifer K.; Akalin, Ali; Homan, Jane; Ostroff, Gary R.

2017-01-01

ABSTRACT Development of a vaccine to protect against cryptococcosis is a priority given the enormous global burden of disease in at-risk individuals. Using glucan particles (GPs) as a delivery system, we previously demonstrated that mice vaccinated with crude Cryptococcus-derived alkaline extracts were protected against lethal challenge with Cryptococcus neoformans and Cryptococcus gattii. The goal of the present study was to identify protective protein antigens that could be used in a subunit vaccine. Using biased and unbiased approaches, six candidate antigens (Cda1, Cda2, Cda3, Fpd1, MP88, and Sod1) were selected, recombinantly expressed in Escherichia coli, purified, and loaded into GPs. Three mouse strains (C57BL/6, BALB/c, and DR4) were then vaccinated with the antigen-laden GPs, following which they received a pulmonary challenge with virulent C. neoformans and C. gattii strains. Four candidate vaccines (GP-Cda1, GP-Cda2, GP-Cda3, and GP-Sod1) afforded a significant survival advantage in at least one mouse model; some vaccine combinations provided added protection over that seen with either antigen alone. Vaccine-mediated protection against C. neoformans did not necessarily predict protection against C. gattii. Vaccinated mice developed pulmonary inflammatory responses that effectively contained the infection; many surviving mice developed sterilizing immunity. Predicted T helper cell epitopes differed between mouse strains and in the degree to which they matched epitopes predicted in humans. Thus, we have discovered cryptococcal proteins that make promising candidate vaccine antigens. Protection varied depending on the mouse strain and cryptococcal species, suggesting that a successful human subunit vaccine will need to contain multiple antigens, including ones that are species specific. PMID:29184017

Time-resolved neuroimaging of visual short term memory consolidation by post-perceptual attention shifts.

PubMed

Hecht, Marcus; Thiemann, Ulf; Freitag, Christine M; Bender, Stephan

2016-01-15

Post-perceptual cues can enhance visual short term memory encoding even after the offset of the visual stimulus. However, both the mechanisms by which the sensory stimulus characteristics are buffered as well as the mechanisms by which post-perceptual selective attention enhances short term memory encoding remain unclear. We analyzed late post-perceptual event-related potentials (ERPs) in visual change detection tasks (100ms stimulus duration) by high-resolution ERP analysis to elucidate these mechanisms. The effects of early and late auditory post-cues (300ms or 850ms after visual stimulus onset) as well as the effects of a visual interference stimulus were examined in 27 healthy right-handed adults. Focusing attention with post-perceptual cues at both latencies significantly improved memory performance, i.e. sensory stimulus characteristics were available for up to 850ms after stimulus presentation. Passive watching of the visual stimuli without auditory cue presentation evoked a slow negative wave (N700) over occipito-temporal visual areas. N700 was strongly reduced by a visual interference stimulus which impeded memory maintenance. In contrast, contralateral delay activity (CDA) still developed in this condition after the application of auditory post-cues and was thereby dissociated from N700. CDA and N700 seem to represent two different processes involved in short term memory encoding. While N700 could reflect visual post processing by automatic attention attraction, CDA may reflect the top-down process of searching selectively for the required information through post-perceptual attention. Copyright © 2015 Elsevier Inc. All rights reserved.

Does visual working memory represent the predicted locations of future target objects? An event-related brain potential study.

PubMed

Grubert, Anna; Eimer, Martin

2015-11-11

During the maintenance of task-relevant objects in visual working memory, the contralateral delay activity (CDA) is elicited over the hemisphere opposite to the visual field where these objects are presented. The presence of this lateralised CDA component demonstrates the existence of position-dependent object representations in working memory. We employed a change detection task to investigate whether the represented object locations in visual working memory are shifted in preparation for the known location of upcoming comparison stimuli. On each trial, bilateral memory displays were followed after a delay period by bilateral test displays. Participants had to encode and maintain three visual objects on one side of the memory display, and to judge whether they were identical or different to three objects in the test display. Task-relevant memory and test stimuli were located in the same visual hemifield in the no-shift task, and on opposite sides in the horizontal shift task. CDA components of similar size were triggered contralateral to the memorized objects in both tasks. The absence of a polarity reversal of the CDA in the horizontal shift task demonstrated that there was no preparatory shift of memorized object location towards the side of the upcoming comparison stimuli. These results suggest that visual working memory represents the locations of visual objects during encoding, and that the matching of memorized and test objects at different locations is based on a comparison process that can bridge spatial translations between these objects. This article is part of a Special Issue entitled SI: Prediction and Attention. Copyright © 2014 Elsevier B.V. All rights reserved.

A glycosylphosphatidylinositol anchor is required for membrane localization but dispensable for cell wall association of chitin deacetylase 2 in Cryptococcus neoformans.

PubMed

Gilbert, Nicole M; Baker, Lorina G; Specht, Charles A; Lodge, Jennifer K

2012-01-01

Cell wall proteins (CWPs) mediate important cellular processes in fungi, including adhesion, invasion, biofilm formation, and flocculation. The current model of fungal cell wall organization includes a major class of CWPs covalently bound to β-1,6-glucan via a remnant of a glycosylphosphatidylinositol (GPI) anchor. This model was established by studies of ascomycetes more than a decade ago, and relatively little work has been done with other fungi, although the presumption has been that proteins identified in the cell wall which contain a predicted GPI anchor are covalently linked to cell wall glucans. The pathogenic basidiomycete Cryptococcus neoformans encodes >50 putatively GPI-anchored proteins, some of which have been identified in the cell wall. One of these proteins is chitin deacetylase 2 (Cda2), an enzyme responsible for converting chitin to chitosan, a cell wall polymer recently established as a virulence factor for C. neoformans infection of mammalian hosts. Using a combination of biochemistry, molecular biology, and genetics, we show that Cda2 is GPI anchored to membranes but noncovalently associated with the cell wall by means independent of both its GPI anchor and β-1,6-glucan. We also show that Cda2 produces chitosan when localized to the plasma membrane, but association with the cell wall is not essential for this process, thereby providing insight into the mechanism of chitosan biosynthesis. These results increase our understanding of the surface of C. neoformans and provide models of cell walls likely applicable to other undercharacterized basidiomycete pathogenic fungi. The surface of a pathogenic microbe is a major interface with its host. In fungi, the outer surface consists of a complex matrix known as the cell wall, which includes polysaccharides, proteins, and other molecules. The mammalian host recognizes many of these surface molecules and mounts appropriate responses to combat the microbial infection. Cryptococcus neoformans is a serious fungal pathogen that kills over 600,000 people annually. It converts most of its chitin, a cell wall polysaccharide, to chitosan, which is necessary for virulence. Chitin deacetylase enzymes have been identified in the cell wall, and our studies were undertaken to understand how the deacetylase is linked to the wall and where it has activity. Our results have implications for the current model of chitosan biosynthesis and further challenge the paradigm of covalent linkages between cell wall proteins and polysaccharides through a lipid modification of the protein.

Preparation of cellulose diacetate/cellulose hybrid fiber by dry-jet wet spinning in tetrabutylammonium acetate/dimethyl sulfoxide solvent

NASA Astrophysics Data System (ADS)

Yu, Yongqi; Zhang, Wentao; Gao, Xin; Jiang, Zeming; Miao, Jiaojiao; Zhang, Liping

2017-12-01

Cellulose diacetate (CDA)/cellulose hybrid fibers with nice properties were prepared by dry-jet wet spinning using a tetrabutylammonium acetate/dimethylsulfoxide system as a solvent at 50 °C. Scanning electron microscopy (SEM) images exhibited the hybrid fibers with circular cross section and smooth surface. In addition, SEM and Fourier transform infrared spectroscopy analysis indicated the nice compatibility of CDA and cellulose. The hybrid fibers with the addition of CDA showed higher thermal stability and a wider range of degradation than pure cellulose material. It was found that the elongation at break of the fibers increased from 4.87 to 13.22% with increasing CDA/cellulose ratio from 0 to 4:6, which was comparable with CDA fiber spun from 1-butyl-3-methylimidazolium chloride. The 1095.5/cm Raman characteristic band of the hybrid fibers with lower intensity was observed, while it did not towards a higher wave number compared to that of fibers containing less CDA. In addition, the shear viscosity of the solutions exhibited a character of typical shear-thinning behaviour with variation of shear rates.

The influence of different cucumariosides on immunogenicity of OmpF porin from Yersinia pseudotuberulosis as a model protein antigen of tubular immunostimulating complex

NASA Astrophysics Data System (ADS)

Sanina, N. M.; Chopenko, N. S.; Davydova, L. A.; Mazeika, A. N.; Portnyagina, O. Yu.; Kim, N. Yu.; Golotin, V. A.; Kostetsky, E. Y.; Shnyrov, V. L.

2017-09-01

Nanoparticulate tubular immunostimulating complex (TI-complex) is a novel promising adjuvant carrier of antigens allowing to create safe and effective vaccines of new generation. The adjuvant activity of TI-complexes based on monogalactosyldyacylglycerol (MGDG) from the sea alga Ulva lactuca and different triterpene glycosides cucumariosides (CDs) from marine invertebrate Cucumaria japonica and their fractions was studied to assess effects of different CDs on the immunogenicity of porin OmpF from Yersinia pseudotuberculosis (YOmpF). TI-complexes with cucumarioside A2-2 (CDA2-2) maximally stimulated anti-porin antibody production. Studies of protein intrinsic fluorescence showed that all CDs had a relaxing effect on the conformation of YOmpF, loosening peripheral region of protein and promoting exposure of the protein antigenic determinants to the water environment. The greatest immunostimulating effect of TI-complexes comprising CDA2-2 was accompanied by mild effect of this CD on the tertiary structure of protein antigen YOmpF, whereas cucumarioside E (CDE) and cucumarioside A2-4 (CDA2-4) caused especially sharp redistribution of spectral form of the YOmpF corresponding to the emission of an intrinsic protein fluorophore tryptophan.

Vaccination with Recombinant Cryptococcus Proteins in Glucan Particles Protects Mice against Cryptococcosis in a Manner Dependent upon Mouse Strain and Cryptococcal Species.

PubMed

Specht, Charles A; Lee, Chrono K; Huang, Haibin; Hester, Maureen M; Liu, Jianhua; Luckie, Bridget A; Torres Santana, Melanie A; Mirza, Zeynep; Khoshkenar, Payam; Abraham, Ambily; Shen, Zu T; Lodge, Jennifer K; Akalin, Ali; Homan, Jane; Ostroff, Gary R; Levitz, Stuart M

2017-11-28

Development of a vaccine to protect against cryptococcosis is a priority given the enormous global burden of disease in at-risk individuals. Using glucan particles (GPs) as a delivery system, we previously demonstrated that mice vaccinated with crude Cryptococcus -derived alkaline extracts were protected against lethal challenge with Cryptococcus neoformans and Cryptococcus gattii The goal of the present study was to identify protective protein antigens that could be used in a subunit vaccine. Using biased and unbiased approaches, six candidate antigens (Cda1, Cda2, Cda3, Fpd1, MP88, and Sod1) were selected, recombinantly expressed in Escherichia coli , purified, and loaded into GPs. Three mouse strains (C57BL/6, BALB/c, and DR4) were then vaccinated with the antigen-laden GPs, following which they received a pulmonary challenge with virulent C. neoformans and C. gattii strains. Four candidate vaccines (GP-Cda1, GP-Cda2, GP-Cda3, and GP-Sod1) afforded a significant survival advantage in at least one mouse model; some vaccine combinations provided added protection over that seen with either antigen alone. Vaccine-mediated protection against C. neoformans did not necessarily predict protection against C. gattii Vaccinated mice developed pulmonary inflammatory responses that effectively contained the infection; many surviving mice developed sterilizing immunity. Predicted T helper cell epitopes differed between mouse strains and in the degree to which they matched epitopes predicted in humans. Thus, we have discovered cryptococcal proteins that make promising candidate vaccine antigens. Protection varied depending on the mouse strain and cryptococcal species, suggesting that a successful human subunit vaccine will need to contain multiple antigens, including ones that are species specific. IMPORTANCE The encapsulated fungi Cryptococcus neoformans and Cryptococcus gattii are responsible for nearly 200,000 deaths annually, mostly in immunocompromised individuals. An effective vaccine could substantially reduce the burden of cryptococcosis. However, a major gap in cryptococcal vaccine development has been the discovery of protective antigens to use in vaccines. Here, six cryptococcal proteins with potential as vaccine antigens were expressed recombinantly and purified. Mice were then vaccinated with glucan particle preparations containing each antigen. Of the six candidate vaccines, four protected mice from a lethal cryptococcal challenge. However, the degree of protection varied as a function of mouse strain and cryptococcal species. These preclinical studies identify cryptococcal proteins that could serve as candidate vaccine antigens and provide a proof of principle regarding the feasibility of protein antigen-based vaccines to protect against cryptococcosis. Copyright © 2017 Specht et al.

Electrophysiological Evidence for a Sensory Recruitment Model of Somatosensory Working Memory.

PubMed

Katus, Tobias; Grubert, Anna; Eimer, Martin

2015-12-01

Sensory recruitment models of working memory assume that information storage is mediated by the same cortical areas that are responsible for the perceptual processing of sensory signals. To test this assumption, we measured somatosensory event-related brain potentials (ERPs) during a tactile delayed match-to-sample task. Participants memorized a tactile sample set at one task-relevant hand to compare it with a subsequent test set on the same hand. During the retention period, a sustained negativity (tactile contralateral delay activity, tCDA) was elicited over primary somatosensory cortex contralateral to the relevant hand. The amplitude of this component increased with memory load and was sensitive to individual limitations in memory capacity, suggesting that the tCDA reflects the maintenance of tactile information in somatosensory working memory. The tCDA was preceded by a transient negativity (N2cc component) with a similar contralateral scalp distribution, which is likely to reflect selection of task-relevant tactile stimuli at the encoding stage. The temporal sequence of N2cc and tCDA components mirrors previous observations from ERP studies of working memory in vision. The finding that the sustained somatosensory delay period activity varies as a function of memory load supports a sensory recruitment model for spatial working memory in touch. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Measurement of total phenolic content and antioxidant activity of aerial parts of medicinal plant Coronopus didymus.

PubMed

Noreen, Hafiza; Semmar, Nabil; Farman, Muhammad; McCullagh, James S O

2017-08-01

To evaluate the total phenolic content and compare the antioxidant activity of various solvent extracts and fractions from the aerial parts of Coronopus didymus through various assays. Total phenolic content was determined using the Folin-Ciocalteu assay and the in vitro antioxidant activity of a number of different extracts was investigated in a dose-dependent manner with three different methods: the 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) and ferric reducing antioxidant power (FRAP) assays. A flavone was isolated from the most active ethanolic extract with high antioxidant activity using size exclusion chromatography. IC 50 values were calculated for the DPPH and ABTS methods. The FRAP activity was assessed in terms of μM Fe (II) equivalent. The phenolic content was found to be highest in the ethanol extract (CDA Et; 47.8 mM GAE) and the lowest in the dichloromethane extract (CDA DCM; 3.13 mM GAE). The ethanol extract showed high radical scavenging activity towards DPPH and ABTS radicals with IC 50 values of (7.80 × 10 2 ) and (4.32 × 10 2 ) μg/mL, respectively. The most active ethanol extract had a FRAP value of 1921.7 μM Fe (II) equivalent. The isolated flavone F10C (5,7,4'-trihydroxy-3'-methoxy flavone) was far more effective for scavenging free radicals in the DPPH and ABTS assays with IC 50 of 43.8 and 0.08 μg/mL, than the standard trolox, with IC 50 values of 97.5 and 21.1 μg/mL, respectively. In addition, the flavone F10C and the standard ascorbic acid had FRAP values of 1621.7 and 16 038.0 μM Fe (II) equivalents, respectively. The total phenolic content of extracts in decreasing order is ethanol extract (CDA Et) > acetone extract (CDA ACE) > phenolic extract (CDA MW) > n-hexane extract (CDA nHX)> chloroform extract (CDA CHL) > dichloromethane extract (CDA DCM). The ordering of extracts in terms of antioxidant activity from highest to lowest is CDA Et > CDA MW > CDA DCM > CDA CHL > CDA ACE > CDA nHX in DPPH, ABTS and FRAP assays. A significant relationship is found between antioxidant potential and total phenolic content, suggesting that phenolic compounds are the major contributors to the antioxidant activity of C. didymus. Copyright © 2017 Hainan Medical University. Production and hosting by Elsevier B.V. All rights reserved.

Cost-utility analysis modeling at 2-year follow-up for cervical disc arthroplasty versus anterior cervical discectomy and fusion: A single-center contribution to the randomized controlled trial

PubMed Central

Warren, Daniel; Andres, Tate; Hoelscher, Christian; Ricart-Hoffiz, Pedro; Bendo, John; Goldstein, Jeffrey

2013-01-01

Background Patients with cervical disc herniations resulting in radiculopathy or myelopathy from single level disease have traditionally been treated with Anterior Cervical Discectomy and Fusion (ACDF), yet Cervical Disc Arthroplasty (CDA) is a new alternative. Expert suggestion of reduced adjacent segment degeneration is a promising future result of CDA. A cost-utility analysis of these procedures with long-term follow-up has not been previously reported. Methods We reviewed single institution prospective data from a randomized trial comparing single-level ACDF and CDA in cervical disc disease. Both Medicare reimbursement schedules and actual hospital cost data for peri-operative care were separately reviewed and analyzed to estimate the cost of treatment of each patient. QALYs were calculated at 1 and 2 years based on NDI and SF-36 outcome scores, and incremental cost effectiveness ratio (ICER) analysis was performed to determine relative cost-effectiveness. Results Patients of both groups showed improvement in NDI and SF-36 outcome scores. Medicare reimbursement rates to the hospital were $11,747 and $10,015 for ACDF and CDA, respectively; these figures rose to $16,162 and $13,171 when including physician and anesthesiologist reimbursement. The estimated actual cost to the hospital of ACDF averaged $16,108, while CDA averaged $16,004 (p = 0.97); when including estimated physicians fees, total hospital costs came to $19,811 and $18,440, respectively. The cost/QALY analyses therefore varied widely with these discrepancies in cost values. The ICERs of ACDF vs CDA with Medicare reimbursements were $18,593 (NDI) and $19,940 (SF-36), while ICERs based on actual total hospital cost were $13,710 (NDI) and $9,140 (SF-36). Conclusions We confirm the efficacy of ACDF and CDA in the treatment of cervical disc disease, as our results suggest similar clinical outcomes at one and two year follow-up. The ICER suggests that the non-significant added benefit via ACDF comes at a reasonable cost, whether we use actual hospital costs or Medicare reimbursement values, though the actual ICER values vary widely depending upon the CUA modality used. Long term follow-up may illustrate a different profile for CDA due to reduced cost and greater long-term utility scores. It is crucial to note that financial modeling plays an important role in how economic treatment dominance is portrayed. PMID:25694905

Attention modulates maintenance of representations in visual short-term memory.

PubMed

Kuo, Bo-Cheng; Stokes, Mark G; Nobre, Anna Christina

2012-01-01

Recent studies have shown that selective attention is of considerable importance for encoding task-relevant items into visual short-term memory (VSTM) according to our behavioral goals. However, it is not known whether top-down attentional biases can continue to operate during the maintenance period of VSTM. We used ERPs to investigate this question across two experiments. Specifically, we tested whether orienting attention to a given spatial location within a VSTM representation resulted in modulation of the contralateral delay activity (CDA), a lateralized ERP marker of VSTM maintenance generated when participants selectively encode memory items from one hemifield. In both experiments, retrospective cues during the maintenance period could predict a specific item (spatial retrocue) or multiple items (neutral retrocue) that would be probed at the end of the memory delay. Our results revealed that VSTM performance is significantly improved by orienting attention to the location of a task-relevant item. The behavioral benefit was accompanied by modulation of neural activity involved in VSTM maintenance. Spatial retrocues reduced the magnitude of the CDA, consistent with a reduction in memory load. Our results provide direct evidence that top-down control modulates neural activity associated with maintenance in VSTM, biasing competition in favor of the task-relevant information.

Persistent axial neck pain after cervical disc arthroplasty: a radiographic analysis.

PubMed

Wagner, Scott C; Formby, Peter M; Kang, Daniel G; Van Blarcum, Gregory S; Cody, John P; Tracey, Robert W; Lehman, Ronald A

2016-07-01

There is very little literature examining optimal radiographic parameters for placement of cervical disc arthroplasty (CDA), nor is there substantial evidence evaluating the relationship between persistent postoperative neck pain and radiographic outcomes. We set out to perform a single-center evaluation of the radiographic outcomes, including associated complications, of CDA. This is a retrospective review. Two hundred eighty-five consecutive patients undergoing CDA were included in the review. The outcome measures were radiological parameters (preoperative facet arthrosis, disc height, CDA placement in sagittal and coronal planes, heterotopic ossification [HO] formation, etc.) and patient outcomes (persistent pain, recurrent pain, new-onset pain, etc.). We performed a retrospective review of all patients from a single military tertiary medical center from August 2008 to August 2012 undergoing CDA. Preoperative, immediate postoperative, and final follow-up films were evaluated. The clinical outcomes and complications associated with the procedure were also examined. The average radiographic follow-up was 13.5 months and the rate of persistent axial neck pain was 17.2%. For patients with persistent neck pain, the rate of HO formation per level studied was 22.6%, whereas the rate was significantly lower for patients without neck pain (11.7%, p=.03). There was no significant association between the severity of HO and the presence of neck pain. Patients with a preoperative diagnosis of cervicalgia, compared to those without cervicalgia, were significantly more likely to experience continued neck pain postoperatively (28.6% vs. 13.1%, p=.01). There were no differences in preoperative facet arthrosis, pre- or postoperative disc height, segmental range of motion, or placement of the device relative to the posterior edge of the vertebral body.However, patients with implants more centered between the uncovertebral joints were more likely to experience posterior neck pain (p=.03). We found that posterior axial neck pain is relatively frequent after CDA, and patients with persistent neck pain were significantly more likely to have preoperative cervicalgia and develop HO postoperatively. We also found that patients with implants that were placed off-centered were less likely to also complain of neck pain, although the reasons for this finding remain unclear. Published by Elsevier Inc.

Molecular cloning of low-temperature-inducible ribosomal proteins from soybean.

PubMed

Kim, Kee-Young; Park, Seong-Whan; Chung, Young-Soo; Chung, Chung-Han; Kim, Jung-In; Lee, Jai-Heon

2004-05-01

Three ribosomal protein genes induced by low-temperature treatment were isolated from soybean. GmRPS13 (742 bp) encodes a 17.1 kDa protein which has 95% identity with the 40S ribosomal protein S13 of Panax ginseng (AB043974). GmRPS6 (925 bp) encodes a 28.1 kDa protein which has 94% identity with the 40S ribosomal protein S6 of Asparagus officinalis (AJ277533). GmRPL37 (494 bp) encodes a 10.7 kDa protein which has 85% identity with the 60S ribosomal protein L37 of Arabidopsis thaliana (AF370216). The expression of these ribosomal protein genes started to increase 3 d after low-temperature treatment, whereas the cold-stress protein src1 was highly induced from the first day. Such late response of these ribosomal protein genes may be due to secondary signals during cold adaptation. The induction of ribosomal protein genes might enhance the translation process or help proper ribosome functioning under low-temperature conditions.

Mechanistic and structural basis of stereospecific Cbeta-hydroxylation in calcium-dependent antibiotic, a daptomycin-type lipopeptide.

PubMed

Strieker, Matthias; Kopp, Florian; Mahlert, Christoph; Essen, Lars-Oliver; Marahiel, Mohamed A

2007-03-20

Non-ribosomally synthesized lipopeptide antibiotics of the daptomycin type are known to contain unnatural beta-modified amino acids, which are essential for bioactivity. Here we present the biochemical and structural basis for the incorporation of 3-hydroxyasparagine at position 9 in the 11-residue acidic lipopeptide lactone calcium-dependent antibiotic (CDA). Direct hydroxylation of l-asparagine by AsnO, a non-heme Fe(2+)/alpha-ketoglutarate-dependent oxygenase encoded by the CDA biosynthesis gene cluster, was validated by Fmoc derivatization of the reaction product and LC/MS analysis. The 1.45, 1.92, and 1.66 A crystal structures of AsnO as apoprotein, Fe(2+) complex, and product complex, respectively, with (2S,3S)-3-hydroxyasparagine and succinate revealed the stereoselectivity and substrate specificity of AsnO. The comparison of native and product-complex structures of AsnO showed a lid-like region (residues F208-E223) that seals the active site upon substrate binding and shields it from sterically demanding peptide substrates. Accordingly, beta-hydroxylated asparagine is synthesized prior to its incorporation into the growing CDA peptide. The AsnO structure could serve as a template for engineering novel enzymes for the synthesis of beta-hydroxylated amino acids.

Novel RepA-MCM proteins encoded in plasmids pTAU4, pORA1 and pTIK4 from Sulfolobus neozealandicus

PubMed Central

Greve, Bo; Jensen, Susanne; Phan, Hoa; Brügger, Kim; Zillig, Wolfram; She, Qunxin; Garrett, Roger A.

2005-01-01

Three plasmids isolated from the crenarchaeal thermoacidophile Sulfolobus neozealandicus were characterized. Plasmids pTAU4 (7,192 bp), pORA1 (9,689 bp) and pTIK4 (13,638 bp) show unusual properties that distinguish them from previously characterized cryptic plasmids of the genus Sulfolobus. Plasmids pORA1 and pTIK4 encode RepA proteins, only the former of which carries the novel polymerase–primase domain of other known Sulfolobus plasmids. Plasmid pTAU4 encodes a mini-chromosome maintenance protein homolog and no RepA protein; the implications for DNA replication are considered. Plasmid pORA1 is the first Sulfolobus plasmid to be characterized that does not encode the otherwise highly conserved DNA-binding PlrA protein. Another encoded protein appears to be specific for the New Zealand plasmids. The three plasmids should provide useful model systems for functional studies of these important crenarchaeal proteins. PMID:15876565

High risk of severe anaemia after chlorproguanil-dapsone+artesunate antimalarial treatment in patients with G6PD (A-) deficiency.

PubMed

Fanello, Caterina I; Karema, Corine; Avellino, Pamela; Bancone, Germana; Uwimana, Aline; Lee, Sue J; d'Alessandro, Umberto; Modiano, David

2008-01-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common inherited human enzyme defect. This deficiency provides some protection from clinical malaria, but it can also cause haemolysis after administration of drugs with oxidant properties. The safety of chlorproguanil-dapsone+artesunate (CD+A) and amodiaquine+sulphadoxine-pyrimethamine (AQ+SP) for the treatment of uncomplicated P. falciparum malaria was evaluated according to G6PD deficiency in a secondary analysis of an open-label, randomized clinical trial. 702 children, treated with CD+A or AQ+SP and followed for 28 days after treatment were genotyped for G6PD A- deficiency. In the first 4 days following CD+A treatment, mean haematocrit declined on average 1.94% (95% CI 1.54 to 2.33) and 1.05% per day (95% CI 0.95 to 1.15) respectively in patients with G6PD deficiency and normal patients; a mean reduction of 1.3% per day was observed among patients who received AQ+SP regardless of G6PD status (95% CI 1.25 to 1.45). Patients with G6PD deficiency recipients of CD+A had significantly lower haematocrit than the other groups until day 7 (p = 0.04). In total, 10 patients had severe post-treatment haemolysis requiring blood transfusion. Patients with G6PD deficiency showed a higher risk of severe anaemia following treatment with CD+A (RR = 10.2; 95% CI 1.8 to 59.3) or AQ+SP (RR = 5.6; 95% CI 1.0 to 32.7). CD+A showed a poor safety profile in individuals with G6PD deficiency most likely as a result of dapsone induced haemolysis. Screening for G6PD deficiency before drug administration of potentially pro-oxidants drugs, like dapsone-containing combinations, although seldom available, is necessary.

Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity.

PubMed

Baudin, Marine; Cinquin, Bertrand; Sclavi, Bianca; Pareau, Dominique; Lopes, Filipa

2017-09-01

Confocal laser scanning microscopy (CLSM) is one of the most relevant technologies for studying biofilms in situ. Several tools have been developed to investigate and quantify the architecture of biofilms. However, an approach to quantify correctly the evolution of intensity of a fluorescent signal as a function of the structural parameters of a biofilm is still lacking. Here we present a tool developed in the ImageJ open source software that can be used to extract both structural and fluorescence intensity from CLSM data: BIAM (Biofilm Intensity and Architecture Measurement). This is of utmost significance when studying the fundamental mechanisms of biofilm growth, differentiation and development or when aiming to understand the effect of external molecules on biofilm phenotypes. In order to provide an example of the potential of such a tool in this study we focused on biofilm dispersion. cis-2-Decenoic acid (CDA) is a molecule known to induce biofilm dispersion of multiple bacterial species. The mechanisms by which CDA induces dispersion are still poorly understood. To investigate the effects of CDA on biofilms, we used a reporter strain of Escherichia coli (E. coli) that expresses the GFPmut2 protein under control of the rrnBP1 promoter. Experiments were done in flow cells and image acquisition was made with CLSM. Analysis carried out using the new tool, BIAM, indicates that CDA affects the fluorescence intensity of the biofilm structures as well as biofilm architectures. Indeed, our results demonstrate that CDA removes more than 35% of biofilm biovolume and suggest that it results in an increase of the biofilm's mean fluorescence intensity (MFI) by more than 26% compared to the control biofilm in the absence of CDA. Copyright © 2017. Published by Elsevier B.V.

Applying Critical Discourse Analysis in Health Policy Research: Case Studies in Regional, Organizational, and Global Health.

PubMed

Evans-Agnew, Robin A; Johnson, Susan; Liu, Fuqin; Boutain, Doris M

2016-08-01

Critical discourse analysis (CDA) is a promising methodology for policy research in nursing. As a critical theoretical methodology, researchers use CDA to analyze social practices and language use in policies to examine whether such policies may promote or impede social transformation. Despite the widespread use of CDA in other disciplines such as education and sociology, nursing policy research employing CDA methodology is sparse. To advance CDA use in nursing science, it is important to outline the overall research strategies and describe the steps of CDA in policy research. This article describes, using exemplar case studies, how nursing and health policy researchers can employ CDA as a methodology. Three case studies are provided to discuss the application of CDA research methodologies in nursing policy research: (a) implementation of preconception care policies in the Zhejiang province of China, (b) formation and enactment of statewide asthma policy in Washington state of the United States, and (c) organizational implementation of employee antibullying policies in hospital systems in the Pacific Northwest of the United States. Each exemplar details how CDA guided the examination of policy within specific contexts and social practices. The variations of the CDA approaches in the three exemplars demonstrated the flexibilities and potentials for conducting policy research grounded in CDA. CDA provides novel insights for nurse researchers examining health policy formation, enactment, and implementation. © The Author(s) 2016.

Exploration of permeability and antifouling performance on modified cellulose acetate ultrafiltration membrane with cellulose nanocrystals.

PubMed

Lv, Jinling; Zhang, Guoquan; Zhang, Hanmin; Yang, Fenglin

2017-10-15

Cellulose nanocrystals (CNCs) were introduced into cellulose diacetate (CDA) matrix via immerged phase-inversion process, aiming to improve the filtration and antifouling performance of CNCs/CDA blending membrane. The effects of CNCs on membrane morphologies, hydrophilicity, permeability and antifouling property were investigated. Results showed that the incorporation of CNCs into CDA membrane could effectively enhance the permeability and antifouling property of CNCs/CDA blending membrane by optimizing membrane microstructure and improving membrane hydrophilicity. A high pure water flux of 173.8L/m 2 h was achieved for the CNCs/CDA blending membrane at 200KPa, which is 24 times that of the CDA membrane (7.2L/m 2 h). The bovine serum albumin (BSA) adsorption amount of the CNCs/CDA blending membrane decreased about 48% compared to that of the CDA membrane. Additionally, the CNCs/CDA blending membrane exhibited better antifouling performance with the flux recovery ratio (FRR) of 89.5% after three fouling cycles, compared to 59.7% for the CDA membrane. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modulation of human cytidine deaminase by specific aminoacids involved in the intersubunit interactions.

PubMed

Vincenzetti, S; Quadrini, B; Mariani, P; De Sanctis, G; Cammertoni, N; Polzonetti, V; Pucciarelli, S; Natalini, P; Vita, A

2008-01-01

An investigation was made of the role exerted by some residues supposed to be involved in the intersubunit interaction and also in the catalytic site of homotetrameric human cytidine deaminase (T-CDA). Attention was focused on Y33, Y60, R68, and F137 residues that are a part of a conserved region in most T-CDAs. Hence, a series of site-directed mutagenesis experiments was set up obtaining seven mutants: Y60G, Y33G, Y33F Y33S, F137A, R68G, and R68Q. Each active purified mutant protein was characterized kinetically, with a series of substrates and inhibitors, and the effect of temperature on enzyme activity and stability was also investigated. Circular dichroism (CD) experiments at different temperatures and in presence of small amounts of sodium dodecyl sulphate (SDS) were performed in all the soluble mutant CDAs. The results obtained by site-directed mutagenesis studies were compared to the crystallographic data of B. subtilis CDA and E. coli CDA and to molecular modeling studies previously performed on human CDA. The mutation of Y60 to glycine produced an enzyme with a more compact quaternary structure with respect to the wild-type; this mutation did not have a dramatic effect on cytidine deamination, but it slightly affected the binding with the substrate. None of the mutant CDAs in Y33 showed enzymatic activity; they existed only as monomers, indicating that this residue, located at the intersubunit interface, may be responsible for the correct folding of human CDA. The insertion of an alanine instead of phenylalanine at position 137 led to a soluble but completely inactive enzyme unable to form a tetramer, suggesting that F137 residue may be important for the assembling of the tetramer and also for the arrangement of the CDA active site. Finally, R68G and R68Q mutations revealed that the presence of the amino group seems to be important for the catalytic process but not for substrate binding, as already shown in B. subtilis CDA. The quaternary structure of R68Q was not affected by the mutation, as shown by the SDS-induced dissociation experiments and CD studies, whereas R68G dissociated very easily in presence of small amounts of SDS. These experiments indicated that in the human CDA, the side chain of arginine 68 involved in the catalytic process in one subunit active site might come from another subunit. The data obtained from these studies confirmed the presence of a complicated set of intersubunit interactions in the active site of human CDA, as shown in other T-CDAs. (c) 2007 Wiley-Liss, Inc.

Anti-inflammatory activity of p-coumaryl alcohol-γ-O-methyl ether is mediated through modulation of interferon-γ production in Th cells

PubMed Central

Yu, E-S; Min, H-J; Lee, K; Lee, M-S; Nam, J-W; Seo, E-K; Hong, J-H; Hwang, E-S

2009-01-01

Background and purpose: p-Coumaryl alcohol-γ-O-methyl ether (CAME) was isolated from Alpinia galanga and shown to contain a phenylpropanoid structure similar to p-coumaryl diacetate (CDA). CDA is known to have antioxidant and anti-inflammatory activity, but the biochemical activities of CAME are unknown. Inflammation is mediated by inflammatory cytokine production, in particular, by CD4+ T helper cells (Th cells), but it is unclear whether phenylpropanoids affect cytokine production in Th cells. In this study, we decided to investigate the functions of CAME and CDA in CD4+ Th cells. Experimental approach: Mouse CD4+ Th cells were isolated from C57BL6 mice and stimulated with an antibody against T cell receptors in the presence of phenylpropanoids. Cytokine production was measured by elisa and intracellular cytokine staining. Gene knockout mice and tetracycline-inducible transgenic mice were used to examine the molecular mechanisms of phenylpropanoids on modulation of cytokine production. Key results: CAME potently reduced intracellular reactive oxygen species in Th cells, as does CDA. However, although CDA was cytotoxic, CAME selectively and potently suppresses interferon-γ (IFNγ) production in CD4+ Th cells, without toxicity. This effect was caused by attenuated expression of the transcription factor, T-box protein expressed in T cells (T-bet), and T-bet was essential for CAME to inhibit IFNγ production in CD4+ Th cells. Conclusions and implications: CAME selectively and substantially suppresses IFNγ production in CD4+ Th cells by decreasing T-bet expression. As increased IFNγ production by CD4+ Th cells can mediate inflammatory immune responses, a selective IFNγ suppressor, such as CAME may be an effective, naturally occurring, compound for modulating inflammatory immune disorders. PMID:19226286

Synthesis of cellulose diacetate based copolymer electrospun nanofibers for tissues scaffold

NASA Astrophysics Data System (ADS)

Liang, Wencheng; Hou, Jia; Fang, Xiangchen; Bai, Fudong; Zhu, Tonghe; Gao, Feifei; Wei, Chao; Mo, Xiumei; Lang, Meidong

2018-06-01

In this study, a novel cellulose diacetate based copolymer used as tissues scaffold, cellulose diacetate-graft-poly(ethylene terephthalate) (CDA-g-PET) was developed by "graft onto" strategy using 3-Isocyanatomethyl-3,5,5-trimethylcyc-lohexyl isocyanate (IPDI) as a coupling reagent of cellulose diacetate and poly(ethylene terephthalate), and using dibutyltin dilaurate (DBTDL) and 1-butyl-3-methylimidazolium chloride salt ([Bmim]Cl) as catalysts. CDA-g-PET copolymers with five different grafting ratios were obtained by the regulation of the reaction time. It was proved by the FT-IR spectra of the purified copolymers that PET had been successfully grafted onto CDA backbone. Afterwards, CDA-g-PET nanofibers were fabricated via electrospinning and further were cross-linked by means of treating in glutaraldehyde (25%wt) aqueous solution for 48 h. The uniform and smooth fiber morphology was proved by SEM and the diameter decreased with the increase of grafting ratio. Moreover, the value of TGA revealed that the grafting PET onto CDA backbone would improve heat-resistant quality of CDA and help to improve the ability of thermo processing. The graft of PET onto CDA significantly enhanced mechanical property of copolymer compared with CDA. The results of hemolysis ratio indicated that hemolysis ratio has decreased compared with CDA, highlighting the potential application in the field of contacting with blood. In vitro cell viability indicated that CDA-g-PET would enhance biocompatibility compared with CDA.

Characterization of rtSH3p13 gene encoding a development protein involved in vesicular traffic in spermiogenesis.

PubMed

Qiao, Yuan; Yang, Ju Xiang; Zhang, Xiao Dong L; Liu, Yu; Zhang, Jian Chao; Zong, Shu Dong; Miao, Shi Ying; Wang, Lin Fang; Koide, Samuel S

2004-06-01

A cDNA, designated as rtSH3p13, was isolated from a rat testis cDNA library. It consists of 1463 bp nuclear acids, which encodes a protein of 312 amino acids and was assigned the GenBank accession number AF227439. The deduced rtSH3p13 protein is a truncated isoform of SH3p13 as a result of mRNA alternative splicing. It is mainly expressed in the rat testis, detected in spermatids at the steps 8-19 of spermiogenesis, and found around the acrosome. During postnatal development, rtSH3p13 appears on day 18 and reaches maximum on day 60. Further experimental results suggested that rtSH3p13 forms a complex with activated epidermal growth factor receptor (EGFR) and interacts with synaptojanin I. Surprisingly, similar to SH3 domain, the V region of rtSH3p13 also inhibits endocytosis in CHO cells. Our results reveal a link between an rtSH3p13-synaptojanin-clathrin complex-mediated formation of pits and the process of spermiogenesis.

Disruption of rimP-SC, encoding a ribosome assembly cofactor, markedly enhances the production of several antibiotics in Streptomyces coelicolor

PubMed Central

2013-01-01

Background Ribosome assembly cofactor RimP is one of the auxiliary proteins required for maturation of the 30S subunit in Escherichia coli. Although RimP in protein synthesis is important, its role in secondary metabolites biosynthesis has not been reported so far. Considering the close relationship between protein synthesis and the production of secondary metabolites, the function of ribosome assembly cofactor RimP on antibiotics production was studied in Streptomyces coelicolor and Streptomyces venezuelae. Results In this study, the rimP homologue rimP-SC was identified and cloned from Streptomyces coelicolor. Disruption of rimP-SC led to enhanced production of actinorhodin and calcium-dependent antibiotics by promoting the transcription of actII-ORF4 and cdaR. Further experiments demonstrated that MetK was one of the reasons for the increment of antibiotics production. In addition, rimP-SC disruption mutant could be used as a host to produce more peptidyl nucleoside antibiotics (polyoxin or nikkomycin) than the wild-type strain. Likewise, disruption of rimP-SV of Streptomyces venezuelae also significantly stimulated jadomycin production, suggesting that enhanced antibiotics production might be widespread in many other Streptomyces species. Conclusion These results established an important relationship between ribosome assembly cofactor and secondary metabolites biosynthesis and provided an approach for yield improvement of secondary metabolites in Streptomyces. PMID:23815792

Population Pharmacokinetics of Cladribine in Patients with Multiple Sclerosis.

PubMed

Savic, Radojka M; Novakovic, Ana M; Ekblom, Marianne; Munafo, Alain; Karlsson, Mats O

2017-10-01

The aims of this study were to characterize the concentration-time course of cladribine (CdA) and its main metabolite 2-chloroadenine (CAde), estimate interindividual variability in pharmacokinetics (PK), and identify covariates explaining variability in the PK of CdA. This population PK analysis was based on the combined dataset from four clinical studies in patients with multiple sclerosis (MS): three phase I studies, including one food and one drug-drug interaction study, and one phase III clinical study. Plasma and urine concentration data of CdA and CAde were modeled simultaneously. The analysis comprised a total of 2619 CdA and CAde plasma and urine concentration observations from 173 patients with MS who received an intravenous infusion or oral tablet doses of CdA as a single agent or in combination with interferon (IFN) β-1a. CdA PK data were best described by a three-compartment model, while a one-compartment model best described the PK of CAde. CdA renal clearance (CL R ) was correlated with creatinine clearance (CL CR ), predicting a decrease in the total clearance of 19%, 30% and 40% for patients with mild (CL CR  = 65 ml/min), moderate (CL CR  = 40 ml/min) and severe (CL CR  = 20 ml/min) renal impairment, respectively. Food decreased the extent of CdA absorption by 11.2% and caused an absorption delay. Coadministration with IFNβ-1a was found to increase non-CL R (CL NR ) by 21%, resulting in an increase of 11% in total clearance. Both CdA and CAde displayed linear PK after intravenous and oral administration of CdA, with CdA renal function depending on CL CR . Trial registration number for study 25643: NCT00213135.

Dust in the Outer Solar System as measured by Cassini-CDA: KBOs, Centaurs and TNOs as parent bodies?

NASA Astrophysics Data System (ADS)

Altobelli, N.; Kempf, S.; Srama, R.

2017-09-01

We analyse 13 years of data acquired by the Cosmic Dust Analyser (CDA)-Entrance Grid (EG) subsystem on-board the Cassini spacecraft around Saturn. We confirm the presence of exogenous dust, originating from the interplanetary space and permanently crossing the Saturnian system. We analyse the range of possible heliocentric orbital elements in order to identify their possible origin. We observe particles whose dynamics is compatible with 'old' collisional debris from the Kuiper-Belt, migrating inward the Solar System under influence of the Poynting-Robertson drag, or relatively fresh grains from recently discovered cometary activity of Centaurs. A population of particles entering the Saturn's system with high velocities can be linked to Halley-type comets as parent bodies.

EEG correlates of visual short-term memory as neuro-cognitive endophenotypes of ADHD.

PubMed

Wiegand, Iris; Hennig-Fast, Kristina; Kilian, Beate; Müller, Hermann J; Töllner, Thomas; Möller, Hans-Jürgen; Engel, Rolf R; Finke, Kathrin

2016-05-01

Attention deficit hyperactivity disorder (ADHD) frequently persists into adulthood. A reduction in visual short-term memory (vSTM) storage capacity was recently suggested as a potential neuro-cognitive endophenotype, i.e., a testable marker of an individual's liability for developing ADHD. This study aimed at identifying markers of the brain abnormalities underlying vSTM reductions in adult ADHD. We combined behavioral parameter-based assessment with electrophysiology in groups of adult ADHD patients and healthy age-matched controls. Amplitudes of ERP markers of vSTM storage capacity, the contralateral delay activity (CDA) and the P3b, were analyzed according to (i) differences between individuals with higher vs. lower storage capacity K and (ii) differences between ADHD patients and control participants. We replicated the finding of reduced storage capacity in adult ADHD. Across groups, individuals with higher relative to lower storage capacity showed a larger CDA and P3b. We further found differences between the patient and control groups in the ERPs: The CDA amplitude was attenuated in an early time window for ADHD patients compared to control participants, and was negatively correlated with ADHD patients' symptom severity ratings. Furthermore, the P3b was larger in ADHD patients relative to control participants. These electrophysiological findings indicate altered brain mechanisms underlying visual storage capacity in ADHD, which are characterized by deficient encoding and maintenance, and increased recruitment of control processes. Accordingly, (quantifiable) ERP markers of vSTM in adult ADHD bear candidacy as neuro-cognitive endophenotypes of the disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

Familiarity Speeds Up Visual Short-term Memory Consolidation: Electrophysiological Evidence from Contralateral Delay Activities.

PubMed

Xie, Weizhen; Zhang, Weiwei

2018-01-01

To test how preexisting long-term memory influences visual STM, this study takes advantage of individual differences in participants' prior familiarity with Pokémon characters and uses an ERP component, the contralateral delay activity (CDA), to assess whether observers' prior stimulus familiarity affects STM consolidation and storage capacity. In two change detection experiments, consolidation speed, as indexed by CDA fractional area latency and/or early-window (500-800 msec) amplitude, was significantly associated with individual differences in Pokémon familiarity. In contrast, the number of remembered Pokémon stimuli, as indexed by Cowan's K and late-window (1500-2000 msec) CDA amplitude, was significantly associated with individual differences in Pokémon familiarity when STM consolidation was incomplete because of a short presentation of Pokémon stimuli (500 msec, Experiment 2), but not when STM consolidation was allowed to complete given sufficient encoding time (1000 msec, Experiment 1). Similar findings were obtained in between-group analyses when participants were separated into high-familiarity and low-familiarity groups based on their Pokémon familiarity ratings. Together, these results suggest that stimulus familiarity, as a proxy for the strength of preexisting long-term memory, primarily speeds up STM consolidation, which may subsequently lead to an increase in the number of remembered stimuli if consolidation is incomplete. These findings thus highlight the importance of research assessing how effects on representations (e.g., STM capacity) are in general related to (or even caused by) effects on processes (e.g., STM consolidation) in cognition.

Dual genetically encoded phage-displayed ligands.

PubMed

Mohan, Kritika; Weiss, Gregory A

2014-05-15

M13 bacteriophage display presents polypeptides as fusions to phage coat proteins. Such phage-displayed ligands offer useful reagents for biosensors. Here, we report a modified phage propagation protocol for the consistent and robust display of two different genetically encoded ligands on the major coat protein, P8. The results demonstrate that the phage surface reaches a saturation point for maximum peptide display. Copyright © 2014 Elsevier Inc. All rights reserved.

Induction of Protective Immunity to Cryptococcal Infection in Mice by a Heat-Killed, Chitosan-Deficient Strain of Cryptococcus neoformans.

PubMed

Upadhya, Rajendra; Lam, Woei C; Maybruck, Brian; Specht, Charles A; Levitz, Stuart M; Lodge, Jennifer K

2016-05-10

Cryptococcus neoformans is a major opportunistic fungal pathogen that causes fatal meningoencephalitis in immunocompromised individuals and is responsible for a large proportion of AIDS-related deaths. The fungal cell wall is an essential organelle which undergoes constant modification during various stages of growth and is critical for fungal pathogenesis. One critical component of the fungal cell wall is chitin, which in C. neoformans is predominantly deacetylated to chitosan. We previously reported that three chitin deacetylase (CDA) genes have to be deleted to generate a chitosan-deficient C. neoformans strain. This cda1Δ2Δ3Δ strain was avirulent in mice, as it was rapidly cleared from the lungs of infected mice. Here, we report that clearance of the cda1Δ2Δ3Δ strain was associated with sharply spiked concentrations of proinflammatory molecules that are known to be critical mediators of the orchestration of a protective Th1-type adaptive immune response. This was followed by the selective enrichment of the Th1-type T cell population in the cda1Δ2Δ3Δ strain-infected mouse lung. Importantly, this response resulted in the development of robust protective immunity to a subsequent lethal challenge with a virulent wild-type C. neoformans strain. Moreover, protective immunity was also induced in mice vaccinated with heat-killed cda1Δ2Δ3Δ cells and was effective in multiple mouse strains. The results presented here provide a strong framework to develop the cda1Δ2Δ3Δ strain as a potential vaccine candidate for C. neoformans infection. The most commonly used anticryptococcal therapies include amphotericin B, 5-fluorocytosine, and fluconazole alone or in combination. Major drawbacks of these treatment options are their limited efficacy, poor availability in limited resource areas, and potential toxicity. The development of antifungal vaccines and immune-based therapeutic interventions is promising and an attractive alternative to chemotherapeutics. Currently, there are no fungal vaccines in clinical use. This is the first report of a C. neoformans deletion strain with an avirulent phenotype in mice exhibiting protective immunity when used as a vaccine after heat inactivation, although other strains that overexpress fungal or murine proteins have recently been shown to induce a protective response. The data presented here demonstrate the potential for developing the avirulent cda1Δ2Δ3Δ strain into a vaccine-based therapy to treat C. neoformans infection. Copyright © 2016 Upadhya et al.

The contralateral delay activity as a neural measure of visual working memory

PubMed Central

Luria, Roy; Balaban, Halely; Awh, Edward; Vogel, Edward K.

2016-01-01

The contralateral delay activity (CDA) is a negative slow wave sensitive to the number of objects maintained in visual working memory (VWM). In recent years, a growing number of labs started to use the CDA in order to investigate VWM, leading to many fascinating discoveries. Here, we discuss the recent developments and contribution of the CDA in various research fields. Importantly, we report two meta-analyses that unequivocally validate the relationship between the set-size increase in the CDA amplitude and the individual VWM capacity, and between the CDA and filtering efficiency. We further discuss how the CDA was used to study the role of VWM in visual search, multiple object tracking, grouping, binding, and whether VWM capacity allocation is determined by the items’ resolution or instead by the number of objects regardless of their complexity. In addition, we report how the CDA has been used to characterize specific VWM deficits in special populations. PMID:26802451

Clinical Document Architecture integration system to support patient referral and reply letters.

PubMed

Lee, Sung-Hyun; Song, Joon Hyun; Kim, Il Kon; Kim, Jeong-Whun

2016-06-01

Many Clinical Document Architecture (CDA) referrals and reply documents have been accumulated for patients since the deployment of the Health Information Exchange System (HIES) in Korea. Clinical data were scattered in many CDA documents and this took too much time for physicians to read. Physicians in Korea spend only limited time per patient as insurances in Korea follow a fee-for-service model. Therefore, physicians were not allowed sufficient time for making medical decisions, and follow-up care service was hindered. To address this, we developed CDA Integration Template (CIT) and CDA Integration System (CIS) for the HIES. The clinical items included in CIT were defined reflecting the Korean Standard for CDA Referral and Reply Letters and requests by physicians. CIS integrates CDA documents of a specified patient into a single CDA document following the format of CIT. Finally, physicians were surveyed after CIT/CIS adoption, and they indicated overall satisfaction. © The Author(s) 2014.

Using archetypes for defining CDA templates.

PubMed

Moner, David; Moreno, Alberto; Maldonado, José A; Robles, Montserrat; Parra, Carlos

2012-01-01

While HL7 CDA is a widely adopted standard for the documentation of clinical information, the archetype approach proposed by CEN/ISO 13606 and openEHR is gaining recognition as a means of describing domain models and medical knowledge. This paper describes our efforts in combining both standards. Using archetypes as an alternative for defining CDA templates permit new possibilities all based on the formal nature of archetypes and their ability to merge into the same artifact medical knowledge and technical requirements for semantic interoperability of electronic health records. We describe the process followed for the normalization of existing legacy data in a hospital environment, from the importation of the HL7 CDA model into an archetype editor, the definition of CDA archetypes and the application of those archetypes to obtain normalized CDA data instances.

iSMART: Ontology-based Semantic Query of CDA Documents

PubMed Central

Liu, Shengping; Ni, Yuan; Mei, Jing; Li, Hanyu; Xie, Guotong; Hu, Gang; Liu, Haifeng; Hou, Xueqiao; Pan, Yue

2009-01-01

The Health Level 7 Clinical Document Architecture (CDA) is widely accepted as the format for electronic clinical document. With the rich ontological references in CDA documents, the ontology-based semantic query could be performed to retrieve CDA documents. In this paper, we present iSMART (interactive Semantic MedicAl Record reTrieval), a prototype system designed for ontology-based semantic query of CDA documents. The clinical information in CDA documents will be extracted into RDF triples by a declarative XML to RDF transformer. An ontology reasoner is developed to infer additional information by combining the background knowledge from SNOMED CT ontology. Then an RDF query engine is leveraged to enable the semantic queries. This system has been evaluated using the real clinical documents collected from a large hospital in southern China. PMID:20351883

Nucleoside analogues in the therapy of Langerhans cell histiocytosis: a survey of members of the histiocyte society and review of the literature.

PubMed

Weitzman, S; Wayne, A S; Arceci, R; Lipton, J M; Whitlock, J A

1999-11-01

Previous reports have suggested activity of the nucleoside analogues 2-chlorodeoxyadenosine (2-CdA) and 2'-deoxycoformycin (2'-DCF) in Langerhans cell histiocytosis (LCH). To assess the efficacy of 2-CdA and 2'-DCF as salvage therapy for LCH, a survey of members of the Histiocyte Society and a literature review were undertaken. Twenty-three patients treated with 2-CdA and 4 treated with 2'-DCF were found, age range 2 months to 49 years. All 15 survey patients had multiorgan involvement, and 14 were heavily pretreated. Doses of 2-CdA ranged from 0.1 mg/kg/day continuous infusion for 5-7 days (majority of patients) to 13 mg/m(2)/day for 5 days, for 1-6 courses. One of the 15 patients had an early death, 5 had no response (NR), 3 had partial response (PR), and 6 achieved complete response (CR). Among 8 published patients, 7 achieved stable CR and 1 NR. Among 4 patients treated with 2'-DCF (4 mg/m(2)/week for 8 weeks then q 2 weekly), 2 achieved CR for 16+ and 18+ months and 2 PR for 2 and 5 months. Toxicity consisted mainly of combined myelo- and immunosuppression but no significant infections occurred and there were no toxic deaths. A cumulative thrombocytopenia was noted, which in 1 case took up to 6 months to resolve. Transient gastrointestinal toxicity and elevation of liver enzymes was seen, and 2 patients developed renal tubular acidosis. The peripheral neuropathy reported in adult patients receiving high doses was not seen. 2-CdA and 2'-DCF appear to have a useful role in LCH and are worthy of prospective trial in patients unresponsive to routine therapy. Copyright 1999 Wiley-Liss, Inc.

A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.

PubMed

Gupta, Amita; Shrivastava, Nimisha; Grover, Payal; Singh, Ajay; Mathur, Kapil; Verma, Vaishali; Kaur, Charanpreet; Chaudhary, Vijay K

2013-01-01

Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.

Comparison of a semi-automatic annotation tool and a natural language processing application for the generation of clinical statement entries.

PubMed

Lin, Ching-Heng; Wu, Nai-Yuan; Lai, Wei-Shao; Liou, Der-Ming

2015-01-01

Electronic medical records with encoded entries should enhance the semantic interoperability of document exchange. However, it remains a challenge to encode the narrative concept and to transform the coded concepts into a standard entry-level document. This study aimed to use a novel approach for the generation of entry-level interoperable clinical documents. Using HL7 clinical document architecture (CDA) as the example, we developed three pipelines to generate entry-level CDA documents. The first approach was a semi-automatic annotation pipeline (SAAP), the second was a natural language processing (NLP) pipeline, and the third merged the above two pipelines. We randomly selected 50 test documents from the i2b2 corpora to evaluate the performance of the three pipelines. The 50 randomly selected test documents contained 9365 words, including 588 Observation terms and 123 Procedure terms. For the Observation terms, the merged pipeline had a significantly higher F-measure than the NLP pipeline (0.89 vs 0.80, p<0.0001), but a similar F-measure to that of the SAAP (0.89 vs 0.87). For the Procedure terms, the F-measure was not significantly different among the three pipelines. The combination of a semi-automatic annotation approach and the NLP application seems to be a solution for generating entry-level interoperable clinical documents. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.comFor numbered affiliation see end of article.

Current practice of cervical disc arthroplasty: a survey among 383 AOSpine International members.

PubMed

Chin-See-Chong, Timothy C; Gadjradj, Pravesh S; Boelen, Robert J; Harhangi, Biswadjiet S

2017-02-01

OBJECTIVE The use of cervical disc arthroplasty (CDA) in spinal practice is controversial. This may be explained by the lack of studies with a large sample size and long-term outcomes. With this survey the authors aimed to evaluate the opinions of spine surgeons on the use of CDA in the current treatment of cervical disc herniation (CDH). METHODS A web-based survey was sent to all members of AOSpine International by email using SurveyMonkey on July 18, 2016. A single reminder was sent on August 18, 2016. Questions included geographic location; specialty; associated practice model; number of discectomies performed annually; the use of CDA, anterior cervical discectomy (ACD), and anterior cervical discectomy and fusion (ACDF); and the expectations for clinical outcomes of these procedures. RESULTS A total of 383 questionnaires were analyzed. Almost all practitioners (97.9%) were male, with a mean of 15.0 ± 9.7 years of clinical experience. The majority of responders were orthopedic surgeons (54.6%). 84.3% performed ACDF as the standard technique for CDH. 47.8% of the surgeons occasionally used CDA, whereas 7.3% used CDA as standard approach for CDH. The most common arthroplasty device used was the ProDisc-C. Low evidence for benefits and higher costs were the most important reasons for not offering CDA. The risk of adjacent-level disease was considered smaller for CDA as compared with ACDF. However, ACDF was expected to have the highest effectiveness on arm pain (87.5%), followed by CDA (77.9%), while ACD had the least (12.6%). CONCLUSIONS In this survey, CDA was not considered to be the routine procedure to treat CDH. Reported benefits included the reduced risk of adjacent-level disease and preservation of motion of the neck. Lack of enough evidence on its effectiveness as well as higher costs were considered to be disadvantages of CDA. More research should be conducted on the implementation impact of CDA and the cost-effectiveness from society's perspective.

Correlation between cervical lordosis and adjacent segment pathology after anterior cervical spinal surgery.

PubMed

Lee, Soo Eon; Jahng, Tae-Ahn; Kim, Hyun Jib

2015-12-01

To evaluate the incidence and risk factors for adjacent segment pathology (ASP) after anterior cervical spinal surgery. Fourteen patients (12 male, mean age 47.1 years) who underwent single-level cervical disk arthroplasty (CDA group) and 28 case-matched patients (24 male, mean age 53.6 years) who underwent single-level anterior cervical discectomy and fusion (ACDF group) were included. Presence of radiologic ASP (RASP) was based on observed changes in anterior osteophytes, disks, and calcification of the anterior longitudinal ligament on lateral radiographs. The mean follow-up period was 43.4 months in the CDA group and 44.6 months in the ACDF group. At final follow-up, ASP was observed in 5 (35.7%) CDA patients and 16 (57.1%) ACDF patients (p = 0.272). The interval between surgery and ASP development was 33.8 months in the CDA group and 16.3 months in the ACDF group (p = 0.046). The ASP risk factor analysis indicated postoperative cervical angle at C3-7 being more lordotic in non-ASP patients in both groups. Restoration of lordosis occurred in the CDA group regardless of the presence of ASP, but heterotopic ossification development was associated with the presence of ASP in the CDA group. And the CDA group had significantly greater clinical improvements than those in the ACDF group when ASP was present. In both CDA and ACDF patients, RASP developed, but CDA was associated with a delay in ASP development. A good clinical outcome was expected in CDA group, even when ASP developed. Restoration of cervical lordosis was an important factor in anterior cervical spine surgery.

Application of portable CDA for secure clinical-document exchange.

PubMed

Huang, Kuo-Hsuan; Hsieh, Sung-Huai; Chang, Yuan-Jen; Lai, Feipei; Hsieh, Sheau-Ling; Lee, Hsiu-Hui

2010-08-01

Health Level Seven (HL7) organization published the Clinical Document Architecture (CDA) for exchanging documents among heterogeneous systems and improving medical quality based on the design method in CDA. In practice, although the HL7 organization tried to make medical messages exchangeable, it is still hard to exchange medical messages. There are many issues when two hospitals want to exchange clinical documents, such as patient privacy, network security, budget, and the strategies of the hospital. In this article, we propose a method for the exchange and sharing of clinical documents in an offline model based on the CDA-the Portable CDA. This allows the physician to retrieve the patient's medical record stored in a portal device, but not through the Internet in real time. The security and privacy of CDA data will also be considered.

Anterior cervical discectomy and fusion (ACDF) versus cervical disc arthroplasty (CDA) for two contiguous levels cervical disc degenerative disease: a meta-analysis of randomized controlled trials.

PubMed

Zou, Shihua; Gao, Junyi; Xu, Bin; Lu, Xiangdong; Han, Yongbin; Meng, Hui

2017-04-01

Anterior cervical discectomy and fusion (ACDF) has been considered as a gold standard for symptomatic cervical disc degeneration (CDD), which may result in progressive degeneration of the adjacent segments. The artificial cervical disc was designed to reduce the number of lesions in the adjacent segments. Clinical studies have demonstrated equivalence of cervical disc arthroplasty (CDA) for anterior cervical discectomy and fusion in single segment cervical disc degeneration. But for two contiguous levels cervical disc degeneration (CDD), which kind of treatment method is better is controversial. To evaluate the clinical effects requiring surgical intervention between anterior cervical discectomy and fusion (ACDF) and cervical disc arthroplasty (CDA) at two contiguous levels cervical disc degeneration. We conducted a comprehensive search in multiple databases, including PubMed, Cochrane Central Register of Controlled Trials, EBSCO and EMBASE. We identified that six reports meet inclusion criteria. Two independent reviewers performed the data extraction from archives. Data analysis was conducted with RevMan 5.3. After applying inclusion and exclusion criteria, six papers were included in meta-analyses. The overall sample size at baseline was 650 patients (317 in the TDR group and 333 in the ACDF group). The results of the meta-analysis indicated that the CDA patients had significant superiorities in mean blood loss (P < 0.00001, standard mean differences (SMD) = -0.85, 95 % confidence interval (CI) = -1.22 to -0.48); reoperation (P = 0.0009, risk ratio (RR) = 0.28, 95 % confidence interval (CI) = 0.13-0.59), adjacent segment degeneration (P < 0.00001, risk ratio (RR) = 0.48, 95 % confidence interval (CI) = 0.40-0.58) and Neck Disability Index (P = 0.002, SMD = 0.31, 95 % CI = 0.12-0.50). No significant difference was identified between the two groups regarding mean surgical time (P = 0.84, SMD = -0.04, 95 % CI = -0.40 to 0.32), neck and arm pain scores (P = 0.52, SMD = 0.06, 95 % CI = -0.13 to 0.25) reported on a visual analog scale and rate of postoperative complications [risk ratio (RR) = 0.79; 95 % CI = 0.50-1.25; P = 0.31]. The CDA group of sagittal range of motion (ROM) of the operated and adjacent levels, functional segment units (FSU) and C2-7 is superior to ACDF group by radiographic data of peroperation, postoperation and follow-up. We can learn from this meta-analysis that the cervical disc arthroplasty (CDA) group is equivalent and in some aspects has more significant clinical outcomes than the ACDF group at two contiguous levels CDD.

Glucose-6-phosphate dehydrogenase deficiency, chlorproguanil-dapsone with artesunate and post-treatment haemolysis in African children treated for uncomplicated malaria.

PubMed

Van Malderen, Carine; Van Geertruyden, Jean-Pierre; Machevo, Sonia; González, Raquel; Bassat, Quique; Talisuna, Ambrose; Yeka, Adoke; Nabasumba, Carolyn; Piola, Patrice; Daniel, Atwine; Turyakira, Eleanor; Forret, Pascale; Van Overmeir, Chantal; van Loen, Harry; Robert, Annie; D' Alessandro, Umberto

2012-07-10

Malaria is a leading cause of mortality, particularly in sub-Saharan African children. Prompt and efficacious treatment is important as patients may progress within a few hours to severe and possibly fatal disease. Chlorproguanil-dapsone-artesunate (CDA) was a promising artemisinin-based combination therapy (ACT), but its development was prematurely stopped because of safety concerns secondary to its associated risk of haemolytic anaemia in glucose-6-phosphate dehydrogenase (G6PD)-deficient individuals. The objective of the study was to assess whether CDA treatment and G6PD deficiency are risk factors for a post-treatment haemoglobin drop in African children<5 years of age with uncomplicated malaria. This case-control study was performed in the context of a larger multicentre randomized clinical trial comparing safety and efficacy of four different ACT in children with uncomplicated malaria. Children, who after treatment experienced a haemoglobin drop≥2 g/dl (cases) within the first four days (days 0, 1, 2, and 3), were compared with those without an Hb drop (controls). Cases and controls were matched for study site, sex, age and baseline haemoglobin measurements. Data were analysed using a conditional logistic regression model. G6PD deficiency prevalence, homo- or hemizygous, was 8.5% (10/117) in cases and 6.8% (16/234) in controls (p=0.56). The risk of a Hb drop≥2 g/dl was not associated with either G6PD deficiency (adjusted odds ratio (AOR): 0.81; p=0.76) or CDA treatment (AOR: 1.28; p=0.37) alone. However, patients having both risk factors tended to have higher odds (AOR: 11.13; p=0.25) of experiencing a Hb drop≥2 g/dl within the first four days after treatment, however this finding was not statistically significant, mainly because G6PD deficient patients treated with CDA were very few. In non-G6PD deficient individuals, the proportion of cases was similar between treatment groups while in G6PD-deficient individuals, haemolytic anaemia occurred more frequently in children treated with CDA (56%) than in those treated with other ACT (29%), though the difference was not significant (p=0.49). The use of CDA for treating uncomplicated malaria may increase the risk of haemolytic anaemia in G6PD-deficient children.

A combination of cis-2-decenoic acid and antibiotics eradicates pre-established catheter-associated biofilms.

PubMed

Rahmani-Badi, Azadeh; Sepehr, Shayesteh; Mohammadi, Parisa; Soudi, Mohammad Reza; Babaie-Naiej, Hamta; Fallahi, Hossein

2014-11-01

The catheterized urinary tract provides ideal conditions for the development of biofilm populations. Catheter-associated urinary tract infections (CAUTIs) are recalcitrant to existing antimicrobial treatments; therefore, established biofilms are not eradicated completely after treatment and surviving biofilm cells will carry on the infection. Cis-2-decenoic acid (CDA), an unsaturated fatty acid, is capable of inhibiting biofilm formation by Pseudomonas aeruginosa and of inducing the dispersion of established biofilms by multiple types of micro-organisms. Here, the ability of CDA to induce dispersal in pre-established single- and dual-species biofilms formed by Escherichia coli and Klebsiella pneumoniae was measured by using both semi-batch and continuous cultures bioassays. Removal of the biofilms by combined CDA and antibiotics (ciprofloxacin or ampicillin) was evaluated using microtitre plate assays (crystal violet staining). The c.f.u. counts were determined to assess the potential of combined CDA treatments to kill and eradicate pre-established biofilms formed on catheters. The effects of combined CDA treatments on biofilm surface area and bacteria viability were evaluated using fluorescence microscopy, digital image analysis and live/dead staining. To investigate the ability of CDA to prevent biofilm formation, single and mixed cultures were grown in the presence and absence of CDA. Treatment of pre-established biofilms with only 310 nM CDA resulted in at least threefold increase in the number of planktonic cells in all cultures tested. Whilst none of the antibiotics alone exerted a significant effect on c.f.u. counts and percentage of surface area covered by the biofilms, combined CDA treatments led to at least a 78% reduction in biofilm biomass in all cases. Moreover, most of the biofilm cells remaining on the surface were killed by antibiotics. The addition of 310 nM CDA significantly prevented biofilm formation by the tested micro-organisms, even within mixed cultures, indicating the ability of CDA to inhibit biofilm formation by other types of bacteria in addition to Pseudomonas aeruginosa. These findings suggested that the biofilm-preventive characteristics of CDA make it a noble candidate for inhibition of biofilm-associated infections such as CAUTIs, which paves the way toward developing new strategies to control biofilms in clinical as well as industrial settings. © 2014 The Authors.

Perceptions on efficacy and side effects of conventional depot antipsychotics (CDA) and atypical depot antipsychotics (ADA): Psychiatrists versus patients in Hong Kong.

PubMed

Tsang, Hector W H; Fong, Mandy W M; Fung, Kelvin M T; Chung, Raymond C K

2010-03-01

Abstract Objectives. We compared the satisfaction level of psychiatrists and psychiatric patients towards conventional (CDA) and atypical (ADA) depot antipsychotics on symptom management, role functioning, and side effects. Method. Patients from an out-patient clinic of a public hospital and psychiatrists from public hospitals participated in the survey in 2007-2008. A total of 153 patients were interviewed by a tailor-made questionnaire and 72 psychiatrists self-administered a similar questionnaire. Results. Both groups shared similar attitudes towards clinical effectiveness and treatment efficacy of ADA and CDA. More patients were ambivalent towards relapse prevention of CDA than psychiatrists (30.7 vs. 16.7%, P<0.044) and three quarters of psychiatrists believed that ADA are associated with less side effects. More than half of the patients showed negative attitudes towards the effectiveness of CDA on improving quality of life (52.40%), work (57.50%), and recreation (55.50%). Psychiatrists were more aware of the limitation of CDA and severity of side effects of CDA. They did not, however, seem to incorporate patients' opinions and research findings into their clinical practice. Conclusion. Evidence-based practice and shared decision-making model between clinicians and mental patients should be advocated. More investigations should be devoted to examine the efficacy of ADA as the alternative to CDA.

Cloning and sequencing of a gene encoding a 21-kilodalton outer membrane protein from Bordetella avium and expression of the gene in Salmonella typhimurium.

PubMed Central

Gentry-Weeks, C R; Hultsch, A L; Kelly, S M; Keith, J M; Curtiss, R

1992-01-01

Three gene libraries of Bordetella avium 197 DNA were prepared in Escherichia coli LE392 by using the cosmid vectors pCP13 and pYA2329, a derivative of pCP13 specifying spectinomycin resistance. The cosmid libraries were screened with convalescent-phase anti-B. avium turkey sera and polyclonal rabbit antisera against B. avium 197 outer membrane proteins. One E. coli recombinant clone produced a 56-kDa protein which reacted with convalescent-phase serum from a turkey infected with B. avium 197. In addition, five E. coli recombinant clones were identified which produced B. avium outer membrane proteins with molecular masses of 21, 38, 40, 43, and 48 kDa. At least one of these E. coli clones, which encoded the 21-kDa protein, reacted with both convalescent-phase turkey sera and antibody against B. avium 197 outer membrane proteins. The gene for the 21-kDa outer membrane protein was localized by Tn5seq1 mutagenesis, and the nucleotide sequence was determined by dideoxy sequencing. DNA sequence analysis of the 21-kDa protein revealed an open reading frame of 582 bases that resulted in a predicted protein of 194 amino acids. Comparison of the predicted amino acid sequence of the gene encoding the 21-kDa outer membrane protein with protein sequences in the National Biomedical Research Foundation protein sequence data base indicated significant homology to the OmpA proteins of Shigella dysenteriae, Enterobacter aerogenes, E. coli, and Salmonella typhimurium and to Neisseria gonorrhoeae outer membrane protein III, Haemophilus influenzae protein P6, and Pseudomonas aeruginosa porin protein F. The gene (ompA) encoding the B. avium 21-kDa protein hybridized with 4.1-kb DNA fragments from EcoRI-digested, chromosomal DNA of Bordetella pertussis and Bordetella bronchiseptica and with 6.0- and 3.2-kb DNA fragments from EcoRI-digested, chromosomal DNA of B. avium and B. avium-like DNA, respectively. A 6.75-kb DNA fragment encoding the B. avium 21-kDa protein was subcloned into the Asd+ vector pYA292, and the construct was introduced into the avirulent delta cya delta crp delta asd S. typhimurium chi 3987 for oral immunization of birds. The gene encoding the 21-kDa protein was expressed equivalently in B. avium 197, delta asd E. coli chi 6097, and S. typhimurium chi 3987 and was localized primarily in the cytoplasmic membrane and outer membrane. In preliminary studies on oral inoculation of turkey poults with S. typhimurium chi 3987 expressing the gene encoding the B. avium 21-kDa protein, it was determined that a single dose of the recombinant Salmonella vaccine failed to elicit serum antibodies against the 21-kDa protein and challenge with wild-type B. avium 197 resulted in colonization of the trachea and thymus with B. avium 197. Images PMID:1447140

Unsaturated fatty acid, cis-2-decenoic acid, in combination with disinfectants or antibiotics removes pre-established biofilms formed by food-related bacteria.

PubMed

Sepehr, Shayesteh; Rahmani-Badi, Azadeh; Babaie-Naiej, Hamta; Soudi, Mohammad Reza

2014-01-01

Biofilm formation by food-related bacteria and food-related pathogenesis are significant problems in the food industry. Even though much disinfection and mechanical procedure exist for removal of biofilms, they may fail to eliminate pre-established biofilms. cis-2 decenoic acid (CDA), an unsaturated fatty acid messenger produced by Pseudomonas aeruginosa, is reportedly capable of inducing the dispersion of established biofilms by multiple types of microorganisms. However, whether CDA has potential to boost the actions of certain antimicrobials is unknown. Here, the activity of CDA as an inducer of pre-established biofilms dispersal, formed by four main food pathogens; Staphylococcus aureus, Bacillus cereus, Salmonella enterica and E. coli, was measured using both semi-batch and continuous cultures bioassays. To assess the ability of CDA combined biocides treatments to remove pre-established biofilms formed on stainless steel discs, CFU counts were performed for both treated and untreated cultures. Eradication of the biofilms by CDA combined antibiotics was evaluated using crystal violet staining. The effect of CDA combined treatments (antibiotics and disinfectants) on biofilm surface area and bacteria viability was evaluated using fluorescence microscopy, digital image analysis and LIVE/DEAD staining. MICs were also determined to assess the probable inhibitory effects of CDA combined treatments on the growth of tested microorganisms' planktonic cells. Treatment of pre-established biofilms with only 310 nM CDA resulted in at least two-fold increase in the number of planktonic cells in all cultures. While antibiotics or disinfectants alone exerted a trivial effect on CFU counts and percentage of surface area covered by the biofilms, combinational treatments with both 310 nM CDA and antibiotics or disinfectants led to approximate 80% reduction in biofilm biomass. These data suggests that combined treatments with CDA would pave the way toward developing new strategies to control biofilms with widespread applications in industry as well as medicine.

Unsaturated Fatty Acid, cis-2-Decenoic Acid, in Combination with Disinfectants or Antibiotics Removes Pre-Established Biofilms Formed by Food-Related Bacteria

PubMed Central

Sepehr, Shayesteh; Rahmani-Badi, Azadeh; Babaie-Naiej, Hamta; Soudi, Mohammad Reza

2014-01-01

Biofilm formation by food-related bacteria and food-related pathogenesis are significant problems in the food industry. Even though much disinfection and mechanical procedure exist for removal of biofilms, they may fail to eliminate pre-established biofilms. cis-2 decenoic acid (CDA), an unsaturated fatty acid messenger produced by Pseudomonas aeruginosa, is reportedly capable of inducing the dispersion of established biofilms by multiple types of microorganisms. However, whether CDA has potential to boost the actions of certain antimicrobials is unknown. Here, the activity of CDA as an inducer of pre-established biofilms dispersal, formed by four main food pathogens; Staphylococcus aureus, Bacillus cereus, Salmonella enterica and E. coli, was measured using both semi-batch and continuous cultures bioassays. To assess the ability of CDA combined biocides treatments to remove pre-established biofilms formed on stainless steel discs, CFU counts were performed for both treated and untreated cultures. Eradication of the biofilms by CDA combined antibiotics was evaluated using crystal violet staining. The effect of CDA combined treatments (antibiotics and disinfectants) on biofilm surface area and bacteria viability was evaluated using fluorescence microscopy, digital image analysis and LIVE/DEAD staining. MICs were also determined to assess the probable inhibitory effects of CDA combined treatments on the growth of tested microorganisms' planktonic cells. Treatment of pre-established biofilms with only 310 nM CDA resulted in at least two-fold increase in the number of planktonic cells in all cultures. While antibiotics or disinfectants alone exerted a trivial effect on CFU counts and percentage of surface area covered by the biofilms, combinational treatments with both 310 nM CDA and antibiotics or disinfectants led to approximate 80% reduction in biofilm biomass. These data suggests that combined treatments with CDA would pave the way toward developing new strategies to control biofilms with widespread applications in industry as well as medicine. PMID:25000301

Para Candidatos en Programas de Centros de Cuidado y Educacion Infantil con Bebes y "Toddlers": Asociado en Desarrollo Infantil Sistema de Evaluacion y Normas de Competencia CDA (Infant/Toddler Caregivers in Center-Based Programs: The Child Development Associate Assessment System and Competency Standards).

ERIC Educational Resources Information Center

Council for Early Childhood Professional Recognition, Washington, DC.

This Spanish-language booklet outlines the requirements of the Child Development Associate (CDA) credential for caregivers working in center-based infant and toddler day care programs. Part 1 provides an overview of the CDA credentialing system and the various options, settings, standards, and stages of the CDA assessment system. Part 2 explains…

Bridging the Gap between HL7 CDA and HL7 FHIR: A JSON Based Mapping.

PubMed

Rinner, Christoph; Duftschmid, Georg

2016-01-01

The Austrian electronic health record (EHR) system ELGA went live in December 2016. It is a document oriented EHR system and is based on the HL7 Clinical Document Architecture (CDA). The HL7 Fast Healthcare Interoperability Resources (FHIR) is a relatively new standard that combines the advantages of HL7 messages and CDA Documents. In order to offer easier access to information stored in ELGA we present a method based on adapted FHIR resources to map CDA documents to FHIR resources. A proof-of-concept tool using Java, the open-source FHIR framework HAPI-FHIR and publicly available FHIR servers was created to evaluate the presented mapping. In contrast to other approaches the close resemblance of the mapping file to the FHIR specification allows existing FHIR infrastructure to be reused. In order to reduce information overload and facilitate the access to CDA documents, FHIR could offer a standardized way to query CDA data on a fine granular base in Austria.

A chitin deacetylase of Podospora anserina has two functional chitin binding domains and a unique mode of action.

PubMed

Hoßbach, Janina; Bußwinkel, Franziska; Kranz, Andreas; Wattjes, Jasper; Cord-Landwehr, Stefan; Moerschbacher, Bruno M

2018-03-01

Chitosan is a structurally diverse biopolymer that is commercially derived from chitin by chemical processing, but chitin deacetylases (CDAs) potentially offer a sustainable and more controllable approach allowing the production of chitosans with tailored structures and biological activities. We investigated the CDA from Podospora anserina (PaCDA) which is closely related to Colletotrichum lindemuthianum CDA in the catalytic domain, but unique in having two chitin-binding domains. We produced recombinant PaCDA in Hansenula polymorpha for biochemical characterization and found that the catalytic domain of PaCDA is also functionally similar to C. lindemuthianum CDA, though differing in detail. When studying the enzyme's mode of action on chitin oligomers by quantitative mass-spectrometric sequencing, we found almost all possible sequences up to full deacetylation but with a clear preference for specific products. Deletion muteins lacking one or both CBDs confirmed their proposed function in supporting the enzymatic conversion of the insoluble substrate colloidal chitin. Copyright © 2017. Published by Elsevier Ltd.

Dark and grey compressional dispersive Alfven solitons in plasmas

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

Shukla, P. K.; Eliasson, B.; Stenflo, L.

2011-06-15

The amplitude modulation of compressional dispersive Alfven (CDA) waves in a low-{beta} plasma is considered. It is shown that the dynamics of modulated CDA waves is governed by a cubic nonlinear Schroedinger equation, which depicts the formation of a dark/grey envelope CDA soliton.

Para Candidatos en Programas de Centros de Cuidado y Educacion Infantil con Ninos de Edad Pre-escolar: Asociado en Desarrollo Infantil Sistema de Evaluacion y Normas de Competencia CDA (Preschool Caregivers in Center-Based Programs: The Child Development Associate Assessment System and Competency Standards).

ERIC Educational Resources Information Center

Council for Early Childhood Professional Recognition, Washington, DC.

This Spanish-language booklet outlines the requirements of the Child Development Associate (CDA) credential for preschool teachers or caregivers who work in center-based preschool day care programs. Part 1 provides an overview of the CDA credentialing system and the various options, settings, standards, and stages of the CDA assessment system.…

Cladribine in a weekly versus daily schedule for untreated active hairy cell leukemia: final report from the Polish Adult Leukemia Group (PALG) of a prospective, randomized, multicenter trial.

PubMed

Robak, Tadeusz; Jamroziak, Krzysztof; Gora-Tybor, Joanna; Blonski, Jerzy Z; Kasznicki, Marek; Dwilewicz-Trojaczek, Jadwiga; Wiater, Elzbieta; Zdunczyk, Andrzej; Dybowicz, Jacek; Dmoszynska, Anna; Wojtaszko, Maria; Zdziarska, Barbara; Calbecka, Malgorzata; Kostyra, Aleksandra; Hellmann, Andrzej; Lewandowski, Krzysztof; Stella-Holowiecka, Beata; Sulek, Kazimierz; Gawronski, Krzysztof; Skotnicki, Aleksander B; Nowak, Wieslaw; Zawilska, Krystyna; Molendowicz-Portala, Lucyna; Kloczko, Janusz; Sokolowski, Jaroslaw; Warzocha, Krzysztof; Seferynska, Ilona; Ceglarek, Bernardeta; Konopka, Lech

2007-05-01

Cladribine (2-chlorodeoxyadenosine, 2-CdA) treatment-associated infections may shorten potentially long-term survival in hairy cell leukemia (HCL). In search of the optimal mode of 2-CdA administration, 132 patients with untreated HCL were randomized to receive either standard 5-day 2-CdA protocol or a novel schedule of 6 weekly 2-CdA infusions suggested to be less toxic. Analysis of treatment response confirmed similar complete remission rates, overall response rates, progression-free survival, and overall survival in both 2-CdA protocols. However, we did not observe lower toxicity in the weekly schedule. Of special interest, no significant differences were found in the rate of grade 3/4 infections (18% for daily and 26% for weekly protocol, difference -8.2%; 95% confidence interval [CI] -23.2% to 6.9%; P = .28) and the rate of septic deaths (3% for daily and 2% for weekly protocol, difference 1.4%; 95% CI -4.3% to 7.0%; P = .64). In conclusion, HCL treatment with weekly 2-CdA infusions is equally effective but no safer than the standard 5-day 2-CdA protocol.

Photorhabdus insect-related (Pir) toxin-like genes in a plasmid of Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (AHPND) of shrimp

PubMed Central

Han, Jee Eun; Tang, Kathy F. J.; Tran, Loc H.; Lightner, Donald V.

2016-01-01

The 69 kb plasmid pVPA3-1 was identified in Vibrio parahaemolyticus strain 13-028/A3 that can cause acute hepatopancreatic necrosis disease (AHPND). This disease is responsible for mass mortalities in farmed penaeid shrimp and is referred to as early mortality syndrome (EMS). The plasmid has a GC content of 45.9% with a copy number of 37 per bacterial cell as determined by comparative quantitative PCR analyses. It consists of 92 open reading frames that encode mobilization proteins, replication enzymes, transposases, virulence-associated proteins, and proteins similar to Photorhabdus insect-related (Pir) toxins. In V. parahaemolyticus, these Pir toxin-like proteins are encoded by 2 genes ( pirA- and pirB-like) located within a 3.5 kb fragment flanked with inverted repeats of a transposase-coding sequence (1 kb). The GC content of these 2 genes is only 38.2%, substantially lower than that of the rest of the plasmid, which suggests that these genes were recently acquired. Based on a proteomic analysis, the pirA-like (336 bp) and pirB-like (1317 bp) genes encode for 13 and 50 kDa proteins, respectively. In laboratory cultures of V. parahaemolyticus 13-028/A3, both proteins were secreted into the culture medium. We developed a duplex PCR diagnostic method, with a detection limit of 105 CFU ml−1 and targeting pirA- and pirB-like genes in this strain of V. parahaemolyticus. This PCR protocol can reliably detect AHPND-causing strains of V. parahaemolyticus and does not cross react with non-pathogenic strains or with other species of Vibrio isolated from shrimp ponds. PMID:25667334

The effect of cervical posterior foraminotomy on segmental range of motion in the setting of total disc arthroplasty.

PubMed

Bevevino, Adam J; Lehman, Ronald A; Kang, Daniel G; Gwinn, David E; Dmitriev, Anton E

2014-09-01

Human cadaveric biomechanical analysis. To investigate the effect on cervical spine segmental stability that results from a posterior foraminotomy after cervical disc arthroplasty (CDA). Posterior foraminotomy offers the ability to decompress cervical nerves roots while avoiding the need to extend a previous fusion or revise an arthroplasty to a fusion. However, the safety of a foraminotomy in the setting of CDA is unknown. Segmental nondestructive range of motion (ROM) was analyzed in 9 human cadaveric cervical spine specimens. After intact testing, each specimen was sequentially tested according to the following 4 experimental groups: group 1=C5-C6 CDA, group 2=C5-C6 CDA with unilateral C5-C6 foraminotomy, group 3=C5-C6 CDA with bilateral C5-C6 foraminotomy, and group 4=C5-C6 CDA with C5-C6 and C4-C5 bilateral foraminotomy. No differences in ROM were found between the intact, CDA, and foraminotomy specimens at C4-C5 or C6-C7. There was a step-wise increase in C5-C6 axial rotation from the intact state (8°) to group 4 (12°), although the difference did not reach statistical significance. At C5-C6, the degree of lateral bending remained relatively constant. Flexion and extension at C5-C6 was significantly higher in the foraminotomy specimens, groups 2 (18.1°), 3 (18.6°), and 4 (18.2°), compared with the intact state, 11.2°. However, no ROM difference was found within foraminotomy groups (2-4) or between the foraminotomy groups and the CDA group (group 1), 15.3°. Our results indicate that cervical stability is not significantly decreased by the presence, number, or level of posterior foraminotomies in the setting of CDA. The addition of foraminotomies to specimens with a pre-existing CDA resulted in small and insignificant increases in segmental ROM. Therefore, biomechanically, posterior foraminotomy/foraminotomies may be considered a safe and viable option in the setting of recurrent or adjacent level radiculopathy after cervical disc replacement. N/A.

Lactobacillus casei Ferments the N-Acetylglucosamine Moiety of Fucosyl-α-1,3-N-Acetylglucosamine and Excretes l-Fucose

PubMed Central

Rodríguez-Díaz, Jesús; Rubio-del-Campo, Antonio

2012-01-01

We have previously characterized from Lactobacillus casei BL23 three α-l-fucosidases, AlfA, AlfB, and AlfC, which hydrolyze in vitro natural fucosyl-oligosaccharides. In this work, we have shown that L. casei is able to grow in the presence of fucosyl-α-1,3-N-acetylglucosamine (Fuc-α-1,3-GlcNAc) as a carbon source. Interestingly, L. casei excretes the l-fucose moiety during growth on Fuc-α-1,3-GlcNAc, indicating that only the N-acetylglucosamine moiety is being metabolized. Analysis of the genomic sequence of L. casei BL23 shows that downstream from alfB, which encodes the α-l-fucosidase AlfB, a gene, alfR, that encodes a transcriptional regulator is present. Divergently from alfB, three genes, alfEFG, that encode proteins with homology to the enzyme IIAB (EIIAB), EIIC, and EIID components of a mannose-class phosphoenolpyruvate:sugar phosphotransferase system (PTS) are present. Inactivation of either alfB or alfF abolishes the growth of L. casei on Fuc-α-1,3-GlcNAc. This proves that AlfB is involved in Fuc-α-1,3-GlcNAc metabolism and that the transporter encoded by alfEFG participates in the uptake of this disaccharide. A mutation in the PTS general component enzyme I does not eliminate the utilization of Fuc-α-1,3-GlcNAc, suggesting that the transport via the PTS encoded by alfEFG is not coupled to phosphorylation of the disaccharide. Transcriptional analysis with alfR and ccpA mutants shows that the two gene clusters alfBR and alfEFG are regulated by substrate-specific induction mediated by the inactivation of the transcriptional repressor AlfR and by carbon catabolite repression mediated by the catabolite control protein A (CcpA). This work reports for the first time the characterization of the physiological role of an α-l-fucosidase in lactic acid bacteria and the utilization of Fuc-α-1,3-GlcNAc as a carbon source for bacteria. PMID:22544237

New Policies Allow High School Child Development Programs to Provide CDA Licensure

ERIC Educational Resources Information Center

Langlais, Amanda G.

2012-01-01

Recent changes made by the Council for Professional Recognition to the Child Development Associate (CDA) credentialing program create an opportunity to redesign high school child development programs. On April 1, 2011, the Council for Professional Recognition lifted the age restriction in the CDA credentialing requirements, now allowing students…

Effect of a new moisturizing lotion on immediate and cumulative skin hydration: Two randomized, intra-individual, vehicle- and comparator-controlled studies.

PubMed

Nogueira, Alessandra; Sidou, Farzaneh; Brocard, Sylvie

2011-08-01

Moisturizers increase skin hydration and can serve as adjunctive care in dermatologic conditions such as xerosis, psoriasis vulgaris, atopic dermatitis and ichthyosis, in which dry skin is implicated. A non-irritating hydrating lotion (CDA lotion) was recently developed. We assessed the effect of CDA lotion on skin hydration in two randomized, evaluator-blind and intra-individual comparison studies. After a single application, CDA lotion induced significantly greater hydration than the non-treated control for at least 24 hours (p < 0.001). After 4 days of twice-daily application, compared with the non-treated control, CDA lotion induced significantly greater skin hydration up to 3 days after treatment cessation (p < 0.05) and significant improvement in the clinical skin dryness score up to 7 days after treatment cessation (p < 0.05). The immediate and cumulative hydration effects of CDA lotion were also compared to those of several currently available moisturizing products. In summary, application of CDA lotion increases skin hydration and alleviates the condition of skin dryness.

Staphylococcus aureus innate immune evasion is lineage-specific: a bioinfomatics study.

PubMed

McCarthy, Alex J; Lindsay, Jodi A

2013-10-01

Staphylococcus aureus is a major human pathogen, and is targeted by the host innate immune system. In response, S. aureus genomes encode dozens of secreted proteins that inhibit complement, chemotaxis and neutrophil activation resulting in successful evasion of innate immune responses. These proteins include immune evasion cluster proteins (IEC; Chp, Sak, Scn), staphylococcal superantigen-like proteins (SSLs), phenol soluble modulins (PSMs) and several leukocidins. Biochemical studies have indicated that genetic variants of these proteins can have unique functions. To ascertain the scale of genetic variation in secreted immune evasion proteins, whole genome sequences of 88 S. aureus isolates, representing 25 clonal complex (CC) lineages, in the public domain were analysed across 43 genes encoding 38 secreted innate immune evasion protein complexes. Twenty-three genes were variable, with between 2 and 15 variants, and the variants had lineage-specific distributions. They include genes encoding Eap, Ecb, Efb, Flipr/Flipr-like, Hla, Hld, Hlg, Sbi, Scin-B/C and 13 SSLs. Most of these protein complexes inhibit complement, chemotaxis and neutrophil activation suggesting that isolates from each S. aureus lineage respond to the innate immune system differently. In contrast, protein complexes that lyse neutrophils (LukSF-PVL, LukMF, LukED and PSMs) were highly conserved, but can be carried on mobile genetic elements (MGEs). MGEs also encode proteins with narrow host-specificities arguing that their acquisition has important roles in host/environmental adaptation. In conclusion, this data suggests that each lineage of S. aureus evades host immune responses differently, and that isolates can adapt to new host environments by acquiring MGEs and the immune evasion protein complexes that they encode. Cocktail therapeutics that targets multiple variant proteins may be the most appropriate strategy for controlling S. aureus infections. Copyright © 2013 Elsevier B.V. All rights reserved.

Solid-state surface luminescence of polycyclic aromatic hydrocarbons adsorbed on cellulose diacetate matrices

NASA Astrophysics Data System (ADS)

Rogacheva, Svetlana M.; Shipovskaya, Anna B.; Volkova, Elena V.; Khurshudyan, Grachia N.; Suska-Malawska, Malgorzata; Gubina, Tamara I.

2018-04-01

The spectral-kinetic characteristics of luminescence of 17 polycyclic aromatic hydrocarbons (PAH) sorbed from a "water-organic solvent" medium on cellulose diacetate (CDA) matrices were studied. A significant increase in the fluorescence signal on the CDA matrix was observed for 13 PAHs in comparison with aqueous solutions. The highest detection sensitivity was found for pyrene, benzo(a)pyrene, and benzo(k)fluoranthene. The fluorescence spectra of two PAH indicator pairs (anthracene-phenanthrene and pyrene-fluoranthene) used to control toxicant emission sources were studied with the simultaneous presence of isomers in the analyte, depending on the excitation wavelength. For both isomer pairs, it has been found that the spectra of their solid-state luminescence overlap insignificantly, the characteristic peaks do not coincide and do not overlap, the sensitivities of detection are close to each other, which makes it possible to consider this technique as promising to control PAH contamination sources.

Isolation and characterization of major histocompatibility complex class IIB genes from the nurse shark.

PubMed

Bartl, S; Weissman, I L

1994-01-04

The major histocompatibility complex (MHC) contains a set of linked genes which encode cell surface proteins involved in the binding of small peptide antigens for their subsequent recognition by T lymphocytes. MHC proteins share structural features and the presence and location of polymorphic residues which play a role in the binding of antigens. In order to compare the structure of these molecules and gain insights into their evolution, we have isolated two MHC class IIB genes from the nurse shark, Ginglymostoma cirratum. Two clones, most probably alleles, encode proteins which differ by 13 amino acids located in the putative antigen-binding cleft. The protein structure and the location of polymorphic residues are similar to their mammalian counterparts. Although these genes appear to encode a typical MHC protein, no T-cell-mediated responses have been demonstrated in cartilaginous fish. The nurse shark represents the most phylogenetically primitive organism in which both class IIA [Kasahara, M., Vazquez, M., Sato, K., McKinney, E.C. & Flajnik, M.F. (1992) Proc. Natl. Acad. Sci USA 89, 6688-6692] and class IIB genes, presumably encoding the alpha/beta heterodimer, have been isolated.

Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L

USDA-ARS?s Scientific Manuscript database

Cytoplasmic male sterility (CMS) is a maternally inherited inability to produce functional pollen. In T-cytoplasm maize, CMS results from the action of the URF13 mitochondrial pore-forming protein, encoded by the unique T-urf13 mitochondrial gene. Full or partial restoration of fertility to T-cyto...

UNC-13L, UNC-13S, and Tomosyn form a protein code for fast and slow neurotransmitter release in Caenorhabditis elegans

PubMed Central

Hu, Zhitao; Tong, Xia-Jing; Kaplan, Joshua M

2013-01-01

Synaptic transmission consists of fast and slow components of neurotransmitter release. Here we show that these components are mediated by distinct exocytic proteins. The Caenorhabditis elegans unc-13 gene is required for SV exocytosis, and encodes long and short isoforms (UNC-13L and S). Fast release was mediated by UNC-13L, whereas slow release required both UNC-13 proteins and was inhibited by Tomosyn. The spatial location of each protein correlated with its effect. Proteins adjacent to the dense projection mediated fast release, while those controlling slow release were more distal or diffuse. Two UNC-13L domains accelerated release. C2A, which binds RIM (a protein associated with calcium channels), anchored UNC-13 at active zones and shortened the latency of release. A calmodulin binding site accelerated release but had little effect on UNC-13’s spatial localization. These results suggest that UNC-13L, UNC-13S, and Tomosyn form a molecular code that dictates the timing of neurotransmitter release. DOI: http://dx.doi.org/10.7554/eLife.00967.001 PMID:23951547

Implementation of Medical Information Exchange System Based on EHR Standard

PubMed Central

Han, Soon Hwa; Kim, Sang Guk; Jeong, Jun Yong; Lee, Bi Na; Choi, Myeong Seon; Kim, Il Kon; Park, Woo Sung; Ha, Kyooseob; Cho, Eunyoung; Kim, Yoon; Bae, Jae Bong

2010-01-01

Objectives To develop effective ways of sharing patients' medical information, we developed a new medical information exchange system (MIES) based on a registry server, which enabled us to exchange different types of data generated by various systems. Methods To assure that patient's medical information can be effectively exchanged under different system environments, we adopted the standardized data transfer methods and terminologies suggested by the Center for Interoperable Electronic Healthcare Record (CIEHR) of Korea in order to guarantee interoperability. Regarding information security, MIES followed the security guidelines suggested by the CIEHR of Korea. This study aimed to develop essential security systems for the implementation of online services, such as encryption of communication, server security, database security, protection against hacking, contents, and network security. Results The registry server managed information exchange as well as the registration information of the clinical document architecture (CDA) documents, and the CDA Transfer Server was used to locate and transmit the proper CDA document from the relevant repository. The CDA viewer showed the CDA documents via connection with the information systems of related hospitals. Conclusions This research chooses transfer items and defines document standards that follow CDA standards, such that exchange of CDA documents between different systems became possible through ebXML. The proposed MIES was designed as an independent central registry server model in order to guarantee the essential security of patients' medical information. PMID:21818447

Implementation of Medical Information Exchange System Based on EHR Standard.

PubMed

Han, Soon Hwa; Lee, Min Ho; Kim, Sang Guk; Jeong, Jun Yong; Lee, Bi Na; Choi, Myeong Seon; Kim, Il Kon; Park, Woo Sung; Ha, Kyooseob; Cho, Eunyoung; Kim, Yoon; Bae, Jae Bong

2010-12-01

To develop effective ways of sharing patients' medical information, we developed a new medical information exchange system (MIES) based on a registry server, which enabled us to exchange different types of data generated by various systems. To assure that patient's medical information can be effectively exchanged under different system environments, we adopted the standardized data transfer methods and terminologies suggested by the Center for Interoperable Electronic Healthcare Record (CIEHR) of Korea in order to guarantee interoperability. Regarding information security, MIES followed the security guidelines suggested by the CIEHR of Korea. This study aimed to develop essential security systems for the implementation of online services, such as encryption of communication, server security, database security, protection against hacking, contents, and network security. The registry server managed information exchange as well as the registration information of the clinical document architecture (CDA) documents, and the CDA Transfer Server was used to locate and transmit the proper CDA document from the relevant repository. The CDA viewer showed the CDA documents via connection with the information systems of related hospitals. This research chooses transfer items and defines document standards that follow CDA standards, such that exchange of CDA documents between different systems became possible through ebXML. The proposed MIES was designed as an independent central registry server model in order to guarantee the essential security of patients' medical information.

The RNA-binding protein, ZC3H14, is required for proper poly(A) tail length control, expression of synaptic proteins, and brain function in mice.

PubMed

Rha, Jennifer; Jones, Stephanie K; Fidler, Jonathan; Banerjee, Ayan; Leung, Sara W; Morris, Kevin J; Wong, Jennifer C; Inglis, George Andrew S; Shapiro, Lindsey; Deng, Qiudong; Cutler, Alicia A; Hanif, Adam M; Pardue, Machelle T; Schaffer, Ashleigh; Seyfried, Nicholas T; Moberg, Kenneth H; Bassell, Gary J; Escayg, Andrew; García, Paul S; Corbett, Anita H

2017-10-01

A number of mutations in genes that encode ubiquitously expressed RNA-binding proteins cause tissue specific disease. Many of these diseases are neurological in nature revealing critical roles for this class of proteins in the brain. We recently identified mutations in a gene that encodes a ubiquitously expressed polyadenosine RNA-binding protein, ZC3H14 (Zinc finger CysCysCysHis domain-containing protein 14), that cause a nonsyndromic, autosomal recessive form of intellectual disability. This finding reveals the molecular basis for disease and provides evidence that ZC3H14 is essential for proper brain function. To investigate the role of ZC3H14 in the mammalian brain, we generated a mouse in which the first common exon of the ZC3H14 gene, exon 13 is removed (Zc3h14Δex13/Δex13) leading to a truncated ZC3H14 protein. We report here that, as in the patients, Zc3h14 is not essential in mice. Utilizing these Zc3h14Δex13/Δex13mice, we provide the first in vivo functional characterization of ZC3H14 as a regulator of RNA poly(A) tail length. The Zc3h14Δex13/Δex13 mice show enlarged lateral ventricles in the brain as well as impaired working memory. Proteomic analysis comparing the hippocampi of Zc3h14+/+ and Zc3h14Δex13/Δex13 mice reveals dysregulation of several pathways that are important for proper brain function and thus sheds light onto which pathways are most affected by the loss of ZC3H14. Among the proteins increased in the hippocampi of Zc3h14Δex13/Δex13 mice compared to control are key synaptic proteins including CaMK2a. This newly generated mouse serves as a tool to study the function of ZC3H14 in vivo. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Nutrition in the Early Childhood Setting: Arizona HSST/CDA Competency Based Training Module #15.

ERIC Educational Resources Information Center

Terrell, Ann

The purpose of this Child Development Associate (CDA) training module is to provide the CDA intern with knowledge of how to use nutrition information with children and parents, as well as how to structure and carry out a nutrition program, including mealtime and food preparation activities. Objectives are presented along with suggested activities…

Music and Creative Movement: Arizona HSST/CDA Competency Based Training Module #23.

ERIC Educational Resources Information Center

Brownrigg, Carolyn

The purpose of this Child Development Associate (CDA) training module is to help the CDA intern increase musical experiences in his or her classroom. Objectives are presented along with suggested activities for achieving each objective, and an assessment checklist. Also provided is a study guide emphasizing the values of musical activities in the…

31 CFR 256.41 - When is reimbursement due for CDA and No FEAR payments?

Code of Federal Regulations, 2010 CFR

2010-07-01

... No FEAR payments? 256.41 Section 256.41 Money and Finance: Treasury Regulations Relating to Money and... When is reimbursement due for CDA and No FEAR payments? Reimbursement for a CDA or No FEAR payment... Management (OPM) regulations, No FEAR reimbursements or payment reimbursement plans must be made within 45...

Evaluation of vertical profiles to design continuous descent approach procedure

NASA Astrophysics Data System (ADS)

Pradeep, Priyank

The current research focuses on predictability, variability and operational feasibility aspect of Continuous Descent Approach (CDA), which is among the key concepts of the Next Generation Air Transportation System (NextGen). The idle-thrust CDA is a fuel economical, noise and emission abatement procedure, but requires increased separation to accommodate for variability and uncertainties in vertical and speed profiles of arriving aircraft. Although a considerable amount of researches have been devoted to the estimation of potential benefits of the CDA, only few have attempted to explain the predictability, variability and operational feasibility aspect of CDA. The analytical equations derived using flight dynamics and Base of Aircraft and Data (BADA) Total Energy Model (TEM) in this research gives insight into dependency of vertical profile of CDA on various factors like wind speed and gradient, weight, aircraft type and configuration, thrust settings, atmospheric factors (deviation from ISA (DISA), pressure and density of the air) and descent speed profile. Application of the derived equations to idle-thrust CDA gives an insight into sensitivity of its vertical profile to multiple factors. This suggests fixed geometric flight path angle (FPA) CDA has higher degree of predictability and lesser variability at the cost of non-idle and low thrust engine settings. However, with optimized design this impact can be overall minimized. The CDA simulations were performed using Future ATM Concept Evaluation Tool (FACET) based on radar-track and aircraft type data (BADA) of the real air-traffic to some of the busiest airports in the USA (ATL, SFO and New York Metroplex (JFK, EWR and LGA)). The statistical analysis of the vertical profiles of CDA shows 1) mean geometric FPAs derived from various simulated vertical profiles are consistently shallower than 3° glideslope angle and 2) high level of variability in vertical profiles of idle-thrust CDA even in absence of uncertainties in external factors. Analysis from operational feasibility perspective suggests that two key features of the performance based Flight Management System (FMS) i.e. required time of arrival (RTA) and geometric descent path would help in reduction of unpredictability associated with arrival time and vertical profile of aircraft guided by the FMS coupled with auto-pilot (AP) and auto-throttle (AT). The statistical analysis of the vertical profiles of CDA also suggests that for procedure design window type, 'AT or above' and 'AT or below' altitude and FPA constraints are more realistic and useful compared to obsolete 'AT' type altitude constraint.

Markers of preparatory attention predict visual short-term memory performance.

PubMed

Murray, Alexandra M; Nobre, Anna C; Stokes, Mark G

2011-05-01

Visual short-term memory (VSTM) is limited in capacity. Therefore, it is important to encode only visual information that is most likely to be relevant to behaviour. Here we asked which aspects of selective biasing of VSTM encoding predict subsequent memory-based performance. We measured EEG during a selective VSTM encoding task, in which we varied parametrically the memory load and the precision of recall required to compare a remembered item to a subsequent probe item. On half the trials, a spatial cue indicated that participants only needed to encode items from one hemifield. We observed a typical sequence of markers of anticipatory spatial attention: early attention directing negativity (EDAN), anterior attention directing negativity (ADAN), late directing attention positivity (LDAP); as well as of VSTM maintenance: contralateral delay activity (CDA). We found that individual differences in preparatory brain activity (EDAN/ADAN) predicted cue-related changes in recall accuracy, indexed by memory-probe discrimination sensitivity (d'). Importantly, our parametric manipulation of memory-probe similarity also allowed us to model the behavioural data for each participant, providing estimates for the quality of the memory representation and the probability that an item could be retrieved. We found that selective encoding primarily increased the probability of accurate memory recall; that ERP markers of preparatory attention predicted the cue-related changes in recall probability. Copyright © 2011. Published by Elsevier Ltd.

Visual working memory gives up attentional control early in learning: ruling out interhemispheric cancellation.

PubMed

Reinhart, Robert M G; Carlisle, Nancy B; Woodman, Geoffrey F

2014-08-01

Current research suggests that we can watch visual working memory surrender the control of attention early in the process of learning to search for a specific object. This inference is based on the observation that the contralateral delay activity (CDA) rapidly decreases in amplitude across trials when subjects search for the same target object. Here, we tested the alternative explanation that the role of visual working memory does not actually decline across learning, but instead lateralized representations accumulate in both hemispheres across trials and wash out the lateralized CDA. We show that the decline in CDA amplitude occurred even when the target objects were consistently lateralized to a single visual hemifield. Our findings demonstrate that reductions in the amplitude of the CDA during learning are not simply due to the dilution of the CDA from interhemispheric cancellation. Copyright © 2014 Society for Psychophysiological Research.

Molecular Cloning and Function of FAS/APO1 Associated Protein in Breast Cancer.

DTIC Science & Technology

1996-06-01

Ariyama T, Abe T, Druck T, Ohta M, Huebner K, Yanagisawa J, Reed JC, Sato T: PTPN13, a Fas-associated protein tyrosine phosphatase, is located on...20. Yang, Q., and Tonks, N. K. (1991). Isolation of a cDNA clone encoding a human protein-tyrosine phosphatase with homology 7. Huebner, K., Druck , T...Acad. Sci. U.S.A. 91, 7477 (1994). Res. 53, 1945 (1993).(Fig. 3D ). In contrast to Jurkat cells which 13. The original description of PTP-BAS (12

Congenital Myasthenic Syndrome Type 19 Is Caused by Mutations in COL13A1, Encoding the Atypical Non-fibrillar Collagen Type XIII α1 Chain.

PubMed

Logan, Clare V; Cossins, Judith; Rodríguez Cruz, Pedro M; Parry, David A; Maxwell, Susan; Martínez-Martínez, Pilar; Riepsaame, Joey; Abdelhamed, Zakia A; Lake, Alice V R; Moran, Maria; Robb, Stephanie; Chow, Gabriel; Sewry, Caroline; Hopkins, Philip M; Sheridan, Eamonn; Jayawant, Sandeep; Palace, Jacqueline; Johnson, Colin A; Beeson, David

2015-12-03

The neuromuscular junction (NMJ) consists of a tripartite synapse with a presynaptic nerve terminal, Schwann cells that ensheathe the terminal bouton, and a highly specialized postsynaptic membrane. Synaptic structural integrity is crucial for efficient signal transmission. Congenital myasthenic syndromes (CMSs) are a heterogeneous group of inherited disorders that result from impaired neuromuscular transmission, caused by mutations in genes encoding proteins that are involved in synaptic transmission and in forming and maintaining the structural integrity of NMJs. To identify further causes of CMSs, we performed whole-exome sequencing (WES) in families without an identified mutation in known CMS-associated genes. In two families affected by a previously undefined CMS, we identified homozygous loss-of-function mutations in COL13A1, which encodes the alpha chain of an atypical non-fibrillar collagen with a single transmembrane domain. COL13A1 localized to the human muscle motor endplate. Using CRISPR-Cas9 genome editing, modeling of the COL13A1 c.1171delG (p.Leu392Sfs(∗)71) frameshift mutation in the C2C12 cell line reduced acetylcholine receptor (AChR) clustering during myotube differentiation. This highlights the crucial role of collagen XIII in the formation and maintenance of the NMJ. Our results therefore delineate a myasthenic disorder that is caused by loss-of-function mutations in COL13A1, encoding a protein involved in organization of the NMJ, and emphasize the importance of appropriate symptomatic treatment for these individuals. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Continuous blade coating for multi-layer large-area organic light-emitting diode and solar cell

NASA Astrophysics Data System (ADS)

Chen, Chun-Yu; Chang, Hao-Wen; Chang, Yu-Fan; Chang, Bo-Jie; Lin, Yuan-Sheng; Jian, Pei-Siou; Yeh, Han-Cheng; Chien, Hung-Ta; Chen, En-Chen; Chao, Yu-Chiang; Meng, Hsin-Fei; Zan, Hsiao-Wen; Lin, Hao-Wu; Horng, Sheng-Fu; Cheng, Yen-Ju; Yen, Feng-Wen; Lin, I.-Feng; Yang, Hsiu-Yuan; Huang, Kuo-Jui; Tseng, Mei-Rurng

2011-11-01

A continuous roll-to-roll compatible blade-coating method for multi-layers of general organic semiconductors is developed. Dissolution of the underlying film during coating is prevented by simultaneously applying heating from the bottom and gentle hot wind from the top. The solvent is immediately expelled and reflow inhibited. This method succeeds for polymers and small molecules. Uniformity is within 10% for 5 cm by 5 cm area with a mean value of tens of nanometers for both organic light-emitting diode (OLED) and solar cell structure with little material waste. For phosphorescent OLED 25 cd/A is achieved for green, 15 cd/A for orange, and 8 cd/A for blue. For fluorescent OLED 4.3 cd/A is achieved for blue, 9 cd/A for orange, and 6.9 cd/A for white. For OLED with 2 cm by 3 cm active area, the luminance variation is within 10%. Power conversion efficiency of 4.1% is achieved for polymer solar cell, similar to spin coating using the same materials. Very-low-cost and high-throughput fabrication of efficient organic devices is realized by the continuous blade-only method.

Molecular cloning and characterization of the spaB gene of Streptococcus sobrinus.

PubMed

Holt, R G; Perry, S E

1990-07-01

A gene of Streptococcus sobrinus 6715 (serotype g) designated spaB and encoding a surface protein antigen was isolated from a cosmid gene bank. A 5.4 kb HindIII/AvaI DNA fragment containing the gene was inserted into plasmid pBR322 to yield plasmid pXI404. Analysis of plasmid-encoded gene products showed that the 5.4 kb fragment of pXI404 encoded a 195 kDa protein. Southern blot experiments revealed that the 5.4 kb chromosomal insert DNA had sequence similarity with genomic DNA of S. sobrinus 6715, S. sobrinus B13 (serotype d) and Streptococcus cricetus HS6 (serotype a). The recombinant SpaB protein (rSpaB) was purified and monospecific antiserum was prepared. With immunological techniques and the anti-rSpaB serum, we have shown: (1) that the rSpaB protein has physico-chemical and antigenic identity with the S. sobrinus SpaB protein, (2) the presence of cross-reactive proteins in the extracellular protein of serotypes a and d of the mutans group of streptococci and (3) that the SpaB protein is expressed on the surface of mutans streptococcal serotypes a, d and g.

In silico analysis of β-1,3-glucanase from a psychrophilic yeast, Glaciozyma antarctica PI12

NASA Astrophysics Data System (ADS)

Mohammadi, Salimeh; Bakar, Farah Diba Abu; Rabu, Amir; Murad, Abdul Munir Abdul

2014-09-01

1,3-beta-glucanase is an industrially important enzyme having wide range of applications especially in food industry. It is crucial to gain an understanding about the structure and functional aspects of various beta-1,3-glucanase produced from diverse sources. In this, study a cDNA encoding β-1,3-glucanase (GaExg55) was isolated from a psychrophilic yeast, Glaciozyma antarctica PI12. The cDNA sequence has been submitted to Genbank with an accession number (KJ436377). Subsequently, the perdition protein was analyzed using various bioinformatics tools to explore the properties of the protein. GaEXG55 is consisting of 1,440-bp nucleotides encoding 480 amino acid residues. Alignment of the deduced amino acid for GaExg55 with other exo-β-1,3-glucanase available at the NCBI database indicate that deduced amino acids shared a consensus motif NEP, which is signature pattern of GH5 hydrolases. Predicted molecular weight of GaExg55 is 53.66 kDa. GaExg55 sequences possesses signal peptide sequence and it is highly conserved with other fungal exo-beta-1,3 glucanase.

Health level seven interoperability strategy: big data, incrementally structured.

PubMed

Dolin, R H; Rogers, B; Jaffe, C

2015-01-01

Describe how the HL7 Clinical Document Architecture (CDA), a foundational standard in US Meaningful Use, contributes to a "big data, incrementally structured" interoperability strategy, whereby data structured incrementally gets large amounts of data flowing faster. We present cases showing how this approach is leveraged for big data analysis. To support the assertion that semi-structured narrative in CDA format can be a useful adjunct in an overall big data analytic approach, we present two case studies. The first assesses an organization's ability to generate clinical quality reports using coded data alone vs. coded data supplemented by CDA narrative. The second leverages CDA to construct a network model for referral management, from which additional observations can be gleaned. The first case shows that coded data supplemented by CDA narrative resulted in significant variances in calculated performance scores. In the second case, we found that the constructed network model enables the identification of differences in patient characteristics among different referral work flows. The CDA approach goes after data indirectly, by focusing first on the flow of narrative, which is then incrementally structured. A quantitative assessment of whether this approach will lead to a greater flow of data and ultimately a greater flow of structured data vs. other approaches is planned as a future exercise. Along with growing adoption of CDA, we are now seeing the big data community explore the standard, particularly given its potential to supply analytic en- gines with volumes of data previously not possible.

Chloride Depletion Alkalosis as a Predictor of Inhospital Mortality in Patients with Decompensated Heart Failure.

PubMed

Khan, Nazia Naz S; Nabeel, Muhammad; Nan, Bin; Ghali, Jalal K

2015-01-01

Chloride depletion alkalosis (CDA) is often seen as a consequence of diuresis in heart failure (HF) but its prognostic significance remains unknown. The purpose of this study was to evaluate the prognostic role of CDA in decompensated HF (DHF). A retrospective cohort analysis was performed on 674 patients who were admitted with DHF. Patients were assigned to 2 groups based on the change in serum bicarbonate (median = 3 mmol/l) after diuresis, which was calculated by computing the difference in the admission and discharge serum bicarbonate: the CDA group (a change in serum bicarbonate ≥3 mmol/l) and the non-CDA group (change in serum bicarbonate <3 mmol/l). The primary end points were inhospital mortality and the composite end point of all-cause 30-day mortality and hospital readmission for HF. In a multivariable logistic regression model, the CDA group, i.e. 374 patients, had a lower inhospital mortality than the non-CDA group, i.e. 300 patients (OR 0.11, 95% CI 0.03-0.38; p = 0.0005) after adjusting for other covariates. There was no statistically significant difference in the combined end point of all-cause 30-day mortality and readmission between the 2 groups (OR 1.26, 95% CI 0.74-2.12; p = 0.39). The presence of CDA during hospitalization for DHF was independently associated with a better inhospital survival rate. © 2015 S. Karger AG, Basel.

Contralateral Delay Activity Tracks Fluctuations in Working Memory Performance.

PubMed

Adam, Kirsten C S; Robison, Matthew K; Vogel, Edward K

2018-01-08

Neural measures of working memory storage, such as the contralateral delay activity (CDA), are powerful tools in working memory research. CDA amplitude is sensitive to working memory load, reaches an asymptote at known behavioral limits, and predicts individual differences in capacity. An open question, however, is whether neural measures of load also track trial-by-trial fluctuations in performance. Here, we used a whole-report working memory task to test the relationship between CDA amplitude and working memory performance. If working memory failures are due to decision-based errors and retrieval failures, CDA amplitude would not differentiate good and poor performance trials when load is held constant. If failures arise during storage, then CDA amplitude should track both working memory load and trial-by-trial performance. As expected, CDA amplitude tracked load (Experiment 1), reaching an asymptote at three items. In Experiment 2, we tracked fluctuations in trial-by-trial performance. CDA amplitude was larger (more negative) for high-performance trials compared with low-performance trials, suggesting that fluctuations in performance were related to the successful storage of items. During working memory failures, participants oriented their attention to the correct side of the screen (lateralized P1) and maintained covert attention to the correct side during the delay period (lateralized alpha power suppression). Despite the preservation of attentional orienting, we found impairments consistent with an executive attention theory of individual differences in working memory capacity; fluctuations in executive control (indexed by pretrial frontal theta power) may be to blame for storage failures.

Construction of a ColD cda promoter-based SOS-green fluorescent protein whole-cell biosensor with higher sensitivity toward genotoxic compounds than constructs based on recA, umuDC, or sulA promoters.

PubMed

Norman, Anders; Hestbjerg Hansen, Lars; Sørensen, Søren J

2005-05-01

Four different green fluorescent protein (GFP)-based whole-cell biosensors were created based on the DNA damage inducible SOS response of Escherichia coli in order to evaluate the sensitivity of individual SOS promoters toward genotoxic substances. Treatment with the known carcinogen N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) revealed that the promoter for the ColD plasmid-borne cda gene had responses 12, 5, and 3 times greater than the recA, sulA, and umuDC promoters, respectively, and also considerably higher sensitivity. Furthermore, we showed that when the SOS-GFP construct was introduced into an E. coli host deficient in the tolC gene, the minimal detection limits toward mitomycin C, MNNG, nalidixic acid, and formaldehyde were lowered to 9.1 nM, 0.16 microM, 1.1 microM, and 141 microM, respectively, which were two to six times lower than those in the wild-type strain. This study thus presents a new SOS-GFP whole-cell biosensor which is not only able to detect minute levels of genotoxins but, due to its use of the green fluorescent protein, also a reporter system which should be applicable in high-throughput screening assays as well as a wide variety of in situ detection studies.

REQUIREMENT VERIFICATION AND SYSTEMS ENGINEERING TECHNICAL REVIEW (SETR) ON A COMMERCIAL DERIVATIVE AIRCRAFT (CDA) PROGRAM

DTIC Science & Technology

2017-09-01

the SETR entrance criteria of these events. Out of 30 evaluated SETR entrance criteria, 22 map to FAA elements. A case study of a military CDA...evaluated SETR entrance criteria, 22 map to FAA elements. A case study of a military CDA program, the Presidential Helicopter Replacement Program...3 C. SCOPE AND METHODOLOGY .................................................. 4 D. ORGANIZATION OF THESIS

Mapping HL7 CDA R2 Formatted Mass Screening Data to OpenEHR Archetypes.

PubMed

Kobayashi, Shinji; Kume, Naoto; Yoshihara, Hiroyuki

2017-01-01

Mass screening of adults was performed to manage employee healthcare. The screening service defined the data collection format as HL7 Clinical Document Architecture (CDA) R2. To capture mass screening data for nationwide electronic health records (her), we programmed a model within the CDA format and mapped the data items to the ISO13606/openEHR archetype for semantic interoperabiilty.

12 CFR 721.3 - What categories of activities are preapproved as incidental powers necessary or requisite to...

Code of Federal Regulations, 2014 CFR

2014-01-01

... establish a CDA using a trust vehicle, the trustee must be regulated by the Office of the Comptroller of the... requirements. The parties to the CDA, typically the funding credit union and trustee or other manager of the... accounting principles; and (D) Indicate the frequency with which the trustee or manager of the CDA will make...

High incidence of Celiac Disease in a Long-term Study of Adolescents With Susceptibility Genotypes

PubMed Central

Liu, Edwin; Dong, Fran; Barón, Anna E.; Taki, Iman; Norris, Jill M.; Frohnert, Brigitte I; Hoffenberg, Edward J; Rewers, Marian

2017-01-01

Background & Aims Little is known about the incidence of celiac disease in the general population of children in the United States. We aimed to estimate the cumulative incidence of celiac disease in adolescents born in the Denver metropolitan area. Methods We collected data on HLA-DR, DQ genotypes of 31,766 infants, born from 1993 through 2004 at St. Joseph’s Hospital in Denver, from the Diabetes Autoimmunity Study in the Young. Subjects with susceptibility genotypes for celiac disease and type 1 diabetes were followed for up to 20 years for development of tissue transglutaminase autoantibodies (tTGA). Outcomes were the development of celiac disease autoimmunity (CDA) or celiac disease. CDA was defined as persistence of tTGA for at least 3 months or development of celiac disease. Celiac disease was defined based on detection of Marsh 2 or greater lesions in biopsies or persistent high levels of tTGA. For each genotype, the cumulative incidence of CDA and celiac disease were determined. To estimate the cumulative incidence in the Denver general population, outcomes by each genotype were weighted according to the frequency of each of these genotypes in the general population. Results Of 1339 subjects followed, 66 developed CDA and met criteria for celiac disease and 46 developed only CDA. Seropositivity for tTGA resolved spontaneously, without treatment, in 21 of the 46 subjects with only CDA (46%). The estimated cumulative incidence for CDA in the Denver general population at 5, 10, and 15 years of age was 2.4%, 4.3%, and 5.1% respectively; incidence values for celiac disease were 1.6%, 2.8%, and 3.1%, respectively. Conclusions In a 20-year prospective study of 1339 children with genetic risk factors for celiac disease, we found the cumulative incidence of CDA and celiac disease to be high within the first 10 years. Although more than 5% of children may experience a period of CDA, not all develop celiac disease or require gluten-free diets. PMID:28188747

High Incidence of Celiac Disease in a Long-term Study of Adolescents With Susceptibility Genotypes.

PubMed

Liu, Edwin; Dong, Fran; Barón, Anna E; Taki, Iman; Norris, Jill M; Frohnert, Brigitte I; Hoffenberg, Edward J; Rewers, Marian

2017-05-01

Little is known about the incidence of celiac disease in the general population of children in the United States. We aimed to estimate the cumulative incidence of celiac disease in adolescents born in the Denver metropolitan area. We collected data on HLA-DR, DQ genotypes of 31,766 infants, born from 1993 through 2004 at St. Joseph's Hospital in Denver, from the Diabetes Autoimmunity Study in the Young. Subjects with susceptibility genotypes for celiac disease and type 1 diabetes were followed up for up to 20 years for development of tissue transglutaminase autoantibodies (tTGA). Outcomes were the development of celiac disease autoimmunity (CDA) or celiac disease. CDA was defined as persistence of tTGA for at least 3 months or development of celiac disease. Celiac disease was defined based on detection of Marsh 2 or greater lesions in biopsy specimens or persistent high levels of tTGA. For each genotype, the cumulative incidence of CDA and celiac disease were determined. To estimate the cumulative incidence in the Denver general population, outcomes by each genotype were weighted according to the frequency of each of these genotypes in the general population. Of 1339 subjects followed up, 66 developed CDA and met criteria for celiac disease and 46 developed only CDA. Seropositivity for tTGA resolved spontaneously, without treatment, in 21 of the 46 subjects with only CDA (46%). The estimated cumulative incidence for CDA in the Denver general population at 5, 10, and 15 years of age was 2.4%, 4.3%, and 5.1%, respectively, and incidence values for celiac disease were 1.6%, 2.8%, and 3.1%, respectively. In a 20-year prospective study of 1339 children with genetic risk factors for celiac disease, we found the cumulative incidence of CDA and celiac disease to be high within the first 10 years. Although more than 5% of children may experience a period of CDA, not all children develop celiac disease or require gluten-free diets. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Cervical disc arthroplasty for symptomatic cervical disc disease: Traditional and Bayesian meta-analysis with trial sequential analysis.

PubMed

Kan, Shun-Li; Yuan, Zhi-Fang; Ning, Guang-Zhi; Liu, Fei-Fei; Sun, Jing-Cheng; Feng, Shi-Qing

2016-11-01

Cervical disc arthroplasty (CDA) has been designed as a substitute for anterior cervical discectomy and fusion (ACDF) in the treatment of symptomatic cervical disc disease (CDD). Several researchers have compared CDA with ACDF for the treatment of symptomatic CDD; however, the findings of these studies are inconclusive. Using recently published evidence, this meta-analysis was conducted to further verify the benefits and harms of using CDA for treatment of symptomatic CDD. Relevant trials were identified by searching the PubMed, EMBASE, and Cochrane Library databases. Outcomes were reported as odds ratio or standardized mean difference. Both traditional frequentist and Bayesian approaches were used to synthesize evidence within random-effects models. Trial sequential analysis (TSA) was applied to test the robustness of our findings and obtain more conservative estimates. Nineteen trials were included. The findings of this meta-analysis demonstrated better overall, neck disability index (NDI), and neurological success; lower NDI and neck and arm pain scores; higher 36-Item Short Form Health Survey (SF-36) Physical Component Summary (PCS) and Mental Component Summary (MCS) scores; more patient satisfaction; greater range of motion at the operative level; and fewer secondary surgical procedures (all P < 0.05) in the CDA group compared with the ACDF group. CDA was not significantly different from ACDF in the rate of adverse events (P > 0.05). TSA of overall success suggested that the cumulative z-curve crossed both the conventional boundary and the trial sequential monitoring boundary for benefit, indicating sufficient and conclusive evidence had been ascertained. For treating symptomatic CDD, CDA was superior to ACDF in terms of overall, NDI, and neurological success; NDI and neck and arm pain scores; SF-36 PCS and MCS scores; patient satisfaction; ROM at the operative level; and secondary surgical procedures rate. Additionally, there was no significant difference between CDA and ACDF in the rate of adverse events. However, as the CDA procedure is a relatively newer operative technique, long-term results and evaluation are necessary before CDA is routinely used in clinical practice. Copyright © 2016 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Application of machine learning using support vector machines for crater detection from Martian digital topography data

NASA Astrophysics Data System (ADS)

Salamunićcar, Goran; Lončarić, Sven

In our previous work, in order to extend the GT-57633 catalogue [PSS, 56 (15), 1992-2008] with still uncatalogued impact-craters, the following has been done [GRS, 48 (5), in press, doi:10.1109/TGRS.2009.2037750]: (1) the crater detection algorithm (CDA) based on digital elevation model (DEM) was developed; (2) using 1/128° MOLA data, this CDA proposed 414631 crater-candidates; (3) each crater-candidate was analyzed manually; and (4) 57592 were confirmed as correct detections. The resulting GT-115225 catalog is the significant result of this effort. However, to check such a large number of crater-candidates manually was a demanding task. This was the main motivation for work on improvement of the CDA in order to provide better classification of craters as true and false detections. To achieve this, we extended the CDA with the machine learning capability, using support vector machines (SVM). In the first step, the CDA (re)calculates numerous terrain morphometric attributes from DEM. For this purpose, already existing modules of the CDA from our previous work were reused in order to be capable to prepare these attributes. In addition, new attributes were introduced such as ellipse eccentricity and tilt. For machine learning purpose, the CDA is additionally extended to provide 2-D topography-profile and 3-D shape for each crater-candidate. The latter two are a performance problem because of the large number of crater-candidates in combination with the large number of attributes. As a solution, we developed a CDA architecture wherein it is possible to combine the SVM with a radial basis function (RBF) or any other kernel (for initial set of attributes), with the SVM with linear kernel (for the cases when 2-D and 3-D data are included as well). Another challenge is that, in addition to diversity of possible crater types, there are numerous morphological differences between the smallest (mostly very circular bowl-shaped craters) and the largest (multi-ring) impact craters. As a solution to this problem, the CDA classifies crater-candidates according to their diameter into 7 groups (D smaller/larger then 2km, 4km, 8km, 16km, 32km and 64km), and for each group uses separate SVMs for training and prediction. For implementation of the machine-learning part and integration with the rest of the CDA, we used C.-J. Lin's et al. [http://www.csie.ntu.edu.tw/˜cjlin/] LIBSVM (A Library for Support Vector Machines) and LIBLINEAR (A Library for Large Linear Classification) libraries. According to the initial evaluation, now the CDA provides much better classification of craters as true and false detections.

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

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

Rodríguez Guilbe, María M.; Protein Research and Development Center, University of Puerto Rico; Alfaro Malavé, Elisa C.

The genetically encoded fluorescent calcium-indicator protein GCaMP2 was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution and the structure was solved by molecular replacement. Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, thismore » protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way.« less

Analysis of Sir2E in the cellular slime mold Dictyostelium discoideum: cellular localization, spatial expression and overexpression.

PubMed

Katayama, Takahiro; Yasukawa, Hiro

2008-10-01

It has been reported that Dictyostelium discoideum encodes four silent information regulator 2 (Sir2) proteins (Sir2A-D) showing sequence similarity to human homologues of Sir2 (SIRT1-3). Further screening in a database revealed that D. discoideum encodes an additional Sir2 homologue (Sir2E). The amino acid sequence of Sir2E is not similar to those of SIRTs but is similar to those of proteins encoded by Giardia lamblia, Cryptosporidium hominis and Cryptosporidium parvum. Fluorescence of Sir2E-green fluorescent protein fusion protein was detected in the D. discoideum nucleus, indicating that Sir2E is a nuclear localizing protein. Reverse transcription-polymerase chain reaction and whole-mount in situ hybridization analyses showed that D. discoideum expressed sir2E in amoebae in the growth phase and in prestalk cells in the developmental phase. D. discoideum overexpressing sir2E grew faster than the wild type. These results indicate that Sir2E plays important roles both in the growth phase and developmental phase of D. discoideum.

Differential gene expression in ripening banana fruit.

PubMed Central

Clendennen, S K; May, G D

1997-01-01

During banana (Musa acuminata L.) fruit ripening ethylene production triggers a developmental cascade that is accompanied by a massive conversion of starch to sugars, an associated burst of respiratory activity, and an increase in protein synthesis. Differential screening of cDNA libraries representing banana pulp at ripening stages 1 and 3 has led to the isolation of 11 nonredundant groups of differentially expressed mRNAs. Identification of these transcripts by partial sequence analysis indicates that two of the mRNAs encode proteins involved in carbohydrate metabolism, whereas others encode proteins thought to be associated with pathogenesis, senescence, or stress responses in plants. Their relative abundance in the pulp and tissue-specific distribution in greenhouse-grown banana plants were determined by northern-blot analyses. The relative abundance of transcripts encoding starch synthase, granule-bound starch synthase, chitinase, lectin, and a type-2 metallothionein decreased in pulp during ripening. Transcripts encoding endochitinase, beta-1,3-glucanase, a thaumatin-like protein, ascorbate peroxidase, metallothionein, and a putative senescence-related protein increased early in ripening. The elucidation of the molecular events associated with banana ripening will facilitate a better understanding and control of these processes, and will allow us to attain our long-term goal of producing candidate oral vaccines in transgenic banana plants. PMID:9342866

Functional display of family 11 endoxylanases on the surface of phage M13.

PubMed

Beliën, T; Hertveldt, K; Van den Brande, K; Robben, J; Van Campenhout, S; Volckaert, G

2005-02-09

Two family 11 endoxylanases (EC 3.2.1.8) were functionally displayed on the surface of bacteriophage M13. The genes encoding endo-1,4-xylanase I from Aspergillus niger (ExlA) and endo-1,4-xylanase A from Bacillus subtilis (XynA) were fused to the gene encoding the minor coat protein g3p in phagemid vector pHOS31. Phage rescue resulted in functional monovalent display of the enzymes as was demonstrated by three independent tests. Firstly, purified recombinant phage particles showed a clear hydrolytic activity in an activity assay based on insoluble, chromagenic arabinoxylan substrate. Secondly, specific binding of endoxylanase displaying phages to immobilized endoxylanase inhibitors was demonstrated by interaction ELISA. Finally, two rounds of selection and amplification in a biopanning procedure against immobilized endoxylanase inhibitor were performed. Phages displaying endoxylanases were strongly enriched from background phages displaying unrelated proteins. These results open perspectives to use phage display for analysing protein-protein interactions at the interface between endoxylanases and their inhibitors. In addition, this technology should enable engineering of endoxylanases into novel variants with altered binding properties towards endoxylanase inhibitors.

Synthesis of pyrimidin-2-one nucleosides as acid-stable inhibitors of cytidine deaminase.

PubMed

Kim, C H; Marquez, V E; Mao, D T; Haines, D R; McCormack, J J

1986-08-01

One of the problems encountered in the use of tetrahydrouridine (THU, 2) and saturated 2-oxo-1,3-diazepine nucleosides as orally administered cytidine deaminase (CDA) inhibitors is their acid instability. Under acid conditions these compounds are rapidly converted into inactive ribopyranoside forms. A solution this problem was sought by functionalizing the acid-stable but less potent CDA inhibitor 1-beta-D-ribofuranosyl-2(1H)-pyrimidinone (1) with the hope of increasing its potency to the level achieved with THU. The selection of the hydroxymethyl substituent at C-4, which led to the synthesis of 4-(hydroxymethyl)-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone (10), 3,4-dihydro-4-(hydroxymethyl)-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone (7), and 3,4,5,6-tetrahydro-4-(dihydroxymethyl)-1-beta-D-ribofuranosyl-2(1H)-p yrimidinone (28) was based on the transition-state (TS) concept. The key intermediate precursor, 4-[(benzoyloxy)methyl]-1-(2,3,5-tri-O-benzoyl-beta-D-ribofuranosyl)-2(H) -pyrimidinone (24), was obtained via the classical Hilbert-Johnson reaction between 2-methoxy-4-[(benzoyloxy)methyl]pyrimidine (20) and 2,3,5-tri-O-benzoyl-1-D-ribofuranosyl bromide (21). Deprotection of 24 afforded compound 10, while its sodium borohydride reduction products afforded compounds 7 and 28 after removal of the blocking groups. Syntheses of 3,4-dihydro-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone (9) and 3,6-dihydro-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone (8), which lack the hydroxymethyl substituent, was accomplished in a similar fashion. The new compounds bearing the hydroxymethyl substituent were more acid stable than THU, and their CDA inhibitory potency, expressed in terms of Ki values, spanned from 10(-4) to 10(-7) M in a manner consistent with the TS theory. Compound 7, in particular, was superior to its parent 1 and equipotent to THU (Ki = 4 X 10(-7) M) when examined against mouse kidney CDA. The superior acid stability of this compound coupled to its potent inhibitory properties against CDA should provide a means of testing oral combinations of rapidly deaminated drugs, viz. ara-C, without the complications associated with the acid instability of THU.

Adherence to Diabetes Dietary Guidelines Assessed Using a Validated Questionnaire Predicts Glucose Control in Adults With Type 2 Diabetes.

PubMed

Raj, Gayathiri Durai; Hashemi, Zohre; Soria Contreras, Diana C; Babwik, Stephanie; Maxwell, Denise; Bell, Rhonda C; Chan, Catherine B

2018-02-01

The purpose of this study was to determine predominant deviations from Canadian Diabetes Association (CDA) nutrition therapy guidelines for Canadians with type 2 diabetes as a prelude to developing relevant interventions. We hypothesized that lack of adherence to these guidelines would be associated with higher glycated hemoglobin (A1C) levels. A cross-sectional trial was conducted to evaluate associations between dietary adherence to CDA and Health Canada guidelines and blood glucose control. Diet was assessed using 3-day diet records and a diabetes-specific validated questionnaire, the Perceived Dietary Adherence Questionnaire (PDAQ). A total of 80 adult participants with type 2 diabetes volunteered. The main outcome measures were A1C levels, adherence to dietary guidelines and food sources of nutrients. Simple and multiple linear regressions that tested the effects of adherence to dietary guidelines concerning A1C levels were conducted; p<0.05 was considered significant. Participants: average age, 61.2±10.4 (standard deviation) years; 48 females and 32 males had A1C levels of 7.3%±1.3% (56±6.3 mmol/mol). Participants' reported mean daily intakes of sodium and saturated fat exceeded CDA nutrition therapy guidelines. Cured meats, fast foods and snack foods were all major contributors to intake of sodium and saturated fat. Saturated fat (r=0.341) and sodium intakes (r=0.296) and total PDAQ scores (r=-0.417) were correlated with A1C levels (p<0.05). This study population had overall good adherence to several CDA nutrition therapy guidelines; however, sodium and saturated fat intakes exceeded these guidelines and should receive particular attention in interventions with patients who have type 2 diabetes. Adherence to diabetes dietary guidelines as assessed by PDAQ is associated with lower A1C levels. Copyright © 2017 Diabetes Canada. Published by Elsevier Inc. All rights reserved.

Triple Resonance Solid State NMR Experiments with Reduced Dimensionality Evolution Periods

NASA Astrophysics Data System (ADS)

Astrof, Nathan S.; Lyon, Charles E.; Griffin, Robert G.

2001-10-01

Two solid state NMR triple resonance experiments which utilize the simultaneous incrementation of two chemical shift evolution periods to obtain a spectrum with reduced dimensionality are described. The CON CA experiment establishes the correlation of 13Ci-1 to 13Cαi and 15Ni by simultaneously encoding the 13COi-1 and 15Ni chemical shifts. The CAN COCA experiment establishes the correlation 13Cai and 15COi to 13Cαi-1 and 15Ni-1 within a single experiment by simultaneous encoding of the 13Cαi and 15Ni chemical shifts. This experiment establishes sequential amino acid correlations in close analogy to the solution state HNCA experiment. Reduced dimensionality 2D experiments are a practical alternative to recording multiple 3D data sets for the purpose of obtaining sequence-specific resonance assignments of peptides and proteins in the solid state.

Cervical arthroplasty: a critical review of the literature.

PubMed

Alvin, Matthew D; Abbott, E Emily; Lubelski, Daniel; Kuhns, Benjamin; Nowacki, Amy S; Steinmetz, Michael P; Benzel, Edward C; Mroz, Thomas E

2014-09-01

Cervical disc arthroplasty (CDA) is a motion-preserving procedure that is an alternative to fusion. Proponents of arthroplasty assert that it will maintain cervical motion and prevent or reduce adjacent segment degeneration. Accordingly, CDA, compared with fusion, would have the potential to improve clinical outcomes. Published studies have varying conclusions on whether CDA reduces complications and/or improves outcomes. As many of these previous studies have been funded by CDA manufacturers, we wanted to ascertain whether there was a greater likelihood for these studies to report positive results. To critically assess the available literature on cervical arthroplasty with a focus on the time of publication and conflict of interest (COI). Review of the literature. All clinical articles about CDA published in English through August 1, 2013 were identified on Medline. Any article that presented CDA clinical results was included. Study design, sample size, type of disc, length of follow-up, use of statistical analysis, quality-of-life (QOL) outcome scores, COI, and complications were recorded. A meta-analysis was conducted stratifying studies by COI and publication date to identify differences in complication rates reported. Seventy-four studies were included that investigated 8 types of disc prosthesis and 22 met the criteria for a randomized controlled trial (RCT). All Level Ib RCTs reported superior quality-of-life outcomes for CDA versus anterior cervical discectomy and fusion (ACDF) at 24 months. Fifty of the 74 articles (68%) had a disclosure section, including all Level Ib RCTs, which had significant COIs related to the respective studies. Those studies without a COI reported mean weighted average adjacent segment disease rates of 6.3% with CDA and 6.2% with ACDF. In contrast, the reverse was reported by studies with a COI, for which the averages were 2.5% with CDA and 6.3% with ACDF. Those studies with a COI (n=31) had an overall weighted average heterotopic ossification rate of 22%, whereas those studies with no COI (n=43) had a rate of 46%. Associated COIs did not influence QOL outcomes. Conflicts of interest were more likely to be present in studies published after 2008, and those with a COI reported greater adjacent segment disease rates for ACDF than CDA. In addition, heterotopic ossification rates were much lower in studies with COI versus those without COI. Thus, COIs did not affect QOL outcomes but were associated with lower complication rates. Copyright © 2014 Elsevier Inc. All rights reserved.

Is cervical disc arthroplasty good for congenital cervical stenosis?

PubMed

Chang, Peng-Yuan; Chang, Hsuan-Kan; Wu, Jau-Ching; Huang, Wen-Cheng; Fay, Li-Yu; Tu, Tsung-Hsi; Wu, Ching-Lan; Cheng, Henrich

2017-05-01

OBJECTIVE Cervical disc arthroplasty (CDA) has been demonstrated to be as safe and effective as anterior cervical discectomy and fusion (ACDF) in the management of 1- and 2-level degenerative disc disease (DDD). However, there has been a lack of data to address the fundamental discrepancy between the two surgeries (CDA vs ACDF), and preservation versus elimination of motion, in the management of cervical myelopathy associated with congenital cervical stenosis (CCS). Although younger patients tend to benefit more from motion preservation, it is uncertain if CCS caused by multilevel DDD can be treated safely with CDA. METHODS Consecutive patients who underwent 3-level anterior cervical discectomy were retrospectively reviewed. Inclusion criteria were age less than 50 years, CCS (Pavlov ratio ≤ 0.82), symptomatic myelopathy correlated with DDD, and stenosis limited to 3 levels of the subaxial cervical (C3-7) spine. Exclusion criteria were ossification of the posterior longitudinal ligament, previous posterior decompression surgery (e.g., laminoplasty or laminectomy), osteoporosis, previous trauma, or other rheumatic diseases that might have caused the cervical myelopathy. All these patients who underwent 3-level discectomy were divided into 2 groups according to the strategies of management: preservation or elimination of motion (the hybrid-CDA group and the ACDF group). The hybrid-CDA group underwent 2-level CDA plus 1-level ACDF, whereas the ACDF group underwent 3-level ACDF. Clinical assessment was measured by the visual analog scales (VAS) for neck and arm pain, Japanese Orthopaedic Association (JOA) scores, and Nurick grades. Radiographic outcomes were measured using dynamic radiographs for evaluation of range of motion (ROM). RESULTS Thirty-seven patients, with a mean (± SD) age of 44.57 ± 5.10 years, were included in the final analysis. There was a male predominance in this series (78.4%, 29 male patients), and the mean follow-up duration was 2.37 ± 1.60 years. There were 20 patients in the hybrid-CDA group, and 17 in the ACDF group. Both groups demonstrated similar clinical improvement at 2 years' follow-up. These patients with 3-level stenosis experienced significant improvement after either type of surgery (hybrid-CDA and ACDF). There were no significant differences between the 2 groups at each of the follow-up visits postoperatively. The preoperative ROM over the operated subaxial levels was similar between both groups (21.9° vs 21.67°; p = 0.94). Postoperatively, the hybrid-CDA group had significantly greater ROM (10.65° vs 2.19°; p < 0.001) than the ACDF group. Complications, adverse events, and reoperations in both groups were similarly low. CONCLUSIONS Hybrid-CDA yielded similar clinical improvement to 3-level ACDF in patients with myelopathy caused by CCS. In this relatively young group of patients, hybrid-CDA demonstrated significantly more ROM than 3-level ACDF without adjacent-segment disease (ASD) at 2 years' follow-up. Therefore, hybrid-CDA appears to be an acceptable option in the management of CCS. The strategy of motion preservation yielded similar improvements of cervical myelopathy to motion elimination (i.e., ACDF) in patients with CCS, while the theoretical benefit of reducing ASD required further validation.

What we know about ST13, a co-factor of heat shock protein, or a tumor suppressor?*

PubMed Central

Shi, Zheng-zheng; Zhang, Jia-wei; Zheng, Shu

2007-01-01

This article is to summarize the molecular and functional analysis of the gene “suppression of tumorigenicity 13” (ST13). ST13 is in fact the gene encoding Hsp70 interacting protein (Hip), a co-factor (co-chaperone) of the 70-kDa heat shock proteins (Hsc/Hsp70). By collaborating with other positive co-factors such as Hsp40 and the Hsp70-Hsp90 organizing protein (Hop), or competing with negative co-factors such as Bcl2-associated athanogen 1 (Bag1), Hip may facilitate the chaperone function of Hsc/Hsp70 in protein folding and repair, and in controlling the activity of regulatory proteins such as steroid receptors and regulators of proliferation or apoptosis. Although the nomenclature of ST13 implies a role in the suppression of tumorigenicity (ST), to date available experimental data are not sufficient to support its role in cancer development, except for the possible down-regulation of ST13 in gastric and colorectal cancers. Further investigation of this gene at the physiological level would benefit our understanding of diseases such as endocrinological disorders, cancer, and neurodegeneration commonly associated with protein misfolding. PMID:17323428

CDA hones its marketing message.

PubMed

Jones, D G

1998-07-01

This article discusses the many tacks CDA has taken with its marketing campaigns over the years. The keys to success have been reasonable goals and sufficient funds to make an impact. The current campaign, while underfunded due to budget constraints, carries on the successful theme of positioning CDA and its member dentists as the trusted sources of dental information for consumers, legislators, and health care decision-makers. An accompanying article discusses the proposed ADA national marketing campaign.

Neuron-specific specificity protein 4 bigenomically regulates the transcription of all mitochondria- and nucleus-encoded cytochrome c oxidase subunit genes in neurons.

PubMed

Johar, Kaid; Priya, Anusha; Dhar, Shilpa; Liu, Qiuli; Wong-Riley, Margaret T T

2013-11-01

Neurons are highly dependent on oxidative metabolism for their energy supply, and cytochrome c oxidase (COX) is a key energy-generating enzyme in the mitochondria. A unique feature of COX is that it is one of only four proteins in mammalian cells that are bigenomically regulated. Of its thirteen subunits, three are encoded in the mitochondrial genome and ten are nuclear-encoded on nine different chromosomes. The mechanism of regulating this multisubunit, bigenomic enzyme poses a distinct challenge. In recent years, we found that nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2) mediate such bigenomic coordination. The latest candidate is the specificity factor (Sp) family of proteins. In N2a cells, we found that Sp1 regulates all 13 COX subunits. However, we discovered recently that in primary neurons, it is Sp4 and not Sp1 that regulates some of the key glutamatergic receptor subunit genes. The question naturally arises as to the role of Sp4 in regulating COX in primary neurons. The present study utilized multiple approaches, including chromatin immunoprecipitation, promoter mutational analysis, knockdown and over-expression of Sp4, as well as functional assays to document that Sp4 indeed functionally regulate all 13 subunits of COX as well as mitochondrial transcription factors A and B. The present study discovered that among the specificity family of transcription factors, it is the less known neuron-specific Sp4 that regulates the expression of all 13 subunits of mitochondrial cytochrome c oxidase (COX) enzyme in primary neurons. Sp4 also regulates the three mitochondrial transcription factors (TFAM, TFB1M, and TFB2M) and a COX assembly protein SURF-1 in primary neurons. © 2013 International Society for Neurochemistry.

Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters

PubMed Central

WANG, JIACHEN; DASGUPTA, INDRANI; FOX, GEORGE E.

2009-01-01

The genomic associations of the archaeal ribosomal proteins, (r-proteins), were examined in detail. The archaeal versions of the universal r-protein genes are typically in clusters similar or identical and to those found in bacteria. Of the 35 nonuniversal archaeal r-protein genes examined, the gene encoding L18e was found to be associated with the conserved L13 cluster, whereas the genes for S4e, L32e and L19e were found in the archaeal version of the spc operon. Eleven nonuniversal protein genes were not associated with any common genomic context. Of the remaining 19 protein genes, 17 were convincingly assigned to one of 10 previously unrecognized gene clusters. Examination of the gene content of these clusters revealed multiple associations with genes involved in the initiation of protein synthesis, transcription or other cellular processes. The lack of such associations in the universal clusters suggests that initially the ribosome evolved largely independently of other processes. More recently it likely has evolved in concert with other cellular systems. It was also verified that a second copy of the gene encoding L7ae found in some bacteria is actually a homolog of the gene encoding L30e and should be annotated as such. PMID:19478915

nab-paclitaxel potentiates gemcitabine activity by reducing cytidine deaminase levels in a mouse model of pancreatic cancer

PubMed Central

Cook, Natalie; Bapiro, Tashinga E.; Lolkema, Martijn P.; Jodrell, Duncan I.; Tuveson, David A.

2016-01-01

nab-paclitaxel, an albumin-stabilized paclitaxel formulation, demonstrates clinical activity when administered in combination with gemcitabine in patients with metastatic pancreatic ductal adenocarcinoma (PDA). The limited availability of patient tissue and exquisite sensitivity of xenografts to chemotherapeutics have limited our ability to address the mechanistic basis of this treatment regimen. Here, we used a mouse model of PDA to show that the co-administration of nab-paclitaxel and gemcitabine uniquely demonstrates evidence of tumor regression. Combination treatment increases intratumoral gemcitabine levels due to a marked decrease in the primary gemcitabine metabolizing enzyme, cytidine deaminase (Cda). Correspondingly, paclitaxel reduced Cda protein levels in cultured cells through reactive oxygen species-mediated degradation, resulting in the increased stabilization of gemcitabine. Our findings support the concept that suboptimal intratumoral concentrations of gemcitabine represent a crucial mechanism of therapeutic resistance in PDA and highlight the advantages of genetically engineered mouse models in preclinical therapeutic trials. PMID:22585996

Design and evaluation of Continuous Descent Approach as a fuel-saving procedure

NASA Astrophysics Data System (ADS)

Jin, Li

Continuous Descent Approach (CDA), which is among the key concepts of the Next Generation Air Transportation System (NextGen), is a fuel economical procedure, but requires increased separation to accommodate spacing uncertainties among arriving aircraft. Such negative impact is often overlooked when benefits are estimated. Although a considerable number of researches have been devoted to the estimation of potential fuel saving of CDA, few have attempted to explain the fuel saving observed in field tests from an analytical point of view. This research gives insights into the reasons why CDA saves fuel, and a number of design guidelines for CDA procedures are derived. The analytical relationship between speed, altitude, and time-cumulative fuel consumption is derived based on Base of Aircraft Data (BADA) Total Energy Model. Theoretical analysis implies that speed profile has an impact as substantial as, if not more than, vertical profile on the fuel consumption in the terminal area. In addition, CDA is not intrinsically a fuel-saving procedure: whether CDA saves fuel or not is contingent upon whether the speed profile is properly designed or not. Based on this model, the potential fuel savings due to CDA at San Francisco International Airport were estimated, and the accuracy of this estimation is analyzed. Possible uncertainties in this fuel estimation primarily resulted from the modeled CDA procedure and the inaccuracy of BADA. This thesis also investigates the fuel savings due to CDAs under high traffic conditions, counting not only the savings benefiting from optimal vertical profiles but also the extra fuel burn resulting from the increased separations. The simulated CDAs traffic is based on radar track data, and deconflicted by a scheduling algorithm that targets minimized delays. The delays are absorbed by speed change and path stretching, accounting for the air traffic controls that are entailed by CDAs. The fuel burn statistics calculated based on the BADA Total Energy Model reveals that the CDAs save on average 171.87 kg per arrival, but the number is discounted by delay absorption. The savings diminish as the arrival demand increases, and could be even negative due to large delays. The throughput analysis demonstrated that the impact of CDA on airport capacity is insignificant and tolerable. The Atlanta International Airport was used as the testbed for sensitivity analysis, and the New York Metroplex was used as the test bed for throughput analysis.

Incidence and risk factors of axial symptoms after cervical disc arthroplasty: a minimum 5-year follow-up study.

PubMed

Chen, Jing; Li, Jia; Qiu, Gang; Wei, Jingchao; Qiu, Yanfen; An, Yonghui; Shen, Yong

2016-09-20

The purpose of this study was to investigate whether uncovertebral joint ossification was a risk factor for axial symptoms (AS) after cervical disc arthroplasty (CDA). This retrospective study included 52 consecutive patients who underwent CDA for single-level cervical disc disease. To examine possible risk factors for AS after CDA, univariate and multivariate logistic regression analyses were conducted to compare data from the patients with and without AS (the AS and no-AS groups, respectively). Among the 52 patients examined, AS were observed in 24 patients (46.2 %), including a stiff neck (n = 11), neck pain and dullness (n = 10), and shoulder pain (n = 3). Uncovertebral joint ossification was detected in 22 (42.3 %) patients, including 17 patients in the AS group and 5 patients in the no-AS group. Clinical outcome improved during the follow-up period for the AS group. According to multivariate logistic regression analysis, uncovertebral joint ossification, cervical kyphosis, and range of motion (ROM) at the index level were identified as significant risk factors for AS after CDA. Satisfactory clinical outcomes were observed following CDA for the treatment of single-level cervical disc disease in the present cohort. In addition, uncovertebral joint ossification, cervical kyphosis, and ROM at the index level were found to affect the incidence of AS after CDA.

Comparison between cervical disc arthroplasty and conservative treatment for patients with single level cervical radiculopathy at C5/6.

PubMed

He, Axiang; Xie, Dong; Qu, Bo; Cai, Xiaomin; Kong, Qin; Yang, Lili; Chen, Xiongsheng; Jia, Lianshun

2018-01-31

Cervical radiculopathy is a common disease that affects millions of people. Patients usually are managed by conservative therapy and surgical treatments. To compare the clinical outcomes between cervical disc arthroplasty (CDA) and conservative management for patients with single level cervical radiculopathy at C5/6. Seventy-two patients with cervical radiculopathy that only affect C5/6 joints were included and thirty-two of them received CDA surgery, and forty patients were treated with conservative management. All the patients were followed up around 4 years. Cervical curvature, cervical range of motion (CROM), horizontal displacement of cervical spine, and intervertebral gap were measured by radiological examination. All the patients have comparable disease severity based on pre-surgical radiological assessments. At the 4-year follow-up examination, patients with CDA surgery had less CROM at C5/6 level, while greater CROM at C4/5 level, than control group. Similarly, the horizontal displacement in CDA group decreased at C5/6 vertebrae, and increased at C4/5 level at the 4-year follow-up examination. The intervertebral gaps of patients in CDA group were larger than control group at one-year and last follow-up examination. CDA surgery stabilized C5/6 vertebrae and increased the CROM and horizontal displacement of upper adjacent C4/5 vertebrae. Copyright © 2018. Published by Elsevier Ltd.

Effect of high doses of 2-CdA on Schwann cells of mouse peripheral nerve.

PubMed

Djaldetti, R; Hart, J; Alexandrova, S; Cohen, S; Beilin, B; Djaldetti, M; Bessler, H

1996-07-01

The present study was undertaken to examine the effect of 2-CdA (Leustatin) on the Schwann cells of myelinated and unmyelinated fibers of peripheral mouse nerve. Two groups of mice were injected intravenously for seven days with 2-CdA: one group received daily doses of 1 mg/kg and the other 0.5 mg/kg. Both doses exceeded those accepted in clinical practice. Mice injected with saline served as controls. The sciatic nerve was then dissected and examined with a transmission electron microscope. The Schwann cells of both the myelinated and unmyelinated nerve fibers of the animals receiving the higher doses of 2-CdA showed nuclear and nucleolus damage, loss of heterochromatin, vacuolization and disorganization of the myelin sheaths. The mesaxons and the axons were also damaged. The Schwann cells of the animals treated with the lower doses appeared undamaged. The results indicate that in contrast to other anticancer drugs known to produce peripheral neuropathy, 2-CdA may cause damage to the Schwann cells only at doses exceeding the therapeutic ones.

Retrospective Evaluation of Hairy Cell Leukemia Patients Treated with Three Different First-Line Treatment Modalities in the Last Two Decades: A Single-Center Experience.

PubMed

Öngören, Şeniz; Eşkazan, Ahmet Emre; Berk, Selin; Elverdi, Tuğrul; Salihoğlu, Ayşe; Ar, Muhlis Cem; Başlar, Zafer; Aydın, Yıldız; Tüzüner, Nükhet; Soysal, Teoman

2017-12-01

In this study, we retrospectively analyzed the clinical outcome, treatment responses, infectious complications, and survival rates of 71 hairy cell leukemia (HCL) cases. Sixty-seven patients received a first-line treatment and 2-chlorodeoxyadenosine (cladribine-2-CdA) was administered in 31 cases, 19 patients received interferon-alpha (INF-α), splenectomy was performed in 16 cases, and rituximab was used in one. Although the highest overall response rate (ORR) was observed in patients receiving 2-CdA upfront, ORRs were comparable in the 2-CdA, INF-α, and splenectomy subgroups. Relapse rates were significantly lower in patients who received first-line 2-CdA. The progression-free survival (PFS) rate with 2-CdA was significantly higher than in patients with INF-α and splenectomy, but we found similar overall survival rates with all three upfront treatment modalities. Infections including tuberculosis were a major problem. Although purine analogues have improved the ORRs and PFS, there is still much progress to make with regard to overall survival and relapsed/refractory disease in patients with HCL.

Whole-exome analysis to detect congenital hemolytic anemia mimicking congenital dyserythropoietic anemia.

PubMed

Hamada, Motoharu; Doisaki, Sayoko; Okuno, Yusuke; Muramatsu, Hideki; Hama, Asahito; Kawashima, Nozomu; Narita, Atsushi; Nishio, Nobuhiro; Yoshida, Kenichi; Kanno, Hitoshi; Manabe, Atsushi; Taga, Takashi; Takahashi, Yoshiyuki; Miyano, Satoru; Ogawa, Seishi; Kojima, Seiji

2018-06-23

Congenital dyserythropoietic anemia (CDA) is a heterogeneous group of rare congenital disorders characterized by ineffective erythropoiesis and dysplastic changes in erythroblasts. Diagnosis of CDA is based primarily on the morphology of bone marrow erythroblasts; however, genetic tests have recently become more important. Here, we performed genetic analysis of 10 Japanese patients who had been diagnosed with CDA based on laboratory findings and morphological characteristics. We examined 10 CDA patients via central review of bone marrow morphology and genetic analysis for congenital bone marrow failure syndromes. Sanger sequencing for CDAN1, SEC23B, and KLF1 was performed for all patients. We performed whole-exome sequencing in patients without mutation in these genes. Three patients carried pathogenic CDAN1 mutations, whereas no SEC23B mutations were identified in our cohort. WES unexpectedly identified gene mutations known to cause congenital hemolytic anemia in two patients: canonical G6PD p.Val394Leu mutation and SPTA1 p.Arg28His mutation. Comprehensive genetic analysis is warranted for more effective diagnosis of patients with suspected CDA.

Inhibitory effects of Cyperus digitatus extract on human platelet function in vitro.

PubMed

Fuentes, Eduardo; Forero-Doria, Oscar; Alarcón, Marcelo; Palomo, Iván

2015-01-01

The purpose of this research was to investigate the mechanisms of antiplatelet action of Cyperus digitatus. The antiplatelet action of C. digitatus was studied on platelet function: secretion, adhesion, aggregation, and sCD40L release. The platelet ATP secretion and aggregation were significantly inhibited by CDA (ethyl acetate extract) at 0.1 mg/ml and after the incubation of whole blood with CDA, the platelet coverage was inhibited by 96 ± 3% (p < 0.001). At the same concentration, CDA significantly decreased sCD40L levels. The mechanism of antiplatelet action of CDA could be by NF-κB inhibition and that is cAMP independent. In conclusion, C. digitatus extract may serve as a new source of antiplatelet agents for food and nutraceutical applications.

Dysfunction of SHANK2 and CHRNA7 in a patient with intellectual disability and language impairment supports genetic epistasis of the two loci.

PubMed

Chilian, B; Abdollahpour, H; Bierhals, T; Haltrich, I; Fekete, G; Nagel, I; Rosenberger, G; Kutsche, K

2013-12-01

Synaptopathies constitute a group of neurological diseases including autism spectrum disorders (ASD) and intellectual disability (ID). They have been associated with mutations in genes encoding proteins important for the formation and stabilization of synapses, such as SHANK1-3. Loss-of-function mutations in the SHANK genes have been identified in individuals with ASD and ID suggesting that other factors modify the neurological phenotype. We report a boy with severe ID, behavioral anomalies, and language impairment who carries a balanced de novo triple translocation 46,XY,t(11;17;19)(q13.3;q25.1;q13.42). The 11q13.3 breakpoint was found to disrupt the SHANK2 gene. The patient also carries copy number variations at 15q13.3 and 10q22.11 encompassing ARHGAP11B and two synaptic genes. The CHRNA7 gene encoding α7-nicotinic acetylcholine receptor subunit and the GPRIN2 gene encoding G-protein-regulated inducer of neurite growth 2 were duplicated. Co-occurrence of a de novo SHANK2 mutation and a CHRNA7 duplication in two reported patients with ASD and ID as well as in the patient with t(11;17;19), severe ID and behavior problems suggests convergence of these genes on a common synaptic pathway. Our results strengthen the oligogenic inheritance model and highlight the presence of a large effect mutation and modifier genes collectively determining phenotypic expression of the synaptopathy. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.)

PubMed Central

Zhao, Jie

2010-01-01

Arabinogalactan proteins (AGPs) comprise a family of hydroxyproline-rich glycoproteins that are implicated in plant growth and development. In this study, 69 AGPs are identified from the rice genome, including 13 classical AGPs, 15 arabinogalactan (AG) peptides, three non-classical AGPs, three early nodulin-like AGPs (eNod-like AGPs), eight non-specific lipid transfer protein-like AGPs (nsLTP-like AGPs), and 27 fasciclin-like AGPs (FLAs). The results from expressed sequence tags, microarrays, and massively parallel signature sequencing tags are used to analyse the expression of AGP-encoding genes, which is confirmed by real-time PCR. The results reveal that several rice AGP-encoding genes are predominantly expressed in anthers and display differential expression patterns in response to abscisic acid, gibberellic acid, and abiotic stresses. Based on the results obtained from this analysis, an attempt has been made to link the protein structures and expression patterns of rice AGP-encoding genes to their functions. Taken together, the genome-wide identification and expression analysis of the rice AGP gene family might facilitate further functional studies of rice AGPs. PMID:20423940

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein.

PubMed

Yan, Winston X; Chong, Shaorong; Zhang, Huaibin; Makarova, Kira S; Koonin, Eugene V; Cheng, David R; Scott, David A

2018-04-19

Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a-Cas13c. Despite their small size, Cas13d orthologs from Eubacterium siraeum (Es) and Ruminococcus sp. (Rsp) are active in both CRISPR RNA processing and targeting, as well as collateral RNA cleavage, with no target-flanking sequence requirements. The RspWYL1 protein stimulates RNA cleavage by both EsCas13d and RspCas13d, demonstrating a common regulatory mechanism for divergent Cas13d orthologs. The small size, minimal targeting constraints, and modular regulation of Cas13d effectors further expands the CRISPR toolkit for RNA manipulation and detection. Copyright © 2018 Elsevier Inc. All rights reserved.

Common nonsynonymous variants in PCSK1 confer risk of obesity.

PubMed

Benzinou, Michael; Creemers, John W M; Choquet, Helene; Lobbens, Stephane; Dina, Christian; Durand, Emmanuelle; Guerardel, Audrey; Boutin, Philippe; Jouret, Beatrice; Heude, Barbara; Balkau, Beverley; Tichet, Jean; Marre, Michel; Potoczna, Natascha; Horber, Fritz; Le Stunff, Catherine; Czernichow, Sebastien; Sandbaek, Annelli; Lauritzen, Torsten; Borch-Johnsen, Knut; Andersen, Gitte; Kiess, Wieland; Körner, Antje; Kovacs, Peter; Jacobson, Peter; Carlsson, Lena M S; Walley, Andrew J; Jørgensen, Torben; Hansen, Torben; Pedersen, Oluf; Meyre, David; Froguel, Philippe

2008-08-01

Mutations in PCSK1 cause monogenic obesity. To assess the contribution of PCSK1 to polygenic obesity risk, we genotyped tag SNPs in a total of 13,659 individuals of European ancestry from eight independent case-control or family-based cohorts. The nonsynonymous variants rs6232, encoding N221D, and rs6234-rs6235, encoding the Q665E-S690T pair, were consistently associated with obesity in adults and children (P = 7.27 x 10(-8) and P = 2.31 x 10(-12), respectively). Functional analysis showed a significant impairment of the N221D-mutant PC1/3 protein catalytic activity.

Acetylcholinesterase of the Sand Fly, Phlebotomus papatasi (Scopoli): cDNA Sequence, Baculovirus Expression, and Biochemical Properties

DTIC Science & Technology

2013-01-01

identity to acetylcholinesterase mRNA sequences of Culex tritaeniorhynchus and Lutzomyia longipalpis, respectively. The P. papatasi cDNA ORF encoded a...tritaeniorhynchus and Lutzomyia longipalpis, respectively. The P. papatasi cDNA ORF encoded a 710-amino acid protein [GenBank: AFP20868] exhibiting 85...improve effectiveness of pesticide application for control of the new world sand fly Lutzomyia longipalpis in chicken sheds [13]. Attempts to control

VizieR Online Data Catalog: Algorithm for correcting CoRoT raw light curves (Mislis+, 2010)

NASA Astrophysics Data System (ADS)

Mislis, D.; Schmitt, J. H. M. M.; Carone, L.; Guenther, E. W.; Patzold, M.

2010-10-01

Requirements : gfortran (or g77, ifort) compiler Input Files : The input files sould be raw CoRoT txt files (http://idoc-corot.ias.u-psud.fr/index.jsp) with names CoRoT*.txt Run the cda by typing C>: ./cda.csh (code and data sould be in the same directory) Output files : CDA creates one ascii output file with name - CoRoT*.R.cor for R filter (2 data files).

D-WISE: Diabetes Web-Centric Information and Support Environment: conceptual specification and proposed evaluation.

PubMed

Abidi, Samina; Vallis, Michael; Raza Abidi, Syed Sibte; Piccinini-Vallis, Helena; Imran, Syed Ali

2014-06-01

To develop and evaluate Diabetes Web-Centric Information and Support Environment (D-WISE) that offers 1) a computerized decision-support system to assist physicians to A) use the Canadian Diabetes Association clinical practice guidelines (CDA CPGs) to recommend evidence-informed interventions; B) offer a computerized readiness assessment strategy to help physicians administer behaviour-change strategies to help patients adhere to disease self-management programs; and 2) a patient-specific diabetes self-management application, accessible through smart mobile devices, that offers behaviour-change interventions to engage patients in self-management. The above-mentioned objectives were pursued through a knowledge management approach that involved 1) Translation of paper-based CDA CPGs and behaviour-change models as computerized decision-support tools that will assist physicians to offer evidence-informed and personalized diabetes management and behaviour-change strategies; 2) Engagement of patients in their diabetes care by generating a diabetes self-management program that takes into account their preferences, challenges and needs; 3) Empowering patients to self-manage their condition by providing them with personalized educational and motivational messages through a mobile self-management application. The theoretical foundation of our research is grounded in behaviour-change models and healthcare knowledge management. We used 1) knowledge modelling to computerize the paper-based CDA CPGs and behaviour-change models, in particular, the behaviour-change strategy elements of A) readiness-to-change assessments; B) motivation-enhancement interventions categorized along the lines of patients' being ready, ambivalent or not ready; and C) self-efficacy enhancement. The CDA CPGs and the behaviour-change models are modelled and computerized in terms of A) a diabetes management ontology that serves as the knowledge resource for all the services offered by D-WISE; B) decision support services that use logic-based reasoning algorithms to utilize the knowledge encoded within the diabetes management ontology to assist physicians by recommending patient-specific diabetes-management interventions and behaviour-change strategies; C) a mobile diabetes self-management application to engage and educate diabetes patients to self-manage their condition in a home-based setting while working in concert with their family physicians. We have been successful in creating and conducting a usability assessment of the physician decision support tool. These results will be published once the patient self- management application has been evaluated. D-WISE will be evaluated through pilot studies measuring 1) the usability of the e-Health interventions; and 2) the impact of the interventions on patients' behaviour changes and diabetes control. Copyright © 2014 Canadian Diabetes Association. Published by Elsevier Inc. All rights reserved.

The change of adjacent segment after cervical disc arthroplasty compared with anterior cervical discectomy and fusion: a meta-analysis of randomized controlled trials.

PubMed

Dong, Liang; Xu, Zhengwei; Chen, Xiujin; Wang, Dongqi; Li, Dichen; Liu, Tuanjing; Hao, Dingjun

2017-10-01

Many meta-analyses have been performed to study the efficacy of cervical disc arthroplasty (CDA) compared with anterior cervical discectomy and fusion (ACDF); however, there are few data referring to adjacent segment within these meta-analyses, or investigators are unable to arrive at the same conclusion in the few meta-analyses about adjacent segment. With the increased concerns surrounding adjacent segment degeneration (ASDeg) and adjacent segment disease (ASDis) after anterior cervical surgery, it is necessary to perform a comprehensive meta-analysis to analyze adjacent segment parameters. To perform a comprehensive meta-analysis to elaborate adjacent segment motion, degeneration, disease, and reoperation of CDA compared with ACDF. Meta-analysis of randomized controlled trials (RCTs). PubMed, Embase, and Cochrane Library were searched for RCTs comparing CDA and ACDF before May 2016. The analysis parameters included follow-up time, operative segments, adjacent segment motion, ASDeg, ASDis, and adjacent segment reoperation. The risk of bias scale was used to assess the papers. Subgroup analysis and sensitivity analysis were used to analyze the reason for high heterogeneity. Twenty-nine RCTs fulfilled the inclusion criteria. Compared with ACDF, the rate of adjacent segment reoperation in the CDA group was significantly lower (p<.01), and the advantage of that group in reducing adjacent segment reoperation increases with increasing follow-up time by subgroup analysis. There was no statistically significant difference in ASDeg between CDA and ACDF within the 24-month follow-up period; however, the rate of ASDeg in CDA was significantly lower than that of ACDF with the increase in follow-up time (p<.01). There was no statistically significant difference in ASDis between CDA and ACDF (p>.05). Cervical disc arthroplasty provided a lower adjacent segment range of motion (ROM) than did ACDF, but the difference was not statistically significant. Compared with ACDF, the advantages of CDA were lower ASDeg and adjacent segment reoperation. However, there was no statistically significant difference in ASDis and adjacent segment ROM. Copyright © 2017 Elsevier Inc. All rights reserved.

The homologous HD-Zip I transcription factors HaHB1 and AtHB13 confer cold tolerance via the induction of pathogenesis-related and glucanase proteins.

PubMed

Cabello, Julieta V; Arce, Agustín L; Chan, Raquel L

2012-01-01

Plants deal with cold temperatures via different signal transduction pathways. The HD-Zip I homologous transcription factors HaHB1 from sunflower and AtHB13 from Arabidopsis were identified as playing a key role in such cold response. The expression patterns of both genes were analyzed indicating an up-regulation by low temperatures. When these genes were constitutively expressed in Arabidopsis, the transgenic plants showed similar phenotypes including cell membrane stabilization under freezing treatments and cold tolerance. An exploratory transcriptomic analysis of HaHB1 transgenic plants indicated that several transcripts encoding glucanases and chitinases were induced. Moreover, under freezing conditions some proteins accumulated in HaHB1 plants apoplasts and these extracts exerted antifreeze activity in vitro. Three genes encoding two glucanases and a chitinase were overexpressed in Arabidopsis and these plants were able to tolerate freezing temperatures. All the obtained transgenic plants exhibited cell membrane stabilization after a short freezing treatment. Finally, HaHB1 and AtHB13 were used to transiently transform sunflower and soybean leading to the up-regulation of HaHB1/AtHB13-target homologues thus indicating the conservation of cold response pathways. We propose that HaHB1 and AtHB13 are involved in plant cold tolerance via the induction of proteins able to stabilize cell membranes and inhibit ice growth. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

[Expression, purification and activity analysis of GGDEF and EAL domain-containing proteins from Lactobacillus acidophilus].

PubMed

He, Jia-Hui; Sun, Jie-Li; Yan, Wen-Juan; Wang, Fang

2017-05-20

To identify the functions of the proteins containing the GGDEF or EAL domain in Lactobacillus acidophilus for investigation of the regulatory mechanism of c-di-GMP in this strain. The DNA fragments of NH13_07045-GGDEF, NH13_07050 and NH13_07055 from Lactobacillus acidophilus ATCC4356 were amplified by PCR and cloned into the expression vector pMAL-His-c2. After sequencing, the recombinant plasmids were transformed into competent Escherichia coli cells, which were induced by IPTG to express the recombinant proteins fused with maltose binding protein (MBP). The fusion proteins were purified using amylose resin column for diguanylate cyclase (DGC) or phosphodiesterase (PDE) activity assays in vitro followed by analysis with high-performance liquid chromatography (HPLC). The target DNA fragments were obtained by PCR, and their sequences were all identical to that in GenBank. The purified and concentrated fusion proteins, which were identified by SDS-PAGE and Western blotting, had relative molecular masses of 59 kD, 67 kD and 72 kD. HPLC analysis showed no DGC activity in NH13_07045-GGDEF, while PDE activity was found in NH13_07050 but not in NH13_07055. We obtained the protein encoded by NH13_07050 that possesses PDE activity in vitro. This protein may facilitate the evaluation of the regulatory function of c-di-GMP in Lactobacillus acidophilus.

Regulatory module involving FGF13, miR-504, and p53 regulates ribosomal biogenesis and supports cancer cell survival

PubMed Central

Bublik, Débora R.; Bursać, Slađana; Sheffer, Michal; Oršolić, Ines; Shalit, Tali; Tarcic, Ohad; Kotler, Eran; Mouhadeb, Odelia; Hoffman, Yonit; Fuchs, Gilad; Levin, Yishai; Volarević, Siniša; Oren, Moshe

2017-01-01

The microRNA miR-504 targets TP53 mRNA encoding the p53 tumor suppressor. miR-504 resides within the fibroblast growth factor 13 (FGF13) gene, which is overexpressed in various cancers. We report that the FGF13 locus, comprising FGF13 and miR-504, is transcriptionally repressed by p53, defining an additional negative feedback loop in the p53 network. Furthermore, we show that FGF13 1A is a nucleolar protein that represses ribosomal RNA transcription and attenuates protein synthesis. Importantly, in cancer cells expressing high levels of FGF13, the depletion of FGF13 elicits increased proteostasis stress, associated with the accumulation of reactive oxygen species and apoptosis. Notably, stepwise neoplastic transformation is accompanied by a gradual increase in FGF13 expression and increased dependence on FGF13 for survival (“nononcogene addiction”). Moreover, FGF13 overexpression enables cells to cope more effectively with the stress elicited by oncogenic Ras protein. We propose that, in cells in which activated oncogenes drive excessive protein synthesis, FGF13 may favor survival by maintaining translation rates at a level compatible with the protein quality-control capacity of the cell. Thus, FGF13 may serve as an enabler, allowing cancer cells to evade proteostasis stress triggered by oncogene activation. PMID:27994142

'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interation

USDA-ARS?s Scientific Manuscript database

A nitrogen-fixing alfalfa-nodulating microsymbiont, Sinorhizobium meliloti, has a genome consisting of a 3.5 Mbp circular chromosome and two megaplasmids totaling 3.0 Mbp, one a 1.3 Mbp pSymA carrying nonessential ‘accessory’ genes including nif, nod and others involved in plant interaction. Predict...

EEG correlates of visual short-term memory in older age vary with adult lifespan cognitive development.

PubMed

Wiegand, Iris; Lauritzen, Martin J; Osler, Merete; Mortensen, Erik Lykke; Rostrup, Egill; Rask, Lene; Richard, Nelly; Horwitz, Anna; Benedek, Krisztina; Vangkilde, Signe; Petersen, Anders

2018-02-01

Visual short-term memory (vSTM) is a cognitive resource that declines with age. This study investigated whether electroencephalography (EEG) correlates of vSTM vary with cognitive development over individuals' lifespan. We measured vSTM performance and EEG in a lateralized whole-report task in a healthy birth cohort, whose cognitive function (intelligence quotient) was assessed in youth and late-middle age. Higher vSTM capacity (K; measured by Bundesen's theory of visual attention) was associated with higher amplitudes of the contralateral delay activity (CDA) and the central positivity (CP). In addition, rightward hemifield asymmetry of vSTM (K λ ) was associated with lower CDA amplitudes. Furthermore, more severe cognitive decline from young adulthood to late-middle age predicted higher CDA amplitudes, and the relationship between K and the CDA was less reliable in individuals who show higher levels of cognitive decline compared to individuals with preserved abilities. By contrast, there was no significant effect of lifespan cognitive changes on the CP or the relationship between behavioral measures of vSTM and the CP. Neither the CDA, nor the CP, nor the relationships between K or K λ and the event-related potentials were predicted by individuals' current cognitive status. Together, our findings indicate complex age-related changes in processes underlying behavioral and EEG measures of vSTM and suggest that the K-CDA relationship might be a marker of cognitive lifespan trajectories. Copyright © 2017 Elsevier Inc. All rights reserved.

Compressive cervical pannus formation in a patient after 2-level disc arthroplasty: a rare complication treated with posterior instrumented fusion.

PubMed

Brophy, Carl M; Hoh, Daniel J

2018-06-01

Cervical disc arthroplasty (CDA) has received widespread attention as an alternative to anterior fusion due to its similar neurological and functional improvement, with the advantage of preservation of segmental motion. As CDA becomes more widely implemented, the potential for unexpected device-related adverse events may be identified. The authors report on a 48-year-old man who presented with progressive neurological deficits 3 years after 2-level CDA was performed. Imaging demonstrated periprosthetic osteolysis of the vertebral endplates at the CDA levels, with a heterogeneously enhancing ventral epidural mass compressing the spinal cord. Diagnostic workup for infectious and neoplastic processes was negative. The presumptive diagnosis was an inflammatory pannus formation secondary to abnormal motion at the CDA levels. Posterior cervical decompression and instrumented fusion was performed without removal of the arthroplasty devices or the ventral epidural mass. Postoperative imaging at 2 months demonstrated complete resolution of the compressive pannus, with associated improvement in clinical symptoms. Follow-up MRI at > 6 months showed no recurrence of the pannus. At 1 year postoperatively, CT scanning revealed improvement in periprosthetic osteolysis. Inflammatory pannus formation may be an unexpected complication of abnormal segmental motion after CDA. This rare etiology of an epidural mass associated with an arthroplasty device should be considered, in addition to workup for other potential infectious or neoplastic mass lesions. In symptomatic individuals, compressive pannus lesions can be effectively treated with fusion across the involved segment without removal of the device.

High-resolution melting analysis of sequence variations in the cytidine deaminase gene (CDA) in patients with cancer treated with gemcitabine.

PubMed

Raynal, Caroline; Ciccolini, Joseph; Mercier, Cédric; Boyer, Jean-Christophe; Polge, Anne; Lallemant, Benjamin; Mouzat, Kévin; Lumbroso, Serge; Brouillet, Jean-Paul; Evrard, Alexandre

2010-02-01

Gemcitabine (2',2'-difluorodeoxycytidine) is a major antimetabolite cytotoxic drug with a wide spectrum of activity against solid tumors. Hepatic elimination of gemcitabine depends on a catabolic pathway through a deamination step driven by the enzyme cytidine deaminase (CDA). Severe hematologic toxicity to gemcitabine was reported in patients harboring genetic polymorphisms in CDA gene. High-resolution melting (HRM) analysis of polymerase chain reaction amplicon emerges today as a powerful technique for both genotyping and gene scanning strategies. In this study, 46 DNA samples from gemcitabine-treated patients were subjected to HRM analysis on a LightCycler 480 platform. Residual serum CDA activity was assayed as a surrogate marker for the overall functionality of this enzyme. Genotyping of three well-described single nucleotide polymorphisms in coding region (c.79A>C, c.208G>A and c.435C>T) was successfully achieved by HRM analysis of small polymerase chain reaction fragments, whereas unknown single nucleotide polymorphisms were searched by a gene scanning strategy with longer amplicons (up to 622 bp). The gene scanning strategy allowed us to find a new intronic mutation c.246+37G>A in a female patient displaying marked CDA deficiency and who had an extreme toxic reaction with a fatal outcome to gemcitabine treatment. Our work demonstrates that HRM-based methods, owing to their simplicity, reliability, and speed, are useful tools for diagnosis of CDA deficiency and could be of interest for personalized medicine.

Engineering M13 for phage display.

PubMed

Sidhu, S S

2001-09-01

Phage display is achieved by fusing polypeptide libraries to phage coat proteins. The resulting phage particles display the polypeptides on their surfaces and they also contain the encoding DNA. Library members with particular functions can be isolated with simple selections and polypeptide sequences can be decoded from the encapsulated DNA. The technology's success depends on the efficiency with which polypeptides can be displayed on the phage surface, and significant progress has been made in engineering M13 bacteriophage coat proteins as improved phage display platforms. Functional display has been achieved with all five M13 coat proteins, with both N- and C-terminal fusions. Also, coat protein mutants have been designed and selected to improve the efficiency of heterologous protein display, and in the extreme case, completely artificial coat proteins have been evolved specifically as display platforms. These studies demonstrate that the M13 phage coat is extremely malleable, and this property can be used to engineer the phage particle specifically for phage display. These improvements expand the utility of phage display as a powerful tool in modern biotechnology.

Organization of the human gene for nucleobindin (NUC) and its chromosomal assignment to 19q13.2-q13.4

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

Miura, Keiji; Kurosawa, Yoshikazu; Hirai, Momoki

1996-06-01

Nucleobindin (Nuc) was first identified as a secreted protein of 55 kDa that promotes production of DNA-specific antibodies in lupus-prone MRL/lpr mice. Analysis of cDNA that encoded Nuc revealed that the protein is composed of a signal peptide, a DNA-binding site, two calcium-binding motifs (EF-hand motifs), and a leucine zipper. In the present study, we analysed the organization of the human gene for Nuc (NUC). It consists of 13 exons that are distributed in a region of 32 kb. The functional motifs listed above are encoded in corresponding exons. NUC was expressed in all organs examined. Comparison of nucleotide sequencesmore » in the promotre regions between human and mouse NCU genes revealed several conserved sequences. Among them, two Sp1-binding sites and a CCAAT box are of particular interest. The promoter is of the TATA-less type, and transcription starts at multiple sites in both the human and the mouse genes. These features suggest that NUC might normally play a role as a housekeeping gene. NUC was located at human chromosome 19q13.2-q13.4. 25 refs., 4 figs., 1 tab.« less

A chitin deacetylase from the endophytic fungus Pestalotiopsis sp. efficiently inactivates the elicitor activity of chitin oligomers in rice cells.

PubMed

Cord-Landwehr, Stefan; Melcher, Rebecca L J; Kolkenbrock, Stephan; Moerschbacher, Bruno M

2016-11-30

To successfully survive in plants, endophytes need strategies to avoid being detected by the plant immune system, as the cell walls of endophytes contain easily detectible chitin. It is possible that endophytes "hide" this chitin from the plant immune system by modifying it, or oligomers derived from it, using chitin deacetylases (CDA). To explore this hypothesis, we identified and expressed a CDA from Pestalotiopsis sp. (PesCDA), an endophytic fungus, in E. coli and characterized this enzyme and its chitosan oligomer products. We found that when PesCDA modifies chitin oligomers, the products are partially deacetylated chitosan oligomers with a specific acetylation pattern: GlcNAc-GlcNAc-(GlcN) n -GlcNAc (n ≥ 1). Then, in a bioactivity assay where suspension-cultured rice cells were incubated with the PesCDA products (processed chitin hexamers), we found that, unlike the substrate hexamers, chitosan oligomer products no longer elicited the plant immune system. Thus, this endophytic enzyme can prevent the endophyte from being recognized by the plant immune system; this might represent a more general hypothesis for how certain fungi are able to live in or on their hosts.

A chitin deacetylase from the endophytic fungus Pestalotiopsis sp. efficiently inactivates the elicitor activity of chitin oligomers in rice cells

PubMed Central

Cord-Landwehr, Stefan; Melcher, Rebecca L. J.; Kolkenbrock, Stephan; Moerschbacher, Bruno M.

2016-01-01

To successfully survive in plants, endophytes need strategies to avoid being detected by the plant immune system, as the cell walls of endophytes contain easily detectible chitin. It is possible that endophytes “hide” this chitin from the plant immune system by modifying it, or oligomers derived from it, using chitin deacetylases (CDA). To explore this hypothesis, we identified and expressed a CDA from Pestalotiopsis sp. (PesCDA), an endophytic fungus, in E. coli and characterized this enzyme and its chitosan oligomer products. We found that when PesCDA modifies chitin oligomers, the products are partially deacetylated chitosan oligomers with a specific acetylation pattern: GlcNAc-GlcNAc-(GlcN)n-GlcNAc (n ≥ 1). Then, in a bioactivity assay where suspension-cultured rice cells were incubated with the PesCDA products (processed chitin hexamers), we found that, unlike the substrate hexamers, chitosan oligomer products no longer elicited the plant immune system. Thus, this endophytic enzyme can prevent the endophyte from being recognized by the plant immune system; this might represent a more general hypothesis for how certain fungi are able to live in or on their hosts. PMID:27901067

A novel Dutch mutation in UNC13D reveals an essential role of the C2B domain in munc13-4 function.

PubMed

Elstak, Edo D; te Loo, Maroeska; Tesselaar, Kiki; van Kerkhof, Peter; Loeffen, Jan; Grivas, Dimitris; Hennekam, Eric; Boelens, Jaap Jan; Hoogerbrugge, Peter M; van der Sluijs, Peter; van Gijn, Marielle E; van de Corput, Lisette

2012-04-01

UNC13D, encoding the protein munc13-4, is essential in intracellular trafficking and exocytosis of lytic granules. Mutations in this gene are associated with familial hemophagocytic lymphohistiocytosis type 3 (FHL3), a genetically heterogeneous, rare autosomal recessive immune disorder. How mutations affect function of munc13-4 is poorly understood. Since 2006 we genetically identified seven FHL patients with mutations in UNC13D. Here, we report for the first time a c.2695C>T (p.Arg899X) mutation in exon 28 of UNC13D in three young unrelated Dutch patients. The mutation causes a premature stop codon and encodes munc13-4(1-899), which lacks the C-terminal C2 domain. Genealogical research and haplotyping of the patient families demonstrated that a single ancestral founder introduced the mutation in the Netherlands. We then characterized the mutant protein phenotypically in cell biological and immunological assays. Munc13-4(1-899) was correctly targeted to CD63-positive secretory lysosomes, although its stability was reduced and dynamic turnover on the granule membrane became uncoupled from receptor signaling. In accord, and in contrast to wild-type munc13-4, ectopically expressed mutant failed to rescue degranulation in cells with silenced endogenous munc13-4. The functional and clinical data showed that this novel Dutch founder mutation leads to severe early onset of FHL3 due to misfolding and degradation of munc13-4(1-899). Copyright © 2011 Wiley Periodicals, Inc.

The MET13 Methylenetetrahydrofolate Reductase Gene Is Essential for Infection-Related Morphogenesis in the Rice Blast Fungus Magnaporthe oryzae

PubMed Central

Wang, Hong; Wang, Congcong; Li, Ya; Yue, Xiaofeng; Ma, Zhonghua; Talbot, Nicholas J.; Wang, Zhengyi

2013-01-01

Methylenetetrahydrofolate reductases (MTHFRs) play a key role in the biosynthesis of methionine in both prokaryotic and eukaryotic organisms. In this study, we report the identification of a novel T-DNA-tagged mutant WH672 in the rice blast fungus Magnaporthe oryzae, which was defective in vegetative growth, conidiation and pathogenicity. Analysis of the mutation confirmed a single T-DNA insertion upstream of MET13, which encodes a 626-amino-acid protein encoding a MTHFR. Targeted gene deletion of MET13 resulted in mutants that were non-pathogenic and significantly impaired in aerial growth and melanin pigmentation. All phenotypes associated with Δmet13 mutants could be overcome by addition of exogenous methionine. The M. oryzae genome contains a second predicted MTHFR-encoding gene, MET12. The deduced amino acid sequences of Met13 and Met12 share 32% identity. Interestingly, Δmet12 mutants produced significantly less conidia compared with the isogenic wild-type strain and grew very poorly in the absence of methionine, but were fully pathogenic. Deletion of both genes resulted in Δmet13Δmet12 mutants that showed similar phenotypes to single Δmet13 mutants. Taken together, we conclude that the MTHFR gene, MET13, is essential for infection-related morphogenesis by the rice blast fungus M. oryzae. PMID:24116181

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

PubMed Central

Rodríguez Guilbe, María M.; Alfaro Malavé, Elisa C.; Akerboom, Jasper; Marvin, Jonathan S.; Looger, Loren L.; Schreiter, Eric R.

2008-01-01

Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, this protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way. PMID:18607093

O(-) identified at high temperatures in CaO-based catalysts for oxidative methane dimerization

NASA Technical Reports Server (NTRS)

Freund, F.; Maiti, G. C.; Batllo, F.; Baerns, M.

1990-01-01

A technique called charge-distribution analysis (CDA) is employed to study mobile charge carriers in the oxidation catalysts CaO, CaO with 11 percent Na2O, and CaO with 10 percent La2O3. A threshold temperature of about 550-600 C is identified at which highly mobile charge carriers are present, and the CDA studies show that they are O(-) states. The present investigation indicates the usefulness of CDA in catalysis research with pressed powder samples and gas/solid reactions.

Direct bone morphogenetic protein 2 and Indian hedgehog gene transfer for articular cartilage repair using bone marrow coagulates.

PubMed

Sieker, J T; Kunz, M; Weißenberger, M; Gilbert, F; Frey, S; Rudert, M; Steinert, A F

2015-03-01

Bone morphogenetic protein 2 (BMP-2, encoded by BMP2) and Indian hedgehog protein (IHH, encoded by IHH) are well known regulators of chondrogenesis and chondrogenic hypertrophy. Despite being a potent chondrogenic factor BMP-2 was observed to induce chondrocyte hypertrophy in osteoarthritis (OA), growth plate cartilage and adult mesenchymal stem cells (MSCs). IHH might induce chondrogenic differentiation through different intracellular signalling pathways without inducing subsequent chondrocyte hypertrophy. The primary objective of this study is to test the efficacy of direct BMP2 and IHH gene delivery via bone marrow coagulates to influence histological repair cartilage quality in vivo. Vector-laden autologous bone marrow coagulates with 10(11) adenoviral vector particles encoding BMP2, IHH or the Green fluorescent protein (GFP) were delivered to 3.2 mm osteochondral defects in the trochlea of rabbit knees. After 13 weeks the histological repair cartilage quality was assessed using the ICRS II scoring system and the type II collagen positive area. IHH treatment resulted in superior histological repair cartilage quality than GFP controls in all of the assessed parameters (with P < 0.05 in five of 14 assessed parameters). Results of BMP2 treatment varied substantially, including severe intralesional bone formation in two of six joints after 13 weeks. IHH gene transfer is effective to improve repair cartilage quality in vivo, whereas BMP2 treatment, carried the risk intralesional bone formation. Therefore IHH protein can be considered as an attractive alternative candidate growth factor for further preclinical research and development towards improved treatments for articular cartilage defects. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Molecular Biology of Archaebacteria

DTIC Science & Technology

1988-03-31

Biology of Archaebacteria i2 PERSONAL AUTHOR(S) Patrick P. Dennis 13a. TYPE OF REPORT 13b- TIME COVERED 114. DATE OF REPORT (Year, Month, Day) 15. PAGE...elucidate at the molecular level some of the features that make archaebacteria unique and distinguish them from eubacteria and eucaryotes. Three types...of genes, encoding rRNAs, ribosomal proteins and superoxide dismutase are phylogenetically conserved in all three kingdoms . The structure, organization

Suppression of HTLV-1 replication by Tax-mediated rerouting of the p13 viral protein to nuclear speckles

PubMed Central

Andresen, Vibeke; Pise-Masison, Cynthia A.; Sinha-Datta, Uma; Bellon, Marcia; Valeri, Valerio; Washington Parks, Robyn; Cecchinato, Valentina; Fukumoto, Risaku; Nicot, Christophe

2011-01-01

Disease development in human T-cell leukemia virus type 1 (HTLV-1)–infected individuals is positively correlated with the level of integrated viral DNA in T cells. HTLV-1 replication is positively regulated by Tax and Rex and negatively regulated by the p30 and HBZ proteins. In the present study, we demonstrate that HTLV-1 encodes another negative regulator of virus expression, the p13 protein. Expressed separately, p13 localizes to the mitochondria, whereas in the presence of Tax, part of it is ubiquitinated, stabilized, and rerouted to the nuclear speckles. The p13 protein directly binds Tax, decreases Tax binding to the CBP/p300 transcriptional coactivator, and, by reducing Tax transcriptional activity, suppresses viral expression. Because Tax stabilizes its own repressor, these findings suggest that HTLV-1 has evolved a complex mechanism to control its own replication. Further, these results highlight the importance of studying the function of the HTLV-1 viral proteins, not only in isolation, but also in the context of full viral replication. PMID:21677314

RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica

PubMed Central

Blackman, Leila M.; Cullerne, Darren P.; Torreña, Pernelyn; Taylor, Jen; Hardham, Adrienne R.

2015-01-01

RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response. PMID:26332397

RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica.

PubMed

Blackman, Leila M; Cullerne, Darren P; Torreña, Pernelyn; Taylor, Jen; Hardham, Adrienne R

2015-01-01

RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.

Solution-Processed n-Type Graphene Doping for Cathode in Inverted Polymer Light-Emitting Diodes

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

Kwon, Sung-Joo; Han, Tae-Hee; Kim, Young-Hoon

n-Type doping with (4-(1,3-dimethyl-2,3-dihydro-1H-benzoimidazol-2-yl)phenyl) dimethylamine (N-DMBI) reduces a work function (WF) of graphene by ~0.45 eV without significant reduction of optical transmittance. Solution process of N-DMBI on graphene provides effective n-type doping effect and air-stability at the same time. Although neutral N-DMBI act as an electron receptor leaving the graphene p-doped, radical N-DMBI acts as an electron donator leaving the graphene n-doped, which is demonstrated by density functional theory. We also verify the suitability of N-DMBI-doped n-type graphene for use as a cathode in inverted polymer light-emitting diodes (PLEDs) by using various analytical methods. Inverted PLEDs using a graphene cathodemore » doped with N-DMBI radical showed dramatically improved device efficiency (~13.8 cd/A) than did inverted PLEDs with pristine graphene (~2.74 cd/A). Finally, N-DMBI-doped graphene can provide a practical way to produce graphene cathodes with low WF in various organic optoelectronics.« less

Solution-Processed n-Type Graphene Doping for Cathode in Inverted Polymer Light-Emitting Diodes

DOE PAGES

Kwon, Sung-Joo; Han, Tae-Hee; Kim, Young-Hoon; ...

2018-01-11

n-Type doping with (4-(1,3-dimethyl-2,3-dihydro-1H-benzoimidazol-2-yl)phenyl) dimethylamine (N-DMBI) reduces a work function (WF) of graphene by ~0.45 eV without significant reduction of optical transmittance. Solution process of N-DMBI on graphene provides effective n-type doping effect and air-stability at the same time. Although neutral N-DMBI act as an electron receptor leaving the graphene p-doped, radical N-DMBI acts as an electron donator leaving the graphene n-doped, which is demonstrated by density functional theory. We also verify the suitability of N-DMBI-doped n-type graphene for use as a cathode in inverted polymer light-emitting diodes (PLEDs) by using various analytical methods. Inverted PLEDs using a graphene cathodemore » doped with N-DMBI radical showed dramatically improved device efficiency (~13.8 cd/A) than did inverted PLEDs with pristine graphene (~2.74 cd/A). Finally, N-DMBI-doped graphene can provide a practical way to produce graphene cathodes with low WF in various organic optoelectronics.« less

Effects of endogenous and exogenous progesterone on emotional intelligence in cocaine dependent men and women who also abuse alcohol

PubMed Central

Milivojevic, V; Sinha, R; Morgan, PT; Sofuoglu, M; Fox, HC

2015-01-01

Objective As sex differences in substance dependence may impinge upon the perception and regulation of emotion, we assess Emotional Intelligence (EI) as a function of gender, menstrual cycle (MC) phase and hormonal changes in early abstinent cocaine dependent individuals who abuse alcohol (CDA). Methods Study 1: The Mayer, Salovey, and Caruso Emotional Intelligence Test (MSCEIT) was administered to 98 CDA (55M/43F) and 56 healthy (28M/28F) individuals. Performance in women was also assessed by MC phase. Study 2: The MSCEIT was administered to 18 CDA (19M/9F) who received exogenous progesterone (400mg/day) versus placebo for 7 days. (Study 2). Results Study 1: Healthy females were better than healthy males at facilitating thought and managing emotions. This gender discrepancy was not observed in the CDA group. Additionally, all women in the high compared with the low progesterone phase of their MC were better at managing their emotions. Study 2: Exogenous progesterone improved ability to facilitate thought in both males and females. Conclusions CDA women may be vulnerable to difficulties managing and regulating emotions. Gonadal hormones may contribute to this gender effect, as increases in both endogenous and exogenous progesterone improved selective aspects of EI. PMID:25363303

Calcium-deficient apatite synthesized by ammonia hydrolysis of dicalcium phosphate dihydrate: influence of temperature, time, and pressure.

PubMed

Obadia, Laetitia; Rouillon, Thierry; Bujoli, Bruno; Daculsi, Guy; Bouler, Jean Michel

2007-01-01

In this work, calcium-deficient apatites (CDA) were synthesized by ammonia hydrolysis reaction of dicalcium phosphate dihydrate (DCPD; CaHPO4 x 2 H2O) to obtain biphasic calcium phosphates (BCP) without any extraionic substitution. The influence of three parameters was studied: temperature of the reaction (70 and 100 degrees C), time of the reaction (4 and 18 h), and the pressure (open and closed system). Experiments were made according to a factorial design method (FDM) allowing optimization of the number of samples as well as statistical analysis of results. Moreover, the influence of temperature (until 200 degrees C) was investigated. The crystal size of CDA was determined according to the Scherrer's formula and from Rietveld refinements taking the CDA anisotropy into account. The last method seems to be a reliable method to determine crystallite sizes of CDA, since crystallite sizes of CDA along <00l> and directions were accessible. The results describe the hydroxyapatite % (HA%) in BCP by a first-order polynomial equation in the experimental area studied and the HA content was found to increase by raising time and temperature of the reaction. Moreover, the type of reaction system (open/closed vessel) appeared to have little influence on HA%. 2006 Wiley Periodicals, Inc.

Effects of endogenous and exogenous progesterone on emotional intelligence in cocaine-dependent men and women who also abuse alcohol.

PubMed

Milivojevic, Verica; Sinha, Rajita; Morgan, Peter T; Sofuoglu, Mehmet; Fox, Helen C

2014-11-01

As sex differences in substance dependence may impinge upon the perception and regulation of emotion, we assess emotional intelligence (EI) as a function of gender, menstrual cycle (MC) phase and hormonal changes in early abstinent cocaine-dependent individuals who abuse alcohol (CDA). Study 1: The Mayer, Salovey, and Caruso Emotional Intelligence Test (MSCEIT) was administered to 98 CDA (55 M/43 F) and 56 healthy (28 M/28 F) individuals. Performance in women was also assessed by MC phase. Study 2: The MSCEIT was administered to 28 CDA (19 M/9 F) who received exogenous progesterone (400 mg/day) versus placebo for 7 days (study 2). Study 1: Healthy females were better than healthy males at facilitating thought and managing emotions. This gender discrepancy was not observed in the CDA group. Additionally, all women in the high compared with the low progesterone phase of their MC were better at managing their emotions. Study 2: Exogenous progesterone improved ability to facilitate thought in both males and females. CDA women may be vulnerable to difficulties managing and regulating emotions. Gonadal hormones may contribute to this gender effect, as increases in both endogenous and exogenous progesterone improved selective aspects of EI. Copyright © 2014 John Wiley & Sons, Ltd.

Cassini-CDA Science in 2014 and beyond

NASA Astrophysics Data System (ADS)

Srama, Ralf

2015-04-01

Today, the German-lead Cosmic Dust Analyser (CDA) is operated continuously for 10 years in orbit around Saturn. Many discoveries like the Saturn nanodust streams or the large extended E-ring were achieved. CDA provided unique results regarding Enceladus, his plume and the liquid water below the icy crust. In 2014 and 2015 CDA focuses on extended inclination and equatorial scans of the ring particle densities. Furthermore, scans are performed of the Pallene and Helene regions. Special attention is also given to the search of the dust cloud around Dione and to the Titan region. Long integration times are needed in order to characterize the flux and composition of exogenous dust (including interstellar dust) or possible retrograde dust particles. Finally, dedicated observation campaigns focus on the coupling of nanodust streams to Saturn's magnetosphere and the search of possible periodicities in the stream data. Saturn's rotation frequency was identified in the impact rate of nanodust particles at a Saturn distance of 40 Saturn radii. In the final three years CDA performs exogenous and interstellar dust campaigns, studies of the composition and origin of Saturn's main rings by unique ring ejecta measurements, long-duration nano-dust stream observations, high-resolution maps of small moon orbit crossings, studies of the dust cloud around Dione and studies of the E-ring interaction with the large moon Titan.

C. elegans HIM-8 functions outside of meiosis to antagonize EGL-13 Sox protein function.

PubMed

Nelms, Brian L; Hanna-Rose, Wendy

2006-05-15

egl-13 encodes a Sox domain protein that is required for proper uterine seam cell development in Caenorhabditis elegans. We demonstrate that mutations of the C2H2 zinc fingers encoded by the him-8 (high incidence of males) gene partially suppress the egg-laying and connection-of-gonad morphology defects caused by incompletely penetrant alleles of egl-13. him-8 alleles have previously characterized recessive effects on recombination and segregation of the X chromosome during meiosis due to failure of X chromosome homolog pairing and subsequent synapsis. However, we show that him-8 alleles are semi-dominant suppressors of egl-13, and the semi-dominant effect is due to haplo-insufficiency of the him-8 locus. Thus, we conclude that the wild-type him-8 gene product acts antagonistically to EGL-13. Null alleles of egl-13 cannot be suppressed, suggesting that this antagonistic interaction most likely occurs either upstream of or in parallel with EGL-13. Moreover, we conclude that suppression of egl-13 is due to a meiosis-independent function of him-8 because suppression is observed in mutants that have severely reduced meiotic germ cell populations and suppression does not depend on the function of him-8 in the maternal germ line. We also show that the chromosomal context of egl-13 seems important in the him-8 suppression mechanism. Interactions between these genes can give insight into function of Sox family members, which are important in many aspects of metazoan development, and into functions of him-8 outside of meiosis.

Identification of a spliced gene from duck enteritis virus encoding a protein homologous to UL15 of herpes simplex virus 1.

PubMed

Zhu, Hongwei; Li, Huixin; Han, Zongxi; Shao, Yuhao; Wang, Yu; Kong, Xiangang

2011-04-06

In herpesviruses, UL15 homologue is a subunit of terminase complex responsible for cleavage and packaging of the viral genome into pre-assembled capsids. However, for duck enteritis virus (DEV), the causative agent of duck viral enteritis (DVE), the genomic sequence was not completely determined until most recently. There is limited information of this putative spliced gene and its encoding protein. DEV UL15 consists of two exons with a 3.5 kilobases (kb) inron and transcribes into two transcripts: the full-length UL15 and an N-terminally truncated UL15.5. The 2.9 kb UL15 transcript encodes a protein of 739 amino acids with an approximate molecular mass of 82 kiloDaltons (kDa), whereas the UL15.5 transcript is 1.3 kb in length, containing a putative 888 base pairs (bp) ORF that encodes a 32 kDa product. We also demonstrated that UL15 gene belonged to the late kinetic class as its expression was sensitive to cycloheximide and phosphonoacetic acid. UL15 is highly conserved within the Herpesviridae, and contains Walker A and B motifs homologous to the catalytic subunit of the bacteriophage terminase as revealed by sequence analysis. Phylogenetic tree constructed with the amino acid sequences of 23 herpesvirus UL15 homologues suggests a close relationship of DEV to the Mardivirus genus within the Alphaherpesvirinae. Further, the UL15 and UL15.5 proteins can be detected in the infected cell lysate but not in the sucrose density gradient-purified virion when reacting with the antiserum against UL15. Within the CEF cells, the UL15 and/or UL15.5 localize(s) in the cytoplasm at 6 h post infection (h p. i.) and mainly in the nucleus at 12 h p. i. and at 24 h p. i., while accumulate(s) in the cytoplasm in the absence of any other viral protein. DEV UL15 is a spliced gene that encodes two products encoded by 2.9 and 1.3 kb transcripts respectively. The UL15 is expressed late during infection. The coding sequences of DEV UL15 are very similar to those of alphaherpesviruses and most similar to the genus Mardivirus. The UL15 and/or UL15.5 accumulate(s) in the cytoplasm during early times post-infection and then are translocated to the nucleus at late times.

Whole-Genome Survey of the Putative ATP-Binding Cassette Transporter Family Genes in Vitis vinifera

PubMed Central

Çakır, Birsen; Kılıçkaya, Ozan

2013-01-01

The ATP-binding cassette (ABC) protein superfamily constitutes one of the largest protein families known in plants. In this report, we performed a complete inventory of ABC protein genes in Vitis vinifera, the whole genome of which has been sequenced. By comparison with ABC protein members of Arabidopsis thaliana, we identified 135 putative ABC proteins with 1 or 2 NBDs in V. vinifera. Of these, 120 encode intrinsic membrane proteins, and 15 encode proteins missing TMDs. V. vinifera ABC proteins can be divided into 13 subfamilies with 79 “full-size,” 41 “half-size,” and 15 “soluble” putative ABC proteins. The main feature of the Vitis ABC superfamily is the presence of 2 large subfamilies, ABCG (pleiotropic drug resistance and white-brown complex homolog) and ABCC (multidrug resistance-associated protein). We identified orthologs of V. vinifera putative ABC transporters in different species. This work represents the first complete inventory of ABC transporters in V. vinifera. The identification of Vitis ABC transporters and their comparative analysis with the Arabidopsis counterparts revealed a strong conservation between the 2 species. This inventory could help elucidate the biological and physiological functions of these transporters in V. vinifera. PMID:24244377

Myasthenic syndromes due to defects in COL13A1 and in the N-linked glycosylation pathway.

PubMed

Beeson, David; Cossins, Judith; Rodriguez-Cruz, Pedro; Maxwell, Susan; Liu, Wei-Wei; Palace, Jacqueline

2018-02-01

The congenital myasthenic syndromes (CMS) are hereditary disorders of neuromuscular transmission. The number of cases recognized, at around 1:100,000 in the United Kingdom, is increasing with improved diagnosis. The advent of next-generation sequencing has facilitated the discovery of many genes that harbor CMS-associated mutations. An emerging group of CMS, characterized by a limb-girdle pattern of muscle weakness, is caused by mutations in genes that encode proteins involved in the initial steps of the N-linked glycosylation pathway, which is surprising, since this pathway is found in all mammalian cells. However, mutations in these genes may also give rise to multisystem disorders (congenital disorders of glycosylation) or muscle disorders where the myasthenic symptoms constitute only one component within a wider phenotypic spectrum. We also report a CMS due to mutations in COL13A1, which encodes an extracellular matrix protein that is concentrated at the neuromuscular junction and highlights a role for these extracellular matrix proteins in maintaining synaptic stability that is independent of the AGRN/MuSK clustering pathway. Knowledge about the neuromuscular synapse and the different proteins involved in maintaining its structure as well as function enables us to tailor treatments to the underlying pathogenic mechanisms. © 2018 New York Academy of Sciences.

Differential expression of odorant-binding proteins in the mandibular glands of the honey bee according to caste and age.

PubMed

Iovinella, Immacolata; Dani, Francesca Romana; Niccolini, Alberto; Sagona, Simona; Michelucci, Elena; Gazzano, Angelo; Turillazzi, Stefano; Felicioli, Antonio; Pelosi, Paolo

2011-08-05

Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) mediate both perception and release of chemical stimuli in insects. The genome of the honey bee contains 21 genes encoding OBPs and 6 encoding CSPs. Using a proteomic approach, we have investigated the expression of OBPs and CSPs in the mandibular glands of adult honey bees in relation to caste and age. OBP13 is mostly expressed in young individuals and in virgin queens, while OBP21 is abundant in older bees and is prevalent in mated queens. OBP14, which had been found in larvae, is produced in hive workers' glands. Quite unexpectedly, the mandibular glands of drones also contain OBPs, mainly OBP18 and OBP21. We have expressed three of the most represented OBPs and studied their binding properties. OBP13 binds with good specificity oleic acid and some structurally related compounds, OBP14 is better tuned to monoterpenoid structures, while OBP21 binds the main components of queen mandibular pheromone as well as farnesol, a compound used as a trail pheromone in the honey bee and other hymenopterans. The high expression of different OBPs in the mandibular glands suggests that such proteins could be involved in solubilization and release of semiochemicals.

Hybrid Corpectomy and Disc Arthroplasty for Cervical Spondylotic Myelopathy Caused by Ossification of Posterior Longitudinal Ligament and Disc Herniation.

PubMed

Chang, Huang-Chou; Tu, Tsung-Hsi; Chang, Hsuan-Kan; Wu, Jau-Ching; Fay, Li-Yu; Chang, Peng-Yuan; Wu, Ching-Lan; Huang, Wen-Cheng; Cheng, Henrich

2016-11-01

The combination of anterior cervical discectomy and fusion (ACDF) and anterior cervical corpectomy and fusion (ACCF) has been demonstrated to be effective for multilevel cervical spondylotic myelopathy (CSM); however, the combination of ACCF and cervical disc arthroplasty (CDA) for 3-level CSM has never been addressed. Consecutive patients (>18 years of age) with CSM caused by segmental ossification of posterior longitudinal ligament (OPLL) and degenerative disc disease (DDD) were reviewed. Inclusion criteria were patients who underwent hybrid ACCF and CDA surgery for symptomatic 3-level CSM with OPLL and DDD. Medical and radiologic records were reviewed retrospectively. A total of 15 patients were analyzed with a mean follow-up of 18.1 ± 7.42 months. Every patient had hybrid surgery composed of 1-level ACCF (for segmental-type OPLL causing spinal stenosis) and 1-level CDA at the adjacent level (for DDD causing stenosis). All clinical outcomes, including visual analogue scale of neck and arm pain, Neck Disability Index, Japanese Orthopedic Association scores, and Nurick scores of myelopathy, demonstrated significant improvement at 12 months after surgery. All patients (100%) achieved arthrodesis for the ACCF (instrumented) and preserved mobility for CDA (preoperation 6.2 ± 3.81° vs. postoperation 7.0 ± 4.18°; P = 0.579). For patients with multilevel CSM caused by segmental OPLL and DDD, the hybrid surgery of ACCF and CDA demonstrated satisfactory clinical and radiologic outcomes. Moreover, although located next to each other, the instrumented ACCF construct and CDA still achieved solid arthrodesis and preserved mobility, respectively. Therefore, hybrid surgery may be a reasonable option for the management of CSM with OPLL. Copyright © 2016 Elsevier Inc. All rights reserved.

Cda Science Today and in Cassini's Final Three Years

NASA Astrophysics Data System (ADS)

Srama, R.

2014-12-01

Today, the German-lead Cosmic Dust Analyser (CDA) is operated continuously for 10 years in orbit around Saturn. The first discovery of CDA related to Saturn was the measurement of nanometer sized dust particles ejected by to interplanetary space with speeds higher than 100 km/s. Their origin and composition was analysed and and their dynamical studies showed a strong link to the conditions of the solar wind plasma flow. A recent surprising result was, that stream particles stem from the interior of Enceladus. Since 2004 CDA measured millions of dust impacts characterizing the dust environment of Saturn. The instrument showed strong evidence for ice geysers located at the south pole of Saturn's moon Enceladus in 2005. Later, a detailed compositional analysis of the salt-rich water ice grains in Saturn's E ring system lead to the discovery of liquid water below the icy crust connected to an ocean at depth feeding the icy jets. CDA was even capable to derive a spatially resolved compositional profile of the plume during close Enceladus flybys. A determination of the dust-magnetosphere interaction and the discovery of the extended E ring allowed the definition of a dynamical dust model of Saturn's E ring describing the observed properties. The measured dust density profiles in the dense E ring revealed geometric asymmetries.In the final three years CDA performs exogenous and interstellar dust campaigns, studies of the composition and origin of Saturn's main rings by unique ring ejecta measurements, long-duration nano-dust stream observations, high-resolution maps of small moon orbit crossings, studies of the dust cloud around Dione and studies of the E-ring interaction with the large moon Titan.

The Cassini Cosmic Dust Analyser CDA - A 10 year exploration of Saturn's dust environment

NASA Astrophysics Data System (ADS)

Srama, Ralf

2014-05-01

The interplanetary space probe Cassini/Huygens reached Saturn in July 2004 after seven years of cruise phase. Since then, the German-lead Cosmic Dust Analyser (CDA) was operated continuously for 10 years in orbit around Saturn. The first discovery of CDA related to Saturn was the measurement of nanometer sized dust particles ejected by its magnetosphere to interplanetary space with speeds higher than 100 km/s. Their origin and composition was analysed and an their dynamical studies showed a strong link to the conditions of the solar wind plasma flow. A recent surprising result was, that stream particles stem from the interior of Enceladus. Since 2004 CDA measured millions of dust impacts characterizing the dust environment of Saturn. The instrument showed strong evidence for ice geysers located at the south pole of Saturn's moon Enceladus in 2005. Later, a detailed compositional analysis of the salt-rich water ice grains in Saturn's E ring system lead to the discovery of liquid water below the crust connected to an ocean at depth feeding the icy jets. CDA was even capable to derive a spatially resolved compositional profile of the plume during close Enceladus flybys. A determination of the dust-magnetosphere interaction and the discovery of the extended E ring (at least twice as large as previously known) allowed the definition of a dynamical dust model of Saturns E ring describing the observed properties. Cassini performed shadow crossings in the ring plane and dust grain charges were measured in shadow regions delivering important data for dust-plasma interaction studies. In the last years, dedicated measurement campaigns were executed by CDA to monitor the flux of interplanetary and interstellar dust particles reaching Saturn.

Contralateral delay activity tracks object identity information in visual short term memory.

PubMed

Gao, Zaifeng; Xu, Xiaotian; Chen, Zhibo; Yin, Jun; Shen, Mowei; Shui, Rende

2011-08-11

Previous studies suggested that ERP component contralateral delay activity (CDA) tracks the number of objects containing identity information stored in visual short term memory (VSTM). Later MEG and fMRI studies implied that its neural source lays in superior IPS. However, since the memorized stimuli in previous studies were displayed in distinct spatial locations, hence possibly CDA tracks the object-location information instead. Moreover, a recent study implied the activation in superior IPS reflected the location load. The current research thus explored whether CDA tracks the object-location load or the object-identity load, and its neural sources. Participants were asked to remember one color, four identical colors or four distinct colors. The four-identical-color condition was the critical one because it contains the same amount of identity information as that of one color while the same amount of location information as that of four distinct colors. To ensure the participants indeed selected four colors in the four-identical-color condition, we also split the participants into two groups (low- vs. high-capacity), analyzed late positive component (LPC) in the prefrontal area, and collected participant's subjective-report. Our results revealed that most of the participants selected four identical colors. Moreover, regardless of capacity-group, there was no difference on CDA between one color and four identical colors yet both were lower than 4 distinct colors. Besides, the source of CDA was located in the superior parietal lobule, which is very close to the superior IPS. These results support the statement that CDA tracks the object identity information in VSTM. Copyright © 2011 Elsevier B.V. All rights reserved.

Common data model for natural language processing based on two existing standard information models: CDA+GrAF.

PubMed

Meystre, Stéphane M; Lee, Sanghoon; Jung, Chai Young; Chevrier, Raphaël D

2012-08-01

An increasing need for collaboration and resources sharing in the Natural Language Processing (NLP) research and development community motivates efforts to create and share a common data model and a common terminology for all information annotated and extracted from clinical text. We have combined two existing standards: the HL7 Clinical Document Architecture (CDA), and the ISO Graph Annotation Format (GrAF; in development), to develop such a data model entitled "CDA+GrAF". We experimented with several methods to combine these existing standards, and eventually selected a method wrapping separate CDA and GrAF parts in a common standoff annotation (i.e., separate from the annotated text) XML document. Two use cases, clinical document sections, and the 2010 i2b2/VA NLP Challenge (i.e., problems, tests, and treatments, with their assertions and relations), were used to create examples of such standoff annotation documents, and were successfully validated with the XML schemata provided with both standards. We developed a tool to automatically translate annotation documents from the 2010 i2b2/VA NLP Challenge format to GrAF, and automatically generated 50 annotation documents using this tool, all successfully validated. Finally, we adapted the XSL stylesheet provided with HL7 CDA to allow viewing annotation XML documents in a web browser, and plan to adapt existing tools for translating annotation documents between CDA+GrAF and the UIMA and GATE frameworks. This common data model may ease directly comparing NLP tools and applications, combining their output, transforming and "translating" annotations between different NLP applications, and eventually "plug-and-play" of different modules in NLP applications. Copyright © 2011 Elsevier Inc. All rights reserved.

Phylogenetic analysis of fungal heterotrimeric G protein-encoding genes and their expression during dimorphism in Mucor circinelloides.

PubMed

Valle-Maldonado, Marco Iván; Jácome-Galarza, Irvin Eduardo; Díaz-Pérez, Alma Laura; Martínez-Cadena, Guadalupe; Campos-García, Jesús; Ramírez-Díaz, Martha Isela; Reyes-De la Cruz, Homero; Riveros-Rosas, Héctor; Díaz-Pérez, César; Meza-Carmen, Víctor

2015-12-01

In fungi, heterotrimeric G proteins are key regulators of biological processes such as mating, virulence, morphology, among others. Mucor circinelloides is a model organism for many biological processes, and its genome contains the largest known repertoire of genes that encode putative heterotrimeric G protein subunits in the fungal kingdom: twelve Gα (McGpa1-12), three Gβ (McGpb1-3), and three Gγ (McGpg1-3). Phylogenetic analysis of fungal Gα showed that they are divided into four distinct groups as reported previously. Fungal Gβ and Gγ are also divided into four phylogenetic groups, and to our understanding this is the first report of a phylogenetic classification for fungal Gβ and Gγ subunits. Almost all genes that encode putative heterotrimeric G subunits in M. circinelloides are differentially expressed during dimorphic growth, except for McGpg1 (Gγ) that showed very low mRNA levels at all developmental stages. Moreover, several of the subunits are expressed in a similar pattern and at the same level, suggesting that they constitute discrete complexes. For example, McGpb3 (Gβ), and McGpg2 (Gγ), are co-expressed during mycelium growth, and McGpa1, McGpb2, and McGpg2, are co-expressed during yeast development. These findings provide the conceptual framework to study the biological role of these genes during M. circinelloides morphogenesis. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Yellow emitting Iridium (III) phenyl-benzothiazole complexes with different β-diketone ancillary ligands as dopants in white organic light-emitting diodes

NASA Astrophysics Data System (ADS)

Ivanov, P.; Petrova, P.; Tomova, R.

2018-03-01

We discuss the influence of the type of β-diketone ancillary ligand in Iridium (III) bis phenyl-benzothiazole complexes ((bt)2Ir(β-diketone)) on their photophysical and electroluminescent properties when they are used as dopants in white organic light-emitting diodes (WOLED). For this purpose, we investigated four novel yellow cyclometalated complexes: (bt)2Ir(dbm), (bt)2Ir(fmtdbm), (bt)2Ir(tta) and (bt)2Ir(bsm), where dbm = 1,3-diphenylpropane-1,3-dionate; fmtdbm = 1-(4-fluorophenyl)-3-(4-methoxyphenyl)propane-1,3-dionate; tta = 4,4,4-trifluoro-1-(thiophene-2-yl)butane-1,3-dionate; and bsm = 1-phenylicosane-1,3-dionate). To obtain white light by mixing emissions of two complementary colors (yellow emitted by the dopant and blue, by another emitter), we chose the following OLED structure: ITO/doped HTL/ElL/ETL/M, where ITO was a transparent anode of In2O3:SnO2; M, a metallic Al cathode; HTL, 4,4’-Bis(9H-carbazol-9-yl)biphenyl (CBP) involved in a poly(N-vinylcarbazole) (PVK) matrix; ElL, an electroluminescent layer of aluminum(III)bis(2-methyl-8-quninolinato)-4-phenylphenolate (BAlq); and ETL, an electron-transporting layer of zinc(II)bis(2-2-hydroxyphenyl)benzothiazole. We found that all complexes are suitable candidates for fabrication of WOLED. The best results were demonstrated by the device doped with 2 wt % of (bt)2Ir(bsm), which had twice as high luminescence (1100 cd/m2) and one-and-a-half as high current efficiency (5 cd/A) as the device doped with 1.25 wt % of the known (bt)2Ir(acac), with its 580 cd/m2 and 3.4 cd/A at approximately the same CIE (Commission Internationale de L’Eclairage) (x/y) coordinates of the warm white light emitted by the two devices.

Immunohistochemical identification of varicella-zoster virus gene 63-encoded protein (IE63) and late (gE) protein on smears and cutaneous biopsies: implications for diagnostic use.

PubMed

Nikkels, A F; Debrus, S; Sadzot-Delvaux, C; Piette, J; Rentier, B; Piérard, G E

1995-12-01

Early and specific recognition of varicella zoster virus (VZV) infection is of vital concern in immunocompromised patients. The aim of this study was to compare the diagnostic accuracy of histochemical and immunohistochemical identification of the VZV ORF63 encoded protein (IE63) and of the VZV late protein gE on smears and formalin-fixed paraffin-embedded skin sections taken from lesions clinically diagnosed as varicella (n = 15) and herpes zoster (n = 51). Microscopic examinations of Tzanck smears and skin sections yielded a diagnostic accuracy of Herpesviridae infections in 66.7% (10/15) and 92.3% (12/13) of varicella, and 74.4% (29/39) and 87.8% (43/49) of herpes zoster, respectively. Immunohistochemistry applied to varicella provided a type-specific virus diagnostic accuracy of 86.7% (13/15; IE63) and 100% (15/15; gE) on smears, and of 92.3% for both VZV proteins on skin sections. In herpes zoster, the diagnostic accuracy of immunohistochemistry reached 92.3% (36/39; IE63) and 94.9% (37/39; gE) on smears, and 91.7% (44/48; IE63) and 91.8% (45/49; gE) on skin sections. These findings indicate that the immunohistochemical detection of IE63 and gE on both smears and skin sections yields a higher specificity and sensitivity than standard microscopic assessments.

49 CFR 192.931 - How may Confirmatory Direct Assessment (CDA) be used?

Code of Federal Regulations, 2010 CFR

2010-10-01

...) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF NATURAL AND OTHER GAS BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Gas Transmission Pipeline Integrity Management § 192.931 How may Confirmatory Direct Assessment (CDA) be used? An...

Surface acetylation of bamboo cellulose: preparation and rheological properties.

PubMed

Cai, Jie; Fei, Peng; Xiong, Zhouyi; Shi, Yongjun; Yan, Kai; Xiong, Hanguo

2013-01-30

In this study, purified bamboo cellulose was used to synthesize cellulose diacetate (B-CDA). The synthesis was controlled by determination of the degree of substitution and insoluble residue content. The product then was characterized by FTIR. The rheological properties of B-CDA solutions in acetone/N,N-dimethylacetamide (DMAc) solvent system were systematically investigated on an advanced rheometer, including the dependence of apparent viscosity η(α), non-Newtonian index n, and structural viscosity index Δη on the concentration and temperature of the solutions. B-CDA-acetone/DMAc solution is a shear-thinning fluid. With increasing solution concentration and decreasing temperature, Δη increased, whereas n decreased, which indicates a deteriorating spinnability. Moreover, the values of the viscous flow activation energy E(η) based on the Arrhenius equation increased when the shear rate γ was enhanced, which indicates that the η(α) of the solution is more sensitive to temperature in the higher γ values. The results are favorable for predicting the B-CDA solution spinnability. Copyright © 2012 Elsevier Ltd. All rights reserved.

Regulation of ciliary retrograde protein trafficking by the Joubert syndrome proteins ARL13B and INPP5E.

PubMed

Nozaki, Shohei; Katoh, Yohei; Terada, Masaya; Michisaka, Saki; Funabashi, Teruki; Takahashi, Senye; Kontani, Kenji; Nakayama, Kazuhisa

2017-02-01

ARL13B (a small GTPase) and INPP5E (a phosphoinositide 5-phosphatase) are ciliary proteins encoded by causative genes of Joubert syndrome. We here showed, by taking advantage of a visible immunoprecipitation assay, that ARL13B interacts with the IFT46 -: IFT56 (IFT56 is also known as TTC26) dimer of the intraflagellar transport (IFT)-B complex, which mediates anterograde ciliary protein trafficking. However, the ciliary localization of ARL13B was found to be independent of its interaction with IFT-B, but dependent on the ciliary-targeting sequence RVEP in its C-terminal region. ARL13B-knockout cells had shorter cilia than control cells and exhibited aberrant localization of ciliary proteins, including INPP5E. In particular, in ARL13B-knockout cells, the IFT-A and IFT-B complexes accumulated at ciliary tips, and GPR161 (a negative regulator of Hedgehog signaling) could not exit cilia in response to stimulation with Smoothened agonist. This abnormal phenotype was rescued by the exogenous expression of wild-type ARL13B, as well as by its mutant defective in the interaction with IFT-B, but not by its mutants defective in INPP5E binding or in ciliary localization. Thus, ARL13B regulates IFT-A-mediated retrograde protein trafficking within cilia through its interaction with INPP5E. © 2017. Published by The Company of Biologists Ltd.

Highlights and discoveries of the Cosmic Dust Analyser (CDA) during its 15 years of exploration

NASA Astrophysics Data System (ADS)

Srama, R.; Moragas-Klostermeyer, G.; Kempf, S.; Postberg, F.; Albin, T.; Auer, S.; Altobelli, N.; Beckmann, U.; Bugiel, S.; Burton, M.; Economou, T.; Fliege, K.; Grande, M.; Gruen, E.; Guglielmino, M.; Hillier, J. K.; Schilling, A.; Schmidt, J.; Seiss, M.; Spahn, F.; Sterken, V.; Trieloff, M.

2014-04-01

The interplanetary space probe Cassini/Huygens reached Saturn in July 2004 after seven years of cruise phase. Today, the German-lead Cosmic Dust Analyser (CDA) is operated continuously for 10 years in orbit around Saturn. During the cruise phase CDA measured the interstellar dust flux at one AU distance from the Sun, the charge and composition of interplanetary dust grains and the composition of the Jovian nanodust streams. The first discovery of CDA related to Saturn was the measurement of nanometer sized dust particles ejected by its magnetosphere to interplanetary space with speeds higher than 100 km/s. Their origin and composition was analysed and an their dynamical studies showed a strong link to the conditions of the solar wind plasma flow. A recent surprising result was, that stream particles stem from the interior of Enceladus. Since 2004 CDA measured millions of dust impacts characterizing the dust environment of Saturn. The instrument showed strong evidence for ice geysers located at the south pole of Saturn's moon Enceladus in 2005. Later, a detailed compositional analysis of the salt-rich water ice grains in Saturn's E ring system lead to the discovery of liquid water below the icy crust connected to an ocean at depth feeding the icy jets. CDA was even capable to derive a spatially resolved compositional profile of the plume during close Enceladus flybys. A determination of the dust-magnetosphere interaction and the discovery of the extended E ring allowed the definition of a dynamical dust model of Saturn's E ring describing the observed properties. The measured dust density profiles in the dense E ring revealed geometric asymmetries. Cassini performed shadow crossings in the ring plane and dust grain charges were measured in shadow regions delivering important data for dust-plasma interaction studies. In the last years, dedicated measurement campaigns were executed by CDA to monitor the flux of interplanetary and interstellar dust particles reaching Saturn. Currently, the composition of interstellar grains and the meteoroid flux into the Saturnian system are in analysis.

New Chromogenic Agar Medium for the Identification of Candida spp.

PubMed Central

Cooke, Venitia M.; Miles, R. J.; Price, R. G.; Midgley, G.; Khamri, W.; Richardson, A. C.

2002-01-01

A new chromogenic agar medium (Candida diagnostic agar [CDA]) for differentiation of Candida spp. is described. This medium is based on Sabouraud dextrose agar (Oxoid CM41) and contains (per liter) 40.0 g of glucose, 10.0 g of mycological peptone, and 15.0 g of agar along with a novel chromogenic glucosaminidase substrate, ammonium 4-{2-[4-(2-acetamido-2-deoxy-β-d-glucopyranosyloxy)-3-methoxyphenyl]-vinyl}-1-(propan-3-yl-oate)-quinolium bromide (0.32 g liter−1). The glucosaminidase substrate in CDA was hydrolyzed by Candida albicans and Candida dubliniensis, yielding white colonies with deep-red spots on a yellow transparent background after 24 to 48 h of incubation at 37°C. Colonies of Candida tropicalis and Candida kefyr were uniformly pink, and colonies of other Candida spp., including Candida glabrata and Candida parapsilosis, were white. CDA was evaluated by using 115 test strains of Candida spp. and other clinically important yeasts and was compared with two commercially available chromogenic agars (Candida ID agar [bioMerieux] and CHROMagar Candida [CHROMagar Company Ltd.]). On all three agars, colonies of C. albicans were not distinguished from colonies of C. dubliniensis. However, for the group containing C. albicans plus C. dubliniensis, both the sensitivity and the specificity of detection when CDA was used were 100%, compared with values of 97.6 and 100%, respectively, with CHROMagar Candida and 100 and 96.8%, respectively, with Candida ID agar. In addition, for the group containing C. tropicalis plus C. kefyr, the sensitivity and specificity of detection when CDA was used were also 100%, compared with 72.7 and 98.1%, respectively, with CHROMagar Candida. Candida ID agar did not differentiate C. tropicalis and C. kefyr strains but did differentiate members of a broader group (C. tropicalis, C. kefyr, Candida lusitaniae plus Candida guilliermondii); the sensitivity and specificity of detection for members of this group were 94.7 and 93.8%, respectively. In addition to the increased sensitivity and/or specificity of Candida detection when CDA was used, differentiation of colony types on CDA (red spotted, pink, or no color) was unambiguous and did not require precise assessment of colony color. PMID:12089051

Complete mitochondrial genome of Chuanzhong black goat in southwest of China (Capra hircus).

PubMed

Huang, Yong-Fu; Chen, Li-Peng; Zhao, Yong-Ju; Zhang, Hao; Na, Ri-Su; Zhao, Zhong-Quan; Zhang, Jia-Hua; Jiang, Cao-De; Ma, Yue-Hui; Sun, Ya-Wang; E, Guang-Xin

2016-09-01

The Chuanzhong black goat (Capra hircus) is a breed native to southwest of China. Its complete mitochondrial genome is 16,641 nt in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.5%, T: 27.3%, C: 26.1%, and G: 13.1%. The complete mitogenome of the Chinese indigenous breed of goat could provide a basic data for further phylogenetics analysis.

The chromosomal mapping of four genes encoding winged helix proteins expressed early in mouse development

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

Labosky, P.A.; Sakaki, Hiroshi; Hogan, B.L.M.

1996-06-01

Members of the winged helix family of transcription factors are required for the normal embryonic development of the mouse. Using the interspecific backcross panel from The Jackson Laboratory, we have determined the chromosomal locations of four genes that encode winged helix containing proteins. Mf1 was assigned to mouse Chromosome 8, Mf2 to Chromosome 4, Mf3 to Chromosome 9, and Mf4 to Chromosome 13. Since Mf3 is located in a region of Chromosome 9 containing many well-characterized mouse mutations such as short ear (se), ashen (ash), and dilute (d), we have analyzed deletion mutants to determine the location of Mf3 moremore » precisely. 14 refs., 3 figs.« less

Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks.

PubMed

Lin, Wen-Hsien; Liu, Wei-Chung; Hwang, Ming-Jing

2009-03-11

Human cells of various tissue types differ greatly in morphology despite having the same set of genetic information. Some genes are expressed in all cell types to perform house-keeping functions, while some are selectively expressed to perform tissue-specific functions. In this study, we wished to elucidate how proteins encoded by human house-keeping genes and tissue-specific genes are organized in human protein-protein interaction networks. We constructed protein-protein interaction networks for different tissue types using two gene expression datasets and one protein-protein interaction database. We then calculated three network indices of topological importance, the degree, closeness, and betweenness centralities, to measure the network position of proteins encoded by house-keeping and tissue-specific genes, and quantified their local connectivity structure. Compared to a random selection of proteins, house-keeping gene-encoded proteins tended to have a greater number of directly interacting neighbors and occupy network positions in several shortest paths of interaction between protein pairs, whereas tissue-specific gene-encoded proteins did not. In addition, house-keeping gene-encoded proteins tended to connect with other house-keeping gene-encoded proteins in all tissue types, whereas tissue-specific gene-encoded proteins also tended to connect with other tissue-specific gene-encoded proteins, but only in approximately half of the tissue types examined. Our analysis showed that house-keeping gene-encoded proteins tend to occupy important network positions, while those encoded by tissue-specific genes do not. The biological implications of our findings were discussed and we proposed a hypothesis regarding how cells organize their protein tools in protein-protein interaction networks. Our results led us to speculate that house-keeping gene-encoded proteins might form a core in human protein-protein interaction networks, while clusters of tissue-specific gene-encoded proteins are attached to the core at more peripheral positions of the networks.

The Complete Set of Genes Encoding Major Intrinsic Proteins in Arabidopsis Provides a Framework for a New Nomenclature for Major Intrinsic Proteins in Plants1

PubMed Central

Johanson, Urban; Karlsson, Maria; Johansson, Ingela; Gustavsson, Sofia; Sjövall, Sara; Fraysse, Laure; Weig, Alfons R.; Kjellbom, Per

2001-01-01

Major intrinsic proteins (MIPs) facilitate the passive transport of small polar molecules across membranes. MIPs constitute a very old family of proteins and different forms have been found in all kinds of living organisms, including bacteria, fungi, animals, and plants. In the genomic sequence of Arabidopsis, we have identified 35 different MIP-encoding genes. Based on sequence similarity, these 35 proteins are divided into four different subfamilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NOD26-like intrinsic proteins also called NOD26-like MIPs, and the recently discovered small basic intrinsic proteins. In Arabidopsis, there are 13 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26-like intrinsic proteins, and three small basic intrinsic proteins. The gene structure in general is conserved within each subfamily, although there is a tendency to lose introns. Based on phylogenetic comparisons of maize (Zea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intron patterns in the subfamilies were formed before the split of monocotyledons and dicotyledons. Although the gene structure is unique for each subfamily, there is a common pattern in how transmembrane helices are encoded on the exons in three of the subfamilies. The nomenclature for plant MIPs varies widely between different species but also between subfamilies in the same species. Based on the phylogeny of all AtMIPs, a new and more consistent nomenclature is proposed. The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species. PMID:11500536

Deregulation of Rab and Rab Effector Genes in Bladder Cancer

PubMed Central

Ho, Joel R.; Chapeaublanc, Elodie; Kirkwood, Lisa; Nicolle, Remy; Benhamou, Simone; Lebret, Thierry; Allory, Yves; Southgate, Jennifer; Radvanyi, François; Goud, Bruno

2012-01-01

Growing evidence indicates that Rab GTPases, key regulators of intracellular transport in eukaryotic cells, play an important role in cancer. We analysed the deregulation at the transcriptional level of the genes encoding Rab proteins and Rab-interacting proteins in bladder cancer pathogenesis, distinguishing between the two main progression pathways so far identified in bladder cancer: the Ta pathway characterized by a high frequency of FGFR3 mutation and the carcinoma in situ pathway where no or infrequent FGFR3 mutations have been identified. A systematic literature search identified 61 genes encoding Rab proteins and 223 genes encoding Rab-interacting proteins. Transcriptomic data were obtained for normal urothelium samples and for two independent bladder cancer data sets corresponding to 152 and 75 tumors. Gene deregulation was analysed with the SAM (significant analysis of microarray) test or the binomial test. Overall, 30 genes were down-regulated, and 13 were up-regulated in the tumor samples. Five of these deregulated genes (LEPRE1, MICAL2, RAB23, STXBP1, SYTL1) were specifically deregulated in FGFR3-non-mutated muscle-invasive tumors. No gene encoding a Rab or Rab-interacting protein was found to be specifically deregulated in FGFR3-mutated tumors. Cluster analysis showed that the RAB27 gene cluster (comprising the genes encoding RAB27 and its interacting partners) was deregulated and that this deregulation was associated with both pathways of bladder cancer pathogenesis. Finally, we found that the expression of KIF20A and ZWINT was associated with that of proliferation markers and that the expression of MLPH, MYO5B, RAB11A, RAB11FIP1, RAB20 and SYTL2 was associated with that of urothelial cell differentiation markers. This systematic analysis of Rab and Rab effector gene deregulation in bladder cancer, taking relevant tumor subgroups into account, provides insight into the possible roles of Rab proteins and their effectors in bladder cancer pathogenesis. This approach is applicable to other group of genes and types of cancer. PMID:22724020

[Mid- to long-term outcomes of cervical disc arthroplasty for symptomatic cervical disc disease: a meta-analysis].

PubMed

Kan, S L; Yang, B; Ning, G Z; Gao, S J; Sun, J C; Feng, S Q

2016-12-01

Objective: To compare the benefits and harms of cervical disc arthroplasty (CDA) with anterior cervical discectomy and fusion(ACDF) for symptomatic cervical disc disease at mid- to long-term follow-up. Methods: Electronic searches were made in PubMed, EMBASE, and the Cochrane Library for randomized controlled trials with at least 48 moths follow-up.Outcomes were reported as relative risk or standardized mean difference.Meta-analysis was carried out using Revman version 5.3 and Stata version 12.0. Results: Seven trials were included, involving 2 302 participants.The results of this meta-analysis indicated that CDA brought about fewer secondary surgical procedures, lower neck disability index (NDI) scores, lower neck and arm pain scores, greater SF-36 Physical Component Summary (PCS) and Mental Component Summary(MCS) scores, greater range of motion (ROM) at the operative level and less superior adjacent-segment degeneration( P <0.05) than ACDF.CDA was not statistically different from ACDF in inferior adjacent-segment degeneration, neurological success, and adverse events ( P >0.05). Conclusions: CDA can significantly reduce the rates of secondary surgical procedures compared with ACDF.Meanwhile, CDA is superior or equivalent to ACDF in other aspects.As some studies without double-blind are included and some potential biases exites, more randomized controlled trials with high quality are required to get more reliable conclusions.

Traveling salesman problems with PageRank Distance on complex networks reveal community structure

NASA Astrophysics Data System (ADS)

Jiang, Zhongzhou; Liu, Jing; Wang, Shuai

2016-12-01

In this paper, we propose a new algorithm for community detection problems (CDPs) based on traveling salesman problems (TSPs), labeled as TSP-CDA. Since TSPs need to find a tour with minimum cost, cities close to each other are usually clustered in the tour. This inspired us to model CDPs as TSPs by taking each vertex as a city. Then, in the final tour, the vertices in the same community tend to cluster together, and the community structure can be obtained by cutting the tour into a couple of paths. There are two challenges. The first is to define a suitable distance between each pair of vertices which can reflect the probability that they belong to the same community. The second is to design a suitable strategy to cut the final tour into paths which can form communities. In TSP-CDA, we deal with these two challenges by defining a PageRank Distance and an automatic threshold-based cutting strategy. The PageRank Distance is designed with the intrinsic properties of CDPs in mind, and can be calculated efficiently. In the experiments, benchmark networks with 1000-10,000 nodes and varying structures are used to test the performance of TSP-CDA. A comparison is also made between TSP-CDA and two well-established community detection algorithms. The results show that TSP-CDA can find accurate community structure efficiently and outperforms the two existing algorithms.

Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns

PubMed Central

2007-01-01

We have converted genome-encoded protein sequences into musical notes to reveal auditory patterns without compromising musicality. We derived a reduced range of 13 base notes by pairing similar amino acids and distinguishing them using variations of three-note chords and codon distribution to dictate rhythm. The conversion will help make genomic coding sequences more approachable for the general public, young children, and vision-impaired scientists. PMID:17477882

Child Development Associate. Conceptual Science: From Atoms to Galaxies.

ERIC Educational Resources Information Center

Oscar Rose Junior Coll., Midwest City, OK.

This Child Development Associate (CDA) training module, one of a series of 18, provides a guide to science activities for preschool children. Objectives state that upon completion of the module the CDA trainee will be able to provide daily opportunities for science concept development; enhance children's problem solving abilities; stimulate…

The 1988 CDA National Survey Results.

ERIC Educational Resources Information Center

Council for Early Childhood Professional Recognition, Washington, DC.

A 44-item questionnare was sent to 11,000 Child Development Associates in the fall of 1988 in an effort to provide an updated view of the constituency served by the Child Development Association (CDA) National Credentialing Program. The questionnaire covered four categories: (1) background information; (2) education and experience; (3) training…

Family Child Care as a Small Business. ECE/CDA Training Series.

ERIC Educational Resources Information Center

Huhn, Susan

This Child Development Associate training module explores the multifaceted aspects of family child care, including zoning, certification, insurance, hours of care, fees, advertising, programming, and parent/provider agreements. The module's purpose is to help individuals interested in a career in family child care understand the CDA requirements…

49 CFR 192.931 - How may Confirmatory Direct Assessment (CDA) be used?

Code of Federal Regulations, 2011 CFR

2011-10-01

... corrosion or internal corrosion. (b) External corrosion plan. An operator's CDA plan for identifying external corrosion must comply with § 192.925 with the following exceptions. (1) The procedures for... criteria of scheduled action must be excavated in each ECDA region. (c) Internal corrosion plan. An...

49 CFR 192.931 - How may Confirmatory Direct Assessment (CDA) be used?

Code of Federal Regulations, 2012 CFR

2012-10-01

... corrosion or internal corrosion. (b) External corrosion plan. An operator's CDA plan for identifying external corrosion must comply with § 192.925 with the following exceptions. (1) The procedures for... criteria of scheduled action must be excavated in each ECDA region. (c) Internal corrosion plan. An...

49 CFR 192.931 - How may Confirmatory Direct Assessment (CDA) be used?

Code of Federal Regulations, 2013 CFR

2013-10-01

... corrosion or internal corrosion. (b) External corrosion plan. An operator's CDA plan for identifying external corrosion must comply with § 192.925 with the following exceptions. (1) The procedures for... criteria of scheduled action must be excavated in each ECDA region. (c) Internal corrosion plan. An...

49 CFR 192.931 - How may Confirmatory Direct Assessment (CDA) be used?

Code of Federal Regulations, 2014 CFR

2014-10-01

... corrosion or internal corrosion. (b) External corrosion plan. An operator's CDA plan for identifying external corrosion must comply with § 192.925 with the following exceptions. (1) The procedures for... criteria of scheduled action must be excavated in each ECDA region. (c) Internal corrosion plan. An...

A General Critical Discourse Analysis Framework for Educational Research

ERIC Educational Resources Information Center

Mullet, Dianna R.

2018-01-01

Critical discourse analysis (CDA) is a qualitative analytical approach for critically describing, interpreting, and explaining the ways in which discourses construct, maintain, and legitimize social inequalities. CDA rests on the notion that the way we use language is purposeful, regardless of whether discursive choices are conscious or…

Effects of CDA Instruction on EFL Analytical Reading Practices

ERIC Educational Resources Information Center

Hazaea, Abduljalil Nasr; Alzubi, Ali Abbas

2017-01-01

Discourse-based approaches to EFL reading have shifted the students' passive role to become 'text resistant'. This paper examines the extent to which Critical Discourse Analysis (CDA) enhances analytical reading practices in English as a Foreign Language (EFL) reading context among Preparatory Year students at Najran University. The paper…

Kinetics and Mechanism of Mammalian Mitochondrial Ribosome Assembly.

PubMed

Bogenhagen, Daniel F; Ostermeyer-Fay, Anne G; Haley, John D; Garcia-Diaz, Miguel

2018-02-13

Mammalian mtDNA encodes only 13 proteins, all essential components of respiratory complexes, synthesized by mitochondrial ribosomes. Mitoribosomes contain greatly truncated RNAs transcribed from mtDNA, including a structural tRNA in place of 5S RNA as a scaffold for binding 82 nucleus-encoded proteins, mitoribosomal proteins (MRPs). Cryoelectron microscopy (cryo-EM) studies have determined the structure of the mitoribosome, but its mechanism of assembly is unknown. Our SILAC pulse-labeling experiments determine the rates of mitochondrial import of MRPs and their assembly into intact mitoribosomes, providing a basis for distinguishing MRPs that bind at early and late stages in mitoribosome assembly to generate a working model for mitoribosome assembly. Mitoribosome assembly is a slow process initiated at the mtDNA nucleoid driven by excess synthesis of individual MRPs. MRPs that are tightly associated in the structure frequently join the complex in a coordinated manner. Clinically significant MRP mutations reported to date affect proteins that bind early on during assembly. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Orphan spin operators enable the acquisition of multiple 2D and 3D magic angle spinning solid-state NMR spectra

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2013-05-01

We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.

Field evaluation of lead effects on Canada geese and mallards in the Coeur d'Alene River Basin, Idaho

USGS Publications Warehouse

Henny, Charles J.; Blus, L.J.; Hoffman, D.J.; Sileo, L.; Audet, Daniel J.; Snyder, Mark R.

2000-01-01

Hatch year (HY) mallards (Anas platyrhynchos) in the Coeur d'Alene (CDA) River Basin had higher concentrations of lead in their blood than HY Western Canada geese (Branta canadensis moffitti) (geometric means 0.98 versus 0.28 μg/g, wet weight). The pattern for adults of both species was similar, although geometric means (1.77 versus 0.41 μg/g) were higher than in HY birds. HY mallards captured in the CDA River Basin in 1987 contained significantly lower lead concentrations in their blood than in 1994–95 (0.36 versus 0.98 μg/g); however, some very young mallards were sampled in 1987, and concentrations in adults were not significantly different in 1987, 1994, or 1995 (1.52, 2.07, 1.55 μg/g, respectively). Both species in the CDA River Basin in 1994–95 showed significantly reduced red blood cell delta-aminolevulinic acid dehydratase (ALAD) activity compared to the reference areas: Canada geese (HY −65.4 to −86.0%, adults −82.3%), and mallards (HY −90.7 to −95.5%, adults −94.1%). Canada goose goslings were divided into size classes, and the two smaller classes from the CDA River Basin had significantly elevated free erythrocyte protoporphyrin (protoporphyrin) levels compared to the reference area (15.2× and 6.9×). HY and adult mallards both had significantly elevated protoporphyrin (5.9× and 7.5×). Recognizing that interspecific differences exist in response and sensitivity to lead, it appears (at least for hemoglobin and hematocrit) that Canada geese were more sensitive to lead than mallards, i.e., adverse hematologic effects occur at lower blood lead concentrations. Only Canada geese from the CDA River Basin, in spite of lower blood lead concentrations, had significantly reduced mean hemoglobin and hematocrit values. No euthanized Canada geese (all HYs) from CDA River Basin were classified as clinically lead poisoned, but 38 Canada geese found dead in the CDA River Basin during a concurrent study succumbed to lead poisoning between 1992 and 1997. Only 6 (15.8%) of these 38 contained ingested lead shot, which contrasts greatly with the 75–94% incidence of ingested lead shot when mortality was due to lead shot ingestion. Lead from other contaminated sources (i.e., sediments and vegetation) in the CDA River Basin was strongly implicated in most Canada goose deaths. Based on the 31 live mallards and Canada geese collected in the CDA River Basin, which were representative of the live populations blood sampled only, the prevalence of subclinical and clinical lead poisoning (as determined by liver lead concentrations, excluding birds with ingested lead shot) was higher in mallards: subclinical (4 of 8, 50% HYs and 6 of 11, 55% adults); clinical (0% HYs and 4 of 11, 36% adults), with less data available for Canada geese (only 1 of 9, 11% HYs marginally subclinical). The clinically lead-poisoned mallards had extremely high concentrations of lead in blood (2.69–8.82 μg/g) and liver (6.39–17.89 μg/g). Eight mallards found dead in the CDA River Basin during a concurrent study were diagnosed as lead poisoned, and only one (12.5%) contained ingested lead shot, which again strongly implicates other lead sources. The finding of dead lead poisoned Canada geese together with the high percentage of live mallards classified as subclinically or clinically lead poisoned, in combination with the low incidence of ingested lead shot causes us concern for both of these species, which live in association with lead-contaminated sediment in the CDA River Basin.

Role of Accessory Proteins of HTLV-1 in Viral Replication, T Cell Activation, and Cellular Gene Expression

PubMed Central

Michael, Bindhu; Nair, Amithraj; Lairmore, Michael D.

2010-01-01

Human T-cell lymphotropic virus type 1 (HTLV-1), causes adult T cell leukemia/lymphoma (ATLL), and initiates a variety of immune mediated disorders. The viral genome encodes common structural and enzymatic proteins characteristic of all retroviruses and utilizes alternative splicing and alternate codon usage to make several regulatory and accessory proteins encoded in the pX region (pX ORF I to IV). Recent studies indicate that the accessory proteins p12I, p27I, p13II, and p30II, encoded by pX ORF I and II, contribute to viral replication and the ability of the virus to maintain typical in vivo expression levels. Proviral clones that are mutated in either pX ORF I or II, while fully competent in cell culture, are severely limited in their replicative capacity in a rabbit model. These HTLV-1 accessory proteins are critical for establishment of viral infectivity, enhance T- lymphocyte activation and potentially alter gene transcription and mitochondrial function. HTLV-1 pX ORF I expression is critical to the viral infectivity in resting primary lymphocytes suggesting a role for the calcineurin-binding protein p12I in lymphocyte activation. The endoplasmic reticulum and cis-Golgi localizing p12I activates NFAT, a key T cell transcription factor, through calcium-mediated signaling pathways and may lower the threshold of lymphocyte activation via the JAK/STAT pathway. In contrast p30II localizes to the nucleus and represses viral promoter activity, but may regulate cellular gene expression through p300/CBP or related co-activators of transcription. The mitochondrial localizing p13II induces morphologic changes in the organelle and may influence energy metabolism infected cells. Future studies of the molecular details HTLV-1 “accessory” proteins interactions will provide important new directions for investigations of HTLV-1 and related viruses associated with lymphoproliferative diseases. Thus, the accessory proteins of HTLV-1, once thought to be dispensable for viral replication, have proven to be directly involved in viral spread in vivo and represent potential targets for therapeutic intervention against HTLV-1 infection and disease. PMID:15358581

Screening and identification of resistance related proteins from apple leaves inoculated with Marssonina coronaria (EII. & J. J. Davis)

PubMed Central

2014-01-01

Background Apple, an invaluable fruit crop worldwide, is often prone to infection by pathogenic fungi. Identification of potentially resistance-conferring apple proteins is one of the most important aims for studying apple resistance mechanisms and promoting the development of disease-resistant apple strains. In order to find proteins which promote resistance to Marssonina coronaria, a deadly pathogen which has been related to premature apple maturation, proteomes from apple leaves inoculated with M. coronaria were characterized at 3 and 6 days post-inoculation by two dimensional electrophoresis (2-DE). Results Overall, 59 differentially accumulated protein spots between inoculation and non-inoculation were successfully identified and aligned as 35 different proteins or protein families which involved in photosynthesis, amino acid metabolism, transport, energy metabolism, carbohydrate metabolism, binding, antioxidant, defense and stress. Quantitative real-time PCR (qRT-PCR) was also used to examine the change of some defense and stress related genes abundance under inoculated conditions. Conclusions In a conclusion, different proteins in response to Marssonina coronaria were identified by proteomic analysis. Among of these proteins, there are some PR proteins, for example class III endo-chitinase, beta-1,3-glucanase and thaumatine-like protein, and some antioxidant related proteins including aldo/keto reductase AKR, ascorbate peroxidase and phi class glutathione S-transferase protein that were associated with disease resistance. The transcription levels of class III endo-chitinase (L13) and beta-1, 3-glucanase (L17) have a good relation with the abundance of the encoded protein’s accumulation, however, the mRNA abundance of thaumatine-like protein (L22) and ascorbate peroxidase (L28) are not correlated with their protein abundance of encoded protein. To elucidate the resistant mechanism, the data in the present study will promote us to investigate further the expression regulation of these target proteins. PMID:24507458

Enhanced Emission Efficiency in Organic Light-Emitting Diodes Using Deoxyribonucleic Acid Complex as an Electron Blocking Layer

DTIC Science & Technology

2006-04-28

1. Color online Photographs of EL emission from several devices: a green Alq3 baseline OLED at 25 V 707 mA/cm2—590 cd/m2, 0.35 cd/A; b green... Alq3 BioLED with DNA EBL at 25 V 308 mA/cm2—21 100 cd/m2, 6.56 cd/A; c blue NPB baseline OLED at 20 V 460 mA/cm2—700 cd/m2, 0.14 cd/A; d blue...al. Appl. Phys. Lett. 88, 171109 2006NPB N ,N-bisnaphthalene-1-yl-N ,N-bisphenyl benzi- dine hole transport layer HTL; Alq3 tris-8

Potential Fuel Economy Improvements from the Implementation of cEGR and CDA on an Atkinson Cycle Engine

EPA Science Inventory

Present the implementation of cEGR and CDA on an Atkinson engine and use steady state fuel consumption maps to estimate the technologies’ potential fuel economy improvements over the FTP and Highway tests. In addition to use fuel weighted modes to determine possible fuel economy...

Child Development Associate. Safety for Young Children.

ERIC Educational Resources Information Center

Oscar Rose Junior Coll., Midwest City, OK.

This Child Development Associate (CDA) training module, one of a series of 18, provides a guide to establishing a safe and healthy preschool environment and promoting health and safety practices among preschool children. Upon completion of the module, CDA trainees are expected to be able to create a safe learning environment for children,…

Child Development Associate. Learning Centers.

ERIC Educational Resources Information Center

Oscar Rose Junior Coll., Midwest City, OK.

One of a series of 18, this Child Development Associate (CDA) training module provides a guide to the construction of learning centers in preschool settings. Upon completion of the module the CDA trainee is expected to be able to analyze and improve the arrangement of space, materials and equipment; specify and rotate learning centers in the…

27 CFR 21.151 - List of denaturants authorized for denatured spirits.

Code of Federal Regulations, 2012 CFR

2012-04-01

....A. 38-B, 38-F. Cinchonidine S.D.A. 39-A. Cinchonidine sulfate, N.F.IX S.D.A. 39-A. Cinnamic aldehyde... ketone C.D.A. 18, 19; S.D.A. 1, 23-H. Methyl n-butyl ketone C.D.A. 18, 19; S.D.A. 1. Methyl salicylate, N...

27 CFR 21.151 - List of denaturants authorized for denatured spirits.

Code of Federal Regulations, 2014 CFR

2014-04-01

....A. 38-B, 38-F. Cinchonidine S.D.A. 39-A. Cinchonidine sulfate, N.F.IX S.D.A. 39-A. Cinnamic aldehyde... ketone C.D.A. 18, 19; S.D.A. 1, 23-H. Methyl n-butyl ketone C.D.A. 18, 19; S.D.A. 1. Methyl salicylate, N...

27 CFR 21.151 - List of denaturants authorized for denatured spirits.

Code of Federal Regulations, 2013 CFR

2013-04-01

....A. 38-B, 38-F. Cinchonidine S.D.A. 39-A. Cinchonidine sulfate, N.F.IX S.D.A. 39-A. Cinnamic aldehyde... ketone C.D.A. 18, 19; S.D.A. 1, 23-H. Methyl n-butyl ketone C.D.A. 18, 19; S.D.A. 1. Methyl salicylate, N...

An HL7-CDA wrapper for facilitating semantic interoperability to rule-based Clinical Decision Support Systems.

PubMed

Sáez, Carlos; Bresó, Adrián; Vicente, Javier; Robles, Montserrat; García-Gómez, Juan Miguel

2013-03-01

The success of Clinical Decision Support Systems (CDSS) greatly depends on its capability of being integrated in Health Information Systems (HIS). Several proposals have been published up to date to permit CDSS gathering patient data from HIS. Some base the CDSS data input on the HL7 reference model, however, they are tailored to specific CDSS or clinical guidelines technologies, or do not focus on standardizing the CDSS resultant knowledge. We propose a solution for facilitating semantic interoperability to rule-based CDSS focusing on standardized input and output documents conforming an HL7-CDA wrapper. We define the HL7-CDA restrictions in a HL7-CDA implementation guide. Patient data and rule inference results are mapped respectively to and from the CDSS by means of a binding method based on an XML binding file. As an independent clinical document, the results of a CDSS can present clinical and legal validity. The proposed solution is being applied in a CDSS for providing patient-specific recommendations for the care management of outpatients with diabetes mellitus. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Molecular cloning and characterization of RGA1 encoding a G protein alpha subunit from rice (Oryza sativa L. IR-36).

PubMed

Seo, H S; Kim, H Y; Jeong, J Y; Lee, S Y; Cho, M J; Bahk, J D

1995-03-01

A cDNA clone, RGA1, was isolated by using a GPA1 cDNA clone of Arabidopsis thaliana G protein alpha subunit as a probe from a rice (Oryza sativa L. IR-36) seedling cDNA library from roots and leaves. Sequence analysis of genomic clone reveals that the RGA1 gene has 14 exons and 13 introns, and encodes a polypeptide of 380 amino acid residues with a calculated molecular weight of 44.5 kDa. The encoded protein exhibits a considerable degree of amino acid sequence similarity to all the other known G protein alpha subunits. A putative TATA sequence (ATATGA), a potential CAAT box sequence (AGCAATAC), and a cis-acting element, CCACGTGG (ABRE), known to be involved in ABA induction are found in the promoter region. The RGA1 protein contains all the consensus regions of G protein alpha subunits except the cysteine residue near the C-terminus for ADP-ribosylation by pertussis toxin. The RGA1 polypeptide expressed in Escherichia coli was, however, ADP-ribosylated by 10 microM [adenylate-32P] NAD and activated cholera toxin. Southern analysis indicates that there are no other genes similar to the RGA1 gene in the rice genome. Northern analysis reveals that the RGA1 mRNA is 1.85 kb long and expressed in vegetative tissues, including leaves and roots, and that its expression is regulated by light.

Detection of sub-kilometer craters in high resolution planetary images using shape and texture features

NASA Astrophysics Data System (ADS)

Bandeira, Lourenço; Ding, Wei; Stepinski, Tomasz F.

2012-01-01

Counting craters is a paramount tool of planetary analysis because it provides relative dating of planetary surfaces. Dating surfaces with high spatial resolution requires counting a very large number of small, sub-kilometer size craters. Exhaustive manual surveys of such craters over extensive regions are impractical, sparking interest in designing crater detection algorithms (CDAs). As a part of our effort to design a CDA, which is robust and practical for planetary research analysis, we propose a crater detection approach that utilizes both shape and texture features to identify efficiently sub-kilometer craters in high resolution panchromatic images. First, a mathematical morphology-based shape analysis is used to identify regions in an image that may contain craters; only those regions - crater candidates - are the subject of further processing. Second, image texture features in combination with the boosting ensemble supervised learning algorithm are used to accurately classify previously identified candidates into craters and non-craters. The design of the proposed CDA is described and its performance is evaluated using a high resolution image of Mars for which sub-kilometer craters have been manually identified. The overall detection rate of the proposed CDA is 81%, the branching factor is 0.14, and the overall quality factor is 72%. This performance is a significant improvement over the previous CDA based exclusively on the shape features. The combination of performance level and computational efficiency offered by this CDA makes it attractive for practical application.

Synthesis and Functional Investigations of Computer Designed Novel Cladribine-Like Compounds for the Treatment of Multiple Sclerosis.

PubMed

Yavuz, Serkan; Çetin, Aysu; Akdemir, Atilla; Doyduk, Doğukan; Dişli, Ali; Çelik Turgut, Gurbet; Şen, Alaattin; Yıldırır, Yılmaz

2017-11-01

Cladribine (2-CdA) is used as an anti-cancer drug but is currently studied as a potential treatment for use in relapsing-remitting multiple sclerosis (MS). In this study, we computer designed, synthesized, and characterized two novel derivatives of 2-CdA, K1-5d and K2-4c, and investigated their underlying mechanism of beneficial effect using the CCRF-CEM and RAJI cell lines. For this purpose, we first determined their effect on MS and DNA damage and repair-related gene expression profiles using custom arrays along with 2-CdA treatment at non-toxic doses. Then, we determined whether cells underwent apoptosis after treatment with 2-CdA, K1-5d, and K2-4c in CCRF-CEM and RAJI cells, using the DNA fragmentation assay. It was found that both derivatives modulated the expression of the pathway-related genes that are important in inflammatory signaling, apoptosis, ATM/ATR, double-strand break repair, and the cell cycle. Furthermore, 2-CdA, K1-5d, and K2-4c significantly activated apoptosis in both cell lines. In summary, our data demonstrate that although both derivatives act as anti-inflammatory and apoptotic agents, inducing the accumulation of DNA strand breaks and activating the ultimate tumor suppressor p53 in T and B lymphocytes, the K1-5d derivative has shown more promising activities for further studies. © 2017 Deutsche Pharmazeutische Gesellschaft.

Are tyrosine residues involved in the photoconversion of the water-soluble chlorophyll-binding protein of Chenopodium album?

PubMed

Takahashi, S; Seki, Y; Uchida, A; Nakayama, K; Satoh, H

2015-05-01

Non-photosynthetic and hydrophilic chlorophyll (Chl) proteins, called water-soluble Chl-binding proteins (WSCPs), are distributed in various species of Chenopodiaceae, Amaranthaceae, Polygonaceae and Brassicaceae. Based on their photoconvertibility, WSCPs are categorised into two classes: Class I (photoconvertible) and Class II (non-photoconvertible). Chenopodium album WSCP (CaWSCP; Class I) is able to convert the chlorin skeleton of Chl a into a bacteriochlorin-like skeleton under light in the presence of molecular oxygen. Potassium iodide (KI) is a strong inhibitor of the photoconversion. Because KI attacks tyrosine residues in proteins, tyrosine residues in CaWSCP are considered to be important amino acid residues for the photoconversion. Recently, we identified the gene encoding CaWSCP and found that the mature region of CaWSCP contained four tyrosine residues: Tyr13, Tyr14, Tyr87 and Tyr134. To gain insight into the effect of the tyrosine residues on the photoconversion, we constructed 15 mutant proteins (Y13A, Y14A, Y87A, Y134A, Y13-14A, Y13-87A, Y13-134A, Y14-87A, Y14-134A, Y87-134A, Y13-14-87A, Y13-14-134A, Y13-87-134A, Y14-87-134A and Y13-14-87-134A) using site-directed mutagenesis. Amazingly, all the mutant proteins retained not only chlorophyll-binding activity, but also photoconvertibility. Furthermore, we found that KI strongly inhibited the photoconversion of Y13-14-87-134A. These findings indicated that the four tyrosine residues are not essential for the photoconversion. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Expression of uncharacterized male germ cell-specific genes and discovery of novel sperm-tail proteins in mice.

PubMed

Kwon, Jun Tae; Ham, Sera; Jeon, Suyeon; Kim, Youil; Oh, Seungmin; Cho, Chunghee

2017-01-01

The identification and characterization of germ cell-specific genes are essential if we hope to comprehensively understand the mechanisms of spermatogenesis and fertilization. Here, we searched the mouse UniGene databases and identified 13 novel genes as being putatively testis-specific or -predominant. Our in silico and in vitro analyses revealed that the expressions of these genes are testis- and germ cell-specific, and that they are regulated in a stage-specific manner during spermatogenesis. We generated antibodies against the proteins encoded by seven of the genes to facilitate their characterization in male germ cells. Immunoblotting and immunofluorescence analyses revealed that one of these proteins was expressed only in testicular germ cells, three were expressed in both testicular germ cells and testicular sperm, and the remaining three were expressed in sperm of the testicular stages and in mature sperm from the epididymis. Further analysis of the latter three proteins showed that they were all associated with cytoskeletal structures in the sperm flagellum. Among them, MORN5, which is predicted to contain three MORN motifs, is conserved between mouse and human sperm. In conclusion, we herein identify 13 authentic genes with male germ cell-specific expression, and provide comprehensive information about these genes and their encoded products. Our finding will facilitate future investigations into the functional roles of these novel genes in spermatogenesis and sperm functions.

cis-4-Decenoic and decanoic acids impair mitochondrial energy, redox and Ca(2+) homeostasis and induce mitochondrial permeability transition pore opening in rat brain and liver: Possible implications for the pathogenesis of MCAD deficiency.

PubMed

Amaral, Alexandre Umpierrez; Cecatto, Cristiane; da Silva, Janaína Camacho; Wajner, Alessandro; Godoy, Kálita Dos Santos; Ribeiro, Rafael Teixeira; Wajner, Moacir

2016-09-01

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is biochemically characterized by tissue accumulation of octanoic (OA), decanoic (DA) and cis-4-decenoic (cDA) acids, as well as by their carnitine by-products. Untreated patients present episodic encephalopathic crises and biochemical liver alterations, whose pathophysiology is poorly known. We investigated the effects of OA, DA, cDA, octanoylcarnitine (OC) and decanoylcarnitine (DC) on critical mitochondrial functions in rat brain and liver. DA and cDA increased resting respiration and diminished ADP- and CCCP-stimulated respiration and complexes II-III and IV activities in both tissues. The data indicate that these compounds behave as uncouplers and metabolic inhibitors of oxidative phosphorylation. Noteworthy, metabolic inhibition was more evident in brain as compared to liver. DA and cDA also markedly decreased mitochondrial membrane potential, NAD(P)H content and Ca(2+) retention capacity in Ca(2+)-loaded brain and liver mitochondria. The reduction of Ca(2+) retention capacity was more pronounced in liver and totally prevented by cyclosporine A and ADP, as well as by ruthenium red, demonstrating the involvement of mitochondrial permeability transition (mPT) and Ca(2+). Furthermore, cDA induced lipid peroxidation in brain and liver mitochondria and increased hydrogen peroxide formation in brain, suggesting the participation of oxidative damage in cDA-induced alterations. Interestingly, OA, OC and DC did not alter the evaluated parameters, implying lower toxicity for these compounds. Our results suggest that DA and cDA, in contrast to OA and medium-chain acylcarnitines, disturb important mitochondrial functions in brain and liver by multiple mechanisms that are possibly involved in the neuropathology and liver alterations observed in MCAD deficiency. Copyright © 2016 Elsevier B.V. All rights reserved.

Lead in hawks, falcons and owls downstream from a mining site on the Coeur D'Alene river, Idaho

USGS Publications Warehouse

Henny, C.J.; Blus, L.J.; Hoffman, D.J.; Grove, R.A.

1994-01-01

Mining and smelting at Kellogg-Smelterville, Idaho, resulted in high concentrations of lead in Coeur d'Alene (CDA) River sediments and the floodplain downstream, where American Kestrels (Falco sparverius), Northern Harriers (Circus cyaneus), Red-tailed Hawks (Buteo jamaicensis), Great Horned Owls (Bubo virginianus), and Western Screech-owls (Otus kennicotti) nested. Nestling American Kestrels contained significantly higher (P=0.0012) blood lead concentrations along the CDA River (0.24 ?g/g, wet wt) than the nearby reference area (0.087 ?g/g). A 35% inhibition of blood *-aminolevulinic acid dehydratase (ALAD) in nestling Northern Harriers (P=0.0001), 55% in nestling American Kestrels (P=0.0001) and 81% in adult American Kestrels (P=0.0004) provided additional evidence of lead exposure in the CDA River population. In nestling American Kestrels and Northern Harriers, ALAD activity was negatively correlated with lead in blood. An earlier report on Ospreys (Pandion haliaetus) showed slightly less inhibition of ALAD than in American Kestrels, but no significant reduction in hemoglobin or hematocrit and no negative influence on production rates. The adult and nestling American Kestrels along the CDA River contained about twice as much blood lead as Ospreys during the same years (adult 0.46 vs. 0.20 ?g/g, and nestling 0.24 vs. 0.09 ?g/g), but adults showed a 7.5% reduction in hemoglobin (P=0.0356) and nestlings an 8.2% reduction in hemoglobin (P=0.0353) and a 5.8% reduction in hematocrit (P=0.0482). We did not observe raptor deaths related to lead, and although the production rate for American Kestrels was slightly lower along the CDA River, we found no significant negative relation between productivity and lead. Limited data on the other raptors provide evidence of exposure to lead along the CDA River. Several traits of raptors apparently reduce their potential for accumulating critical levels of lead which is primarily stored in bones of prey species.

10 years of Cassini/VIMS observations at Titan

NASA Astrophysics Data System (ADS)

Sotin, C.; Brown, R. H.; Baines, K. H.; Barnes, J.; Buratti, B. J.; Clark, R. N.; Jaumann, R.; LeMouelic, S.; Nicholson, P. D.; Rodriguez, S.; Soderblom, J.; Soderblom, L.; Stephan, K.

2014-04-01

The interplanetary space probe Cassini/Huygens reached Saturn in July 2004 after seven years of cruise phase. Today, the German-lead Cosmic Dust Analyser (CDA) is operated continuously for 10 years in orbit around Saturn. During the cruise phase CDA measured the interstellar dust flux at one AU distance from the Sun, the charge and composition of interplanetary dust grains and the composition of the Jovian nanodust streams. The first discovery of CDA related to Saturn was the measurement of nanometer sized dust particles ejected by its magnetosphere to interplanetary space with speeds higher than 100 km/s. Their origin and composition was analysed and an their dynamical studies showed a strong link to the conditions of the solar wind plasma flow. A recent surprising result was, that stream particles stem from the interior of Enceladus. Since 2004 CDA measured millions of dust impacts characterizing the dust environment of Saturn. The instrument showed strong evidence for ice geysers located at the south pole of Saturn's moon Enceladus in 2005. Later, a detailed compositional analysis of the salt-rich water ice grains in Saturn's E ring system lead to the discovery of liquid water below the icy crust connected to an ocean at depth feeding the icy jets. CDA was even capable to derive a spatially resolved compositional profile of the plume during close Enceladus flybys. A determination of the dust-magnetosphere interaction and the discovery of the extended E ring allowed the definition of a dynamical dust model of Saturn's E ring describing the observed properties. The measured dust density profiles in the dense E ring revealed geometric asymmetries. Cassini performed shadow crossings in the ring plane and dust grain charges were measured in shadow regions delivering important data for dust-plasma interaction studies. In the last years, dedicated measurement campaigns were executed by CDA to monitor the flux of interplanetary and interstellar dust particles reaching Saturn. Currently, the composition of interstellar grains and the meteoroid flux into the Saturnian system are in analysis.

Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome.

PubMed

Lake, Nicole J; Webb, Bryn D; Stroud, David A; Richman, Tara R; Ruzzenente, Benedetta; Compton, Alison G; Mountford, Hayley S; Pulman, Juliette; Zangarelli, Coralie; Rio, Marlene; Boddaert, Nathalie; Assouline, Zahra; Sherpa, Mingma D; Schadt, Eric E; Houten, Sander M; Byrnes, James; McCormick, Elizabeth M; Zolkipli-Cunningham, Zarazuela; Haude, Katrina; Zhang, Zhancheng; Retterer, Kyle; Bai, Renkui; Calvo, Sarah E; Mootha, Vamsi K; Christodoulou, John; Rötig, Agnes; Filipovska, Aleksandra; Cristian, Ingrid; Falk, Marni J; Metodiev, Metodi D; Thorburn, David R

2017-08-03

The synthesis of all 13 mitochondrial DNA (mtDNA)-encoded protein subunits of the human oxidative phosphorylation (OXPHOS) system is carried out by mitochondrial ribosomes (mitoribosomes). Defects in the stability of mitoribosomal proteins or mitoribosome assembly impair mitochondrial protein translation, causing combined OXPHOS enzyme deficiency and clinical disease. Here we report four autosomal-recessive pathogenic mutations in the gene encoding the small mitoribosomal subunit protein, MRPS34, in six subjects from four unrelated families with Leigh syndrome and combined OXPHOS defects. Whole-exome sequencing was used to independently identify all variants. Two splice-site mutations were identified, including homozygous c.321+1G>T in a subject of Italian ancestry and homozygous c.322-10G>A in affected sibling pairs from two unrelated families of Puerto Rican descent. In addition, compound heterozygous MRPS34 mutations were identified in a proband of French ancestry; a missense (c.37G>A [p.Glu13Lys]) and a nonsense (c.94C>T [p.Gln32 ∗ ]) variant. We demonstrated that these mutations reduce MRPS34 protein levels and the synthesis of OXPHOS subunits encoded by mtDNA. Examination of the mitoribosome profile and quantitative proteomics showed that the mitochondrial translation defect was caused by destabilization of the small mitoribosomal subunit and impaired monosome assembly. Lentiviral-mediated expression of wild-type MRPS34 rescued the defect in mitochondrial translation observed in skin fibroblasts from affected subjects, confirming the pathogenicity of MRPS34 mutations. Our data establish that MRPS34 is required for normal function of the mitoribosome in humans and furthermore demonstrate the power of quantitative proteomic analysis to identify signatures of defects in specific cellular pathways in fibroblasts from subjects with inherited disease. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Contamination control methods for gases used in the microlithography process

NASA Astrophysics Data System (ADS)

Rabellino, Larry; Applegarth, Chuck; Vergani, Giorgio

2002-07-01

Sensitivity to contamination continues to increase as the technology shrinks from 365 nm I-line lamp illumination to 13.4 nm Extreme Ultraviolet laser activated plasma. Gas borne impurities can be readily distributed within the system, remaining both suspended in the gas and attached to critical surfaces. Effects from a variety of contamination, some well characterized and others not, remain a continuing obstacle for stepper manufacturers and users. Impurities like oxygen, moisture and hydrocarbons in parts per billion levels can absorb light, reducing the light intensity and subsequently reducing the consistence of the process. Moisture, sulfur compounds, ammonia, acid compounds and organic compounds such as hydrocarbons can deposit on lens or mirror surfaces affecting image quality. Regular lens replacement or removal for cleaning is a costly option and in-situ cleaning processes must be carefully managed to avoid recontamination of the system. The contamination can come from outside the controlled environment (local gas supply, piping system, & leaks), or from the materials moving into the controlled environment; or contamination may be generated inside the controlled environment as a result of the process itself. The release of amines can occur as a result of the degassing of the photo-resists. For the manufacturer and user of stepper equipment, the challenge is not in predictable contamination, but the variable or unpredictable contamination in the process. One type of unpredictable contamination may be variation in the environmental conditions when producing the nitrogen gas and Clean Dry Air (CDA). Variation in the CDA, nitrogen and xenon may range from parts per billion to parts per million. The risk due to uncontrolled or unmonitored variation in gas quality can be directly related to product defects. Global location can significantly affect the gas quality, due to the ambient air quality (for nitrogen and CDA), production methods, gas handling equipment maintenance, transportation and storage processes. Fortunately, technology has been developed which can remove the killer impurities from these processes. This paper will review processes, and purification media that can be used in the photolithography processes, and detail the advances in purification technologies for removal of hydrocarbons, oxygen (where applicable), moisture, carbon dioxide, carbon monoxide, hydrogen, nitrogen (where applicable), sulfur compounds, ammonia and acid compounds from process gases such as nitrogen, CDA, argon, krypton and xenon.

Wheel-like Ln18 Cluster Organic Frameworks for Magnetic Refrigeration and Conversion of CO2.

PubMed

Song, Tian-Qun; Dong, Jie; Yang, An-Fei; Che, Xue-Jing; Gao, Hong-Ling; Cui, Jian-Zhong; Zhao, Bin

2018-03-19

Two isostructural 2D MOFs ([Ln 7 (CDA) 6 (HCOO) 3 (μ 3 -OH) 6 (H 2 O) 8 ] n , abbreviated as 1-Gd and 2-Dy) were successfully synthesized under solvothermal conditions. The self-assembly of lanthanide(III) nitrate and 1,1'-cyclopropane-dicarboxylic acid (H 2 CDA) resulted in wheel-like Ln 18 cluster second building units (SBU), which are further linked to six neighboring wheels to generate a 2D ordered honeycomb array. Both 1-Gd and 2-Dy exhibit high thermal stability and decompose above 330 °C. Moreover, they have good solvent stability in ten common solvents and pH stability with pH values from 1 to 13. Magnetic studies reveal that 1-Gd exhibits weak antiferromagnetic coupling between adjacent Gd 3+ ions and has a large magnetocaloric effect of 47.30 J kg -1 K -1 (Δ H = 7.0 T at 2 K), while 2-Dy shows ferromagnetic interaction between adjacent Dy 3+ ions. Interestingly, 1-Gd and 2-Dy can catalyze the cycloaddition of CO 2 to epoxides under mild conditions and can be reused at least five rounds with negligible loss of catalytic performance.

Mechanism of Protein Biosynthesis in Mammalian Mitochondria

PubMed Central

Christian, Brooke E.; Spremulli, Linda L.

2011-01-01

Protein synthesis in mammalian mitochondria produces 13 proteins that are essential subunits of the oxidative phosphorylation complexes. This review provides a detailed outline of each phase of mitochondrial translation including initiation, elongation, termination, and ribosome recycling. The roles of essential proteins involved in each phase are described. All of the products of mitochondrial protein synthesis in mammals are inserted into the inner membrane. Several proteins that may help bind ribosomes to the membrane during translation are described, although much remains to be learned about this process. Mutations in mitochondrial or nuclear genes encoding components of the translation system often lead to severe deficiencies in oxidative phosphorylation, and a summary of these mutations is provided. PMID:22172991

The plastid ribosomal proteins. Identification of all the proteins in the 30 S subunit of an organelle ribosome (chloroplast).

PubMed

Yamaguchi, K; von Knoblauch, K; Subramanian, A R

2000-09-15

Identification of all the protein components of a plastid (chloroplast) ribosomal 30 S subunit has been achieved, using two-dimensional gel electropholesis, high performance liquid chromatography purification, N-terminal sequencing, polymerase chain reaction-based screening of cDNA library, nucleotide sequencing, and mass spectrometry (electrospray ionization, matrix-assisted laser desorption/ionization time-of-flight, and reversed-phase HPLC coupled with electrospray ionization mass spectrometry). 25 proteins were identified, of which 21 are orthologues of all Escherichia coli 30 S ribosomal proteins (S1-S21), and 4 are plastid-specific ribosomal proteins (PSRPs) that have no homologues in the mitochondrial, archaebacterial, or cytosolic ribosomal protein sequences in data bases. 12 of the 25 plastid 30 S ribosomal proteins (PRPs) are encoded in the plastid genome, whereas the remaining 13 are encoded by the nuclear genome. Post-translational transit peptide cleavage sites for the maturation of the 13 cytosolically synthesized PRPs, and post-translational N-terminal processing in the maturation of the 12 plastid synthesized PRPs are described. Post-translational modifications in several PRPs were observed: alpha-N-acetylation of S9, N-terminal processings leading to five mature forms of S6 and two mature forms of S10, C-terminal and/or internal modifications in S1, S14, S18, and S19, leading to two distinct forms differing in mass and/or charge (the corresponding modifications are not observed in E. coli). The four PSRPs in spinach plastid 30 S ribosomal subunit (PSRP-1, 26.8 kDa, pI 6.2; PSRP-2, 21.7 kDa, pI 5.0; PSRP-3, 13.8 kDa, pI 4.9; PSRP-4, 5.2 kDa, pI 11.8) comprise 16% (67.6 kDa) of the total protein mass of the 30 S subunit (429.3 kDa). PSRP-1 and PSRP-3 show sequence similarities with hypothetical photosynthetic bacterial proteins, indicating their possible origins in photosynthetic bacteria. We propose the hypothesis that PSRPs form a "plastid translational regulatory module" on the 30 S ribosomal subunit structure for the possible mediation of nuclear factors on plastid translation.

Identification of novel serine proteinase gene transcripts in the midguts of two tropical insect pests, Scirpophaga incertulas (Wk.) and Helicoverpa armigera (Hb.).

PubMed

Mazumdar-Leighton, S; Babu, C R; Bennett, J

2000-01-01

We have used RT PCR and 3'RACE to identify diverse serine proteinase genes expressed in the midguts of the rice yellow stem borer (Scirpophaga incertulas) and Asian corn borer (Helicoverpa armigera). The RT-PCR primers encoded the conserved regions around the active site histidine57 and serine195 of Drosophila melanogaster alpha trypsin, including aspartate189 of the specificity pocket. These primers amplified three transcripts (SiP1-3) from midguts of S. incertulas, and two transcripts (HaP1-2) from midguts of H. armigera. The five RT PCR products were sequenced to permit design of gene-specific forward primers for use with anchored oligo dT primers in 3'RACE. Sequencing of the 3'RACE products indicated that SiP1, SiP2 and HaP1 encoded trypsin-like serine proteinases, while HaP2 encoded a chymotrypsin-like serine proteinases. The SiP3 transcript proved to be an abundant 960 nt mRNA encoding a trypsin-like protein in which the active site serine195 was replaced by aspartate. The possible functions of this unusual protein are discussed.

Nucleic acid compositions and the encoding proteins

DOEpatents

Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

2014-09-02

The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

Genome-wide identification and characterization of the apple (Malus domestica) HECT ubiquitin-protein ligase family and expression analysis of their responsiveness to abiotic stresses.

PubMed

Xu, Jianing; Xing, Shanshan; Cui, Haoran; Chen, Xuesen; Wang, Xiaoyun

2016-04-01

The ubiquitin-protein ligases (E3s) directly participate in ubiquitin (Ub) transferring to the target proteins in the ubiquitination pathway. The HECT ubiquitin-protein ligase (UPL), one type of E3s, is characterized as containing a conserved HECT domain of approximately 350 amino acids in the C terminus. Some UPLs were found to be involved in trichome development and leaf senescence in Arabidopsis. However, studies on plant UPLs, such as characteristics of the protein structure, predicted functional motifs of the HECT domain, and the regulatory expression of UPLs have all been limited. Here, we present genome-wide identification of the genes encoding UPLs (HECT gene) in apple. The 13 genes (named as MdUPL1-MdUPL13) from ten different chromosomes were divided into four groups by phylogenetic analysis. Among these groups, the encoding genes in the intron-exon structure and the included additional functional domains were quite different. Notably, the F-box domain was first found in MdUPL7 in plant UPLs. The HECT domain in different MdUPL groups also presented different spatial features and three types of conservative motifs were identified. The promoters of each MdUPL member carried multiple stress-response related elements by cis-acting element analysis. Experimental results demonstrated that the expressions of several MdUPLs were quite sensitive to cold-, drought-, and salt-stresses by qRT-PCR assay. The results of this study helped to elucidate the functions of HECT proteins, especially in Rosaceae plants.

Expression cloning and chromosomal mapping of the leukocyte activation antigen CD97, a new seven-span transmembrane molecule of the secretin receptor superfamily with an unusual extracellular domain

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

Hamann, J.; Hamann, D.; Lier, R.A.W.

1995-08-15

CD97 is a monomeric glycoprotein of 75 to 85 kDa that is induced rapidly on the surface of most leukocytes upon activation. We herein report the isolation of a cDNA encoding human CD97 by expression cloning in COS cells. The 3-kb cDNA clone encodes a mature polypeptide chain of 722 amino acids with a predicted molecular mass of 79 kDa. Within the C-terminal part of the protein, a region with seven hydrophobic segments was identified, suggesting that CD97 is a seven-span transmembrane molecule. Sequence comparison indicates that CD97 is the first leukocyte Ag in a recently described superfamily that includesmore » the receptors for secretin, calcitonin, and other mammalian and insect peptide hormones. Different from these receptors, CD97 has an extended extracellular region of 433 amino acids that possesses three N-terminal epidermal growth factor-like domains, two of them with a calcium-binding site, and single Arg-Gly-Asp (RGD) motif. The existence of structural elements characteristic for extracellular matrix proteins in a seven-span transmembrane molecule makes CD97 a receptor potentially involved in both adhesion and signaling processes early after leukocyte activation. The gene encoding CD97 is localized on chromosome 19 (19p13.12-13.2).« less

Frame-Insensitive Expression Cloning of Fluorescent Protein from Scolionema suvaense.

PubMed

Horiuchi, Yuki; Laskaratou, Danai; Sliwa, Michel; Ruckebusch, Cyril; Hatori, Kuniyuki; Mizuno, Hideaki; Hotta, Jun-Ichi

2018-01-26

Expression cloning from cDNA is an important technique for acquiring genes encoding novel fluorescent proteins. However, the probability of in-frame cDNA insertion following the first start codon of the vector is normally only 1/3, which is a cause of low cloning efficiency. To overcome this issue, we developed a new expression plasmid vector, pRSET-TriEX, in which transcriptional slippage was induced by introducing a DNA sequence of (dT) 14 next to the first start codon of pRSET. The effectiveness of frame-insensitive cloning was validated by inserting the gene encoding eGFP with all three possible frames to the vector. After transformation with one of these plasmids, E. coli cells expressed eGFP with no significant difference in the expression level. The pRSET-TriEX vector was then used for expression cloning of a novel fluorescent protein from Scolionema suvaense . We screened 3658 E. coli colonies transformed with pRSET-TriEX containing Scolionema suvaense cDNA, and found one colony expressing a novel green fluorescent protein, ScSuFP. The highest score in protein sequence similarity was 42% with the chain c of multi-domain green fluorescent protein like protein "ember" from Anthoathecata sp. Variations in the N- and/or C-terminal sequence of ScSuFP compared to other fluorescent proteins indicate that the expression cloning, rather than the sequence similarity-based methods, was crucial for acquiring the gene encoding ScSuFP. The absorption maximum was at 498 nm, with an extinction efficiency of 1.17 × 10⁵ M -1 ·cm -1 . The emission maximum was at 511 nm and the fluorescence quantum yield was determined to be 0.6. Pseudo-native gel electrophoresis showed that the protein forms obligatory homodimers.

EXPOSURE-DISEASE CONTINUUM FOR 2-CHLORO-2'-DEOXYADENOSINE (2CDA), A PROTOTYPE OCULAR TERATOGEN. 1. DOSE-RESPONSE ANALYSIS

EPA Science Inventory

Treatment of pregnant mice with 2-chloro-2'-deoxyadenosine (2CdA) on day 8 of gestation induces coloboma, microphthalmia and anophthalmia through a mechanism coupled to the effects of the p53 tumor suppressor gene (Wubah et al.'96). The present study defines the dosimetry for 2Cd...

Examining the Barriers to the Continuing Education of Early Childhood Teacher Assistants

ERIC Educational Resources Information Center

Wright, Colleen Louise

2017-01-01

The Improving Head Start for School Readiness Act of 2007 required teacher assistants (TAs) to obtain their child development associate (CDA) credential by September of 2015. TAs who had not obtained their CDA within the required timeframe were either demoted or terminated from their positions. However, with the increase of working parents, the…

Exposing Ideology within University Policies: A Critical Discourse Analysis of Faculty Hiring, Promotion and Remuneration Practices

ERIC Educational Resources Information Center

Uzuner-Smith, Sedef; Englander, Karen

2015-01-01

Using critical discourse analysis (CDA), this paper exposes the neoliberal ideology of the knowledge-based economy embedded within university policies, specifically those that regulate faculty hiring, promotion, and remuneration in two national contexts: Turkey and Mexico. The paper follows four stages of CDA: (1) focus upon a social wrong in its…

Color-tunable and high-efficiency organic light-emitting diode by adjusting exciton bilateral migration zone

NASA Astrophysics Data System (ADS)

Liu, Shengqiang; Wu, Ruofan; Huang, Jiang; Yu, Junsheng

2013-09-01

A voltage-controlled color-tunable and high-efficiency organic light-emitting diode (OLED) by inserting 16-nm N,N'-dicarbazolyl-3,5-benzene (mCP) interlayer between two complementary emitting layers (EMLs) was fabricated. The OLED emitted multicolor ranging from blue (77.4 cd/A @ 6 V), white (70.4 cd/A @ 7 V), to yellow (33.7 cd/A @ 9 V) with voltage variation. An equivalent model was proposed to reveal the color-tunable and high-efficiency emission of OLEDs, resulting from the swing of exciton bilateral migration zone near mCP/blue-EML interface. Also, the model was verified with a theoretical arithmetic using single-EML OLEDs to disclose the crucial role of mCP exciton adjusting layer.

DNA vaccine encoding central conserved region of G protein induces Th1 predominant immune response and protection from RSV infection in mice.

PubMed

Hua, Ying; Jiao, Yue-Ying; Ma, Yao; Peng, Xiang-Lei; Fu, Yuan-Hui; Zheng, Yan-Peng; Hong, Tao; He, Jin-Sheng

2016-11-01

Human respiratory syncytial virus (RSV) can cause serious infection in the lower respiratory tract, especially in infants, young children, the elderly and the immunocompromised population worldwide. Previous study demonstrated the polypeptide (amino acids 148-198) of RSV attachment (G) glycoprotein, corresponding to the central conserved region and encompassing CX3C chemokine motif, could induce antibodies and protection from RSV challenge in mice [1,2]. In this study, we evaluated the immune efficacy of the recombinant DNA vaccine of pVAX1/3G 148-198 encoding RSV G protein polypeptide. RSV specific serum IgG antibodies with neutralizing activity were stimulated following prime-boost immunization of pVAX1/3G 148-198 intramuscularly, and the ratio of IgG2a/IgG1 was 4.93, indicating a Th1 biased immune response. After challenged intranasally with RSV Long, the vaccinated mice showed both decreased lung RSV titers, pulmonary inflammation and body weight loss. The results suggest that pVAX1/3G 148-198 DNA vaccine may be an effective RSV vaccine candidate, and deserves further exploration. Copyright © 2016 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Chromosomal localization and cDNA cloning of the human DBP and TEF genes

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

Khatib, Z.A.; Inaba, T.; Valentine, M.

1994-09-15

The authors have isolated cDNA and genomic clones and determined the human chromosome positions of two genes encoding transcription factors expressed in the liver and the pituitary gland: albumin D-site-binding protein (DBP) and thyrotroph embryonic factor (TEF). Both proteins have been identified as members of the PAR (proline and acidic amino acid-rich) subfamily of bZIP transcription factors in the rat, but human homologues have not been characterized. Using a fluorescence in situ hybridization technique, the DBP locus was assigned to chromosome 19q13, and TEF to chromosome 22q13. Each assignment was confirmed by means of human chromosome segregation in somatic cellmore » hybrids. Coding sequences of DBP and TEF, extending beyond the bZIP domain to the PAR region, were highly conserved in both human-human and interspecies comparisons. Conservation of the exon-intron boundaries of each bZIP domain-encoding exon suggested derivation from a common ancestral gene. DBP and TEF mRNAs were expressed in all tissues and cell lines examined, including brain, lung, liver, spleen, and kidney. Knowledge of the human chromosome locations of these PAR proteins will facilitate studies to assess their involvement in carcinogenesis and other fundamental biological processes. 37 refs., 5 figs., 1 tab.« less

Genetic and functional characterization of PCSK1.

PubMed

Choquet, Hélène; Stijnen, Pieter; Creemers, John W M

2011-01-01

PC1/3 is a neuroendocrine-specific member of the mammalian subtilisin-like proprotein convertase family. This seven-member family is involved in the endoproteolytic cleavage of a large number of precursor proteins including prohormones, proneuropeptides, zymogens, and proreceptors. PC1/3 is synthesized as a zymogen, proPC1/3, and its propeptide is rapidly and autocatalytically cleaved in the endoplasmic reticulum. The mature protein is sorted and stored in dense-core secretory vesicles, together with its substrates. Compound-inactivating mutations in the PCSK1 gene, which encodes PC1/3, cause monogenic obesity. Furthermore, the contribution of two common nonsynonymous variants in PCSK1 to polygenic obesity risk has recently been established. Additional rare variants have been identified in non-consanguineous extremely obese Europeans but functional characterization has not yet been described. Sequencing efforts of larger cohorts of obese patients might reveal more variants conferring risk of obesity.

Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom

PubMed Central

2013-01-01

Background Nucleoside phosphorylases (NPs) have been extensively investigated in human and bacterial systems for their role in metabolic nucleotide salvaging and links to oncogenesis. In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins function as an important ecophysiological adaptation for inter- and intra-seasonal nitrogen storage and cycling. Results We conducted phylogenetic analyses to determine the distribution and evolution of NP-like proteins in plants. These analyses revealed two major clusters of NP-like proteins in plants. Group I proteins were encoded by genes across a wide range of plant taxa while proteins encoded by Group II genes were dominated by species belonging to the order Malpighiales and included the Populus Bark Storage Protein (BSP) and WIN4-like proteins. Additionally, we evaluated the NP-like genes in Populus by examining the transcript abundance of the 13 NP-like genes found in the Populus genome in various tissues of plants exposed to long-day (LD) and short-day (SD) photoperiods. We found that all 13 of the Populus NP-like genes belonging to either Group I or II are expressed in various tissues in both LD and SD conditions. Tests of natural selection and expression evolution analysis of the Populus genes suggests that divergence in gene expression may have occurred recently during the evolution of Populus, which supports the adaptive maintenance models. Lastly, in silico analysis of cis-regulatory elements in the promoters of the 13 NP-like genes in Populus revealed common regulatory elements known to be involved in light regulation, stress/pathogenesis and phytohormone responses. Conclusion In Populus, the evolution of the NP-like protein and gene family has been shaped by duplication events and natural selection. Expression data suggest that previously uncharacterized NP-like proteins may function in nutrient sensing and/or signaling. These proteins are members of Group I NP-like proteins, which are widely distributed in many plant taxa. We conclude that NP-like proteins may function in plants, although this function is undefined. PMID:23957885

Catalytic diversity and homotropic allostery of two Cytochrome P450 monooxygenase like proteins from Trichoderma brevicompactum.

PubMed

Hussain, Razak; Kumari, Indu; Sharma, Shikha; Ahmed, Mushtaq; Khan, Tabreiz Ahmad; Akhter, Yusuf

2017-12-01

Trichothecenes are the secondary metabolites produced by Trichoderma spp. Some of these molecules have been reported for their ability to stimulate plant growth by suppressing plant diseases and hence enabling Trichoderma spp. to be efficiently used as biocontrol agents in modern agriculture. Many of the proteins involved in the trichothecenes biosynthetic pathway in Trichoderma spp. are encoded by the genes present in the tri cluster. Tri4 protein catalyzes three consecutive oxygenation reaction steps during biosynthesis of isotrichodiol in the trichothecenes biosynthetic pathway, while tri11 protein catalyzes the C4 hydroxylation of 12, 13-epoxytrichothec-9-ene to produce trichodermol. In the present study, we have homology modelled the three-dimensional structures of tri4 and tri11 proteins. Furthermore, molecular dynamics simulations were carried out to elucidate the mechanism of their action. Both tri4 and tri11 encode for cytochrome P450 monooxygenase like proteins. These data also revealed effector-induced allosteric changes on substrate binding at an alternative binding site and showed potential homotropic negative cooperativity. These analyses also showed that their catalytic mechanism relies on protein-ligand and protein-heme interactions controlled by hydrophobic and hydrogen-bonding interactions which orient the complex in optimal conformation within the active sites.

Phage as a template to grow bone mineral nanocrystals.

PubMed

Cao, Binrui; Xu, Hong; Mao, Chuanbin

2014-01-01

Phage display is a biotechnique that fuses functional peptides on the outer surface of filamentous phage by inserting DNA encoding the peptides into the genes of its coat proteins. The resultant peptide-displayed phage particles have been widely used as biotemplates for the synthesis of functional hybrid nanomaterials. Here, we describe the bioengineering of M13 filamentous phage to surface-display bone mineral (hydroxyapatite (HAP))-nucleating peptides derived from dentin matrix protein-1 and using the engineered phage as a biotemplate to grow HAP nanocrystals.

Study of the plant COPII vesicle coat subunits by functional complementation of yeast Saccharomyces cerevisiae mutants.

PubMed

De Craene, Johan-Owen; Courte, Fanny; Rinaldi, Bruno; Fitterer, Chantal; Herranz, Mari Carmen; Schmitt-Keichinger, Corinne; Ritzenthaler, Christophe; Friant, Sylvie

2014-01-01

The formation and budding of endoplasmic reticulum ER-derived vesicles depends on the COPII coat protein complex that was first identified in yeast Saccharomyces cerevisiae. The ER-associated Sec12 and the Sar1 GTPase initiate the COPII coat formation by recruiting the Sec23-Sec24 heterodimer following the subsequent recruitment of the Sec13-Sec31 heterotetramer. In yeast, there is usually one gene encoding each COPII protein and these proteins are essential for yeast viability, whereas the plant genome encodes multiple isoforms of all COPII subunits. Here, we used a systematic yeast complementation assay to assess the functionality of Arabidopsis thaliana COPII proteins. In this study, the different plant COPII subunits were expressed in their corresponding temperature-sensitive yeast mutant strain to complement their thermosensitivity and secretion phenotypes. Secretion was assessed using two different yeast cargos: the soluble α-factor pheromone and the membranous v-SNARE (vesicle-soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptor) Snc1 involved in the fusion of the secretory vesicles with the plasma membrane. This complementation study allowed the identification of functional A. thaliana COPII proteins for the Sec12, Sar1, Sec24 and Sec13 subunits that could represent an active COPII complex in plant cells. Moreover, we found that AtSec12 and AtSec23 were co-immunoprecipitated with AtSar1 in total cell extract of 15 day-old seedlings of A. thaliana. This demonstrates that AtSar1, AtSec12 and AtSec23 can form a protein complex that might represent an active COPII complex in plant cells.

Enhancement of heterogeneous alkaline xylanase production in Pichia pastoris GS115

NASA Astrophysics Data System (ADS)

Zheng, Wei

2017-08-01

A series of strategies were applied to improve expression level of the recombinant alkaline xylanase from Bacillus pumilus G1-3 in Pichia pastoris GS115. Codon optimization of xylanase gene xynG1-3 from B. pumilus G1-3 were carried out for its heterogeneous expression in P. pastoris. The activity of xylanase encoded by optimized gene (xynG1-3-opt) was up to 33641 U/mL, which was 37% higher than that by wild-type (xynG1-3) gene. The results will greatly contribute to increasing the production of recombinant proteins in P. pastoris and improving the industrial production of the alkaline xylanase.

A retrospective analysis of the Dermatology Foundation's Career Development Award Program.

PubMed

Boris, Chris; Lessin, Stuart R; Wintroub, Bruce U; Yancey, Kim B

2012-11-01

To provide research support that develops and retains leaders, educators, and investigators in dermatology and cutaneous biology, the Dermatology Foundation (DF) has designed and implemented a comprehensive Career Development Award (CDA) Program. To assess the impact of the DF's 3-year CDA, a comprehensive survey of recipients who received this mechanism of support between 1990 and 2007 was performed. Of 196 individuals receiving a DF CDA, 181 were identified and asked to complete a comprehensive questionnaire concerning their career status, employment history, professional rank, and record of independent research funding (private foundation, federal, other). A personal assessment of the impact of this funding on these individuals' career trajectory was also requested. Eighty percent of 181 CDA recipients identified currently hold full- or part-time positions in academic medicine. The faculty rank of 112 survey respondents included 46 assistant professors (41%), 41 associate professors (37%), 18 professors (16%), and 7 division or departmental chairs (6%). Of respondents, 84% reported that they have received subsequent independent research funding; 95 of these individuals (86%) have received funding from a federal agency (235 federal grants awarded to date with funding >$318M). The study was retrospective and self-reported; some awardees did not respond to the survey. The DF's CDA Program has succeeded in supporting the early career development of talented investigators, educators, and leaders; fostered the promotion and retention of these individuals in academic medicine; and nucleated numerous investigative careers that have successfully acquired independent research funding. Copyright © 2012 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

High cytidine deaminase expression in the liver provides sanctuary for cancer cells from decitabine treatment effects.

PubMed

Ebrahem, Quteba; Mahfouz, Reda Z; Ng, Kwok Peng; Saunthararajah, Yogen

2012-10-01

We document for the first time that sanctuary in an organ which expresses high levels of the enzyme cytidine deaminase (CDA) is a mechanism of cancer cell resistance to cytidine analogues. This mechanism could explain why historically, cytidine analogues have not been successful chemotherapeutics against hepatotropic cancers, despite efficacy in vitro. Importantly, this mechanism of resistance can be readily reversed, without increasing toxicity to sensitive organs, by combining a cytidine analogue with an inhibitor of cytidine deaminase (tetrahydrouridine). Specifically, CDA rapidly metabolizes cytidine analogues into inactive uridine counterparts. Hence, to determine if sheltering/protection of cancer cells in organs which express high levels of CDA (e.g., liver) is a mechanism of resistance, we utilized a murine xenotransplant model of myeloid cancer that is sensitive to epigenetic therapeutic effects of the cytidine analogue decitabine in vitro and hepato-tropic in vivo. Treatment of tumor-bearing mice with decitabine (subcutaneous 0.2mg/kg 2X/week) doubled median survival and significantly decreased extra-hepatic tumor burden, but hepatic tumor burden remained substantial, to which the animals eventually succumbed. Combining a clinically-relevant inhibitor of CDA (tetrahydrouridine) with a lower dose of decitabine (subcutaneous 0.1mg/kg 2X/week) markedly decreased liver tumor burden without blood count or bone marrow evidence of myelotoxicity, and with further improvement in survival. In conclusion, sanctuary in a CDA-rich organ is a mechanism by which otherwise susceptible cancer cells can resist the effects of decitabine epigenetic therapy. This protection can be reversed without increasing myelotoxicity by combining tetrahydrouridine with a lower dose of decitabine.

Working memory delay period activity marks a domain-unspecific attention mechanism.

PubMed

Katus, Tobias; Müller, Matthias M

2016-03-01

Working memory (WM) recruits neural circuits that also perform perception- and action-related functions. Among the functions that are shared between the domains of WM and perception is selective attention, which supports the maintenance of task-relevant information during the retention delay of WM tasks. The tactile contralateral delay activity (tCDA) component of the event-related potential (ERP) marks the attention-based rehearsal of tactile information in somatosensory brain regions. We tested whether the tCDA reflects the competition for shared attention resources between a WM task and a perceptual task under dual-task conditions. The two tasks were always performed on opposite hands. In different blocks, the WM task had higher or lower priority than the perceptual task. The tCDA's polarity consistently reflected the hand where the currently prioritized task was performed. This suggests that the process indexed by the tCDA is not specific to the domain of WM, but mediated by a domain-unspecific attention mechanism. The analysis of transient ERP components evoked by stimuli in the two tasks further supports the interpretation that the tCDA marks a goal-directed bias in the allocation of selective attention. Larger spatially selective modulations were obtained for stimulus material related to the high-, as compared to low-priority, task. While our results generally indicate functional overlap between the domains of WM and perception, we also found evidence suggesting that selection in internal (mnemonic) and external (perceptual) stimulus representations involves processes that are not active during shifts of preparatory attention. Copyright © 2016 Elsevier Inc. All rights reserved.

Global Genetic Determinants of Mitochondrial DNA Copy Number

PubMed Central

Zhang, Hengshan; Singh, Keshav K.

2014-01-01

Many human diseases including development of cancer is associated with depletion of mitochondrial DNA (mtDNA) content. These diseases are collectively described as mitochondrial DNA depletion syndrome (MDS). High similarity between yeast and human mitochondria allows genomic study of the budding yeast to be used to identify human disease genes. In this study, we systematically screened the pre-existing respiratory-deficient Saccharomyces cerevisiae yeast strains using fluorescent microscopy and identified 102 nuclear genes whose deletions result in a complete mtDNA loss, of which 52 are not reported previously. Strikingly, these genes mainly encode protein products involved in mitochondrial protein biosynthesis process (54.9%). The rest of these genes either encode protein products associated with nucleic acid metabolism (14.7%), oxidative phosphorylation (3.9%), or other protein products (13.7%) responsible for bud-site selection, mitochondrial intermembrane space protein import, assembly of cytochrome-c oxidase, vacuolar protein sorting, protein-nucleus import, calcium-mediated signaling, heme biosynthesis and iron homeostasis. Thirteen (12.7%) of the genes encode proteins of unknown function. We identified human orthologs of these genes, conducted the interaction between the gene products and linked them to human mitochondrial disorders and other pathologies. In addition, we screened for genes whose defects affect the nuclear genome integrity. Our data provide a systematic view of the nuclear genes involved in maintenance of mitochondrial DNA. Together, our studies i) provide a global view of the genes regulating mtDNA content; ii) provide compelling new evidence toward understanding novel mechanism involved in mitochondrial genome maintenance and iii) provide useful clues in understanding human diseases in which mitochondrial defect and in particular depletion of mitochondrial genome plays a critical role. PMID:25170845

Critical Discourse Analysis of Martin Luther King's Speech in Socio-Political Perspective

ERIC Educational Resources Information Center

Sipra, Muhammad Aslam; Rashid, Athar

2013-01-01

The article presents the Critical Discourse Analysis (CDA) of the first part of King Martin Luther's speech "When I Have a Dream" in socio-political context. The study investigates how it lies on the basis of application of Fairclough version of CDA in the first part of the text. Moreover, it explicates the terms like social, cultural…

Exploring Ways to Provide Diagnostic Feedback with an ESL Placement Test: Cognitive Diagnostic Assessment of L2 Reading Ability

ERIC Educational Resources Information Center

Kim, Ah-Young

2015-01-01

Previous research in cognitive diagnostic assessment (CDA) of L2 reading ability has been frequently conducted using large-scale English proficiency exams (e.g., TOEFL, MELAB). Using CDA, it is possible to analyze individual learners' strengths and weaknesses in multiple attributes (i.e., knowledge, skill, strategy) measured at the item level.…

Molecular cloning and expression of rat brain endopeptidase 3.4.24.16.

PubMed

Dauch, P; Vincent, J P; Checler, F

1995-11-10

We have isolated by immunological screening of a lambda ZAPII cDNA library constructed from rat brain mRNAs a cDNA clone encoding endopeptidase 3.4.24.16. The longest open reading frame encodes a 704-amino acid protein with a theoretical molecular mass of 80,202 daltons and bears the consensus sequence of the zinc metalloprotease family. The sequence exhibits a 60.2% homology with those of another zinc metallopeptidase, endopeptidase 3.4.24.15. Northern blot analysis reveals two mRNA species of about 3 and 5 kilobases in rat brain, ileum, kidney, and testis. We have transiently transfected COS-7 cells with pcDNA3 containing the cloned cDNA and established the overexpression of a 70-75-kDa immunoreactive protein. This protein hydrolyzes QFS, a quenched fluorimetric substrate of endopeptidase 3.4.24.16, and cleaves neurotensin at a single peptide bond, leading to the formation of neurotensin (1-10) and neurotensin (11-13). QFS and neurotensin hydrolysis are potently inhibited by the selective endopeptidase 3.4.24.16 dipeptide blocker Pro-Ile and by dithiothreitol, while the enzymatic activity remains unaffected by phosphoramidon and captopril, the specific inhibitors of endopeptidase 3.4.24.11 and angiotensin-converting enzyme, respectively. Altogether, these physicochemical, biochemical, and immunological properties unambiguously identify endopeptidase 3.4.24.16 as the protein encoded by the isolated cDNA clone.

Complete mitochondrial genome of the a rare subspecies of genus Bos, Tianzhu white yak from Tibetan area in China.

PubMed

E, Guangxin; Na, Ri-Su; Zhao, Yong-Ju; Gao, Hui-Jiang; An, Tian-Wu; Huang, Yong-Fu

2016-01-01

The population of domestic yak, Tianzhu white yak, from Tibetan area in China is considered as a rare Bos grunniens species. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,319 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.7%, T: 27.2%, C: 25.8% and G: 13.2%. The complete mitogenome of the new subspecies of Bos grunniens could provide an important data to further explore the taxonomic status of the subspecies.

Lead-rich sediments, Coeur d'Alene River Valley, Idaho: area, volume, tonnage, and lead content

USGS Publications Warehouse

Bookstrom, Arthur A.; Box, Stephen E.; Campbell, Julie K.; Foster, Kathryn I.; Jackson, Berne L.

2001-01-01

In north Idaho, downstream from the Coeur d?Alene (CdA) silver-lead-zinc mining district, lead-rich sediments, containing at least 1,000 ppm of lead, cover approximately 61 km2 (or 73 percent) of the 84-km2 floor of the CdA River valley, from the confluence of its North and South Forks to the top of its delta-front slope, in CdA Lake. Concentrations of lead (Pb) in surface sediments range from 15 to about 38,500 ppm, and average 3,370 ppm, which is 112 times the mean background concentration (30 ppm) of Pb in uncontaminated sediments of the CdA and St. Joe River valleys. Most of the highest concentrations of Pb are in sediments within or near the river channel, or near the base of the stratigraphic section of Pb-rich sediments. Ranges of Pb concentration in Pb-rich sediments gradually decrease with increasing distance from the river and its distributaries. Ranges of thickness of Pb-rich sediments generally decrease abruptly with increasing distance from the river, from about 3 + 3 m in the river channel to about 1 + 1m on upland riverbanks, levees and sand splays, to about 0.3 + 0.3 m in back-levee marshes and lateral lakes. Thickness of Pb-rich dredge spoils (removed from the river and deposited on Cataldo-Mission Flats) is mostly in the range 4 + 4 m, thinning away from an outfall zone north and west of the river, near the formerly dredged channel reach near Cataldo Landing. We attribute lateral variation in ranges of thickness and Pb content of Pb-rich sediments to the dynamic balance between decreasing floodwater flow velocity with increasing distance from the river and the quantity, size, density, and Pb content of particles mobilized, transported, and deposited. We present alternative median- and mean-based estimates of the volume of Pbrich sediments, their wet and dry tonnage, and their tonnage of contained Pb. We calculate separate pairs of estimates for 23 Estimation Units, each of which corresponds to a major depositional environment, divided into down-valley segments. We favor median-based estimates of the thickness and thickness-interval weighted-average Pb concentration, because uncommonly thick and Pb-rich sections may excessively influence mean estimates. Nevertheless, data from partial sections of Pb-rich sediments are included in most estimates, and these tend to reduce both median- and mean-based estimates. Median-based estimates indicate a volume of 32 M m3 of Pb-rich sediments in the CdA River valley, with a dry tonnage of 47 + 4 M t, containing 250 + 75 kt of Pb (considering analytical uncertainties only). An equivalent tonnage of dry CdA River valley sediments of the pre-mining era, with the mean background concentration of 30 ppm of Pb, would contain about 1.4 kt of Pb. Thus, the amount of Pb added to CdA River valley sediments deposited since the onset of mining is estimated as 249 + 75 kt of Pb, or about 99.5 percent of the estimated Pb contained. Of an estimated 850 + 10 kt of Pb lost to streams as a result of mining-related activities, an estimated total of 739 + 319 kt of Pb has been deposited in sediments of the South Fork drainage basin, the CdA River valley, and the bottom of CdA Lake (combined). Based on mid-range values from a set of preferred estimates with uncertainty ranges up to + 50 percent, roughly 24 percent of the 850 + 10 kt of mining-derived Pb lost to streams has been added to sediments of the South Fork drainage basin, 29 percent to sediments of the CdA River valley floor, and 34 percent to sediments on the bottom of CdA Lake. This amounts to roughly 87 percent of the Pb lost to streams, not including Pb contained in sediments of the North Fork drainage basin and the Spokane River valley, the tonnages of which have not yet estimated.

Hxt13, Hxt15, Hxt16 and Hxt17 from Saccharomyces cerevisiae represent a novel type of polyol transporters

PubMed Central

Jordan, Paulina; Choe, Jun-Yong; Boles, Eckhard; Oreb, Mislav

2016-01-01

The genome of S. cerevisae encodes at least twenty hexose transporter-like proteins. Despite extensive research, the functions of Hxt8-Hxt17 have remained poorly defined. Here, we show that Hxt13, Hxt15, Hxt16 and Hxt17 transport two major hexitols in nature, mannitol and sorbitol, with moderate affinities, by a facilitative mechanism. Moreover, Hxt11 and Hxt15 are capable of transporting xylitol, a five-carbon polyol derived from xylose, the most abundant pentose in lignocellulosic biomass. Hxt11, Hxt13, Hxt15, Hxt16 and Hxt17 are phylogenetically and functionally distinct from known polyol transporters. Based on docking of polyols to homology models of transporters, we propose the architecture of their active site. In addition, we determined the kinetic parameters of mannitol and sorbitol dehydrogenases encoded in the yeast genome, showing that they discriminate between mannitol and sorbitol to a much higher degree than the transporters. PMID:26996892

Identification and characterization of Rhox13, a novel X-linked mouse homeobox gene

PubMed Central

Geyer, Christopher B.; Eddy, Edward M.

2008-01-01

Homeobox genes encode transcription factors whose expression organizes programs of development. A number of homeobox genes expressed in reproductive tissues have been identified recently, including a colinear cluster on the X chromosome in mice. This has led to an increased interest in understanding the role(s) of homeobox genes in regulating development of reproductive tissues including the testis, ovary, and placenta. Here we report the identification and characterization of a novel homeobox gene of the paired-like class on the X chromosome distal to the reproductive homeobox (Rhox) cluster in mice. Transcripts are found in the testis and ovary as early as 13.5 days post-coitum (dpc). Transcription ceases in the ovary by 3 days post-partum (dpp), but continues in the testis through adulthood. The Rhox13 gene encodes a 25.3 kDa protein expressed in the adult testis in germ cells at the basal aspect of the seminiferous epithelium. PMID:18675325

Transgenic cells with increased plastoquinone levels and methods of use

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

Sayre, Richard T.; Subramanian, Sowmya; Cahoon, Edgar

Disclosed herein are transgenic cells expressing a heterologous nucleic acid encoding a prephenate dehydrogenase (PDH) protein, a heterologous nucleic acid encoding a homogentisate solanesyl transferase (HST) protein, a heterologous nucleic acid encoding a deoxyxylulose phosphate synthase (DXS) protein, or a combination of two or more thereof. In particular examples, the disclosed transgenic cells have increased plastoquinone levels. Also disclosed are methods of increasing cell growth rates or production of biomass by cultivating transgenic cells expressing a heterologous nucleic acid encoding a PDH protein, a heterologous nucleic acid encoding an HST protein, a heterologous nucleic acid encoding a DXS protein, ormore » a combination of two or more thereof under conditions sufficient to produce cell growth or biomass.« less

Molecular Cloning and Ethylene Induction of mRNA Encoding a Phytoalexin Elicitor-Releasing Factor, beta-1,3-Endoglucanase, in Soybean.

PubMed

Takeuchi, Y; Yoshikawa, M; Takeba, G; Tanaka, K; Shibata, D; Horino, O

1990-06-01

Soybean (Glycine max) beta-1,3-endoglucanase (EC 3.2. 1.39) is involved in one of the earliest plant-pathogen interactions that may lead to active disease resistance by releasing elicitor-active carbohydrates from the cell walls of fungal pathogens. Ethylene induced beta-1,3-endoglucanase activity to 2- to 3-fold higher levels in cotyledons of soybean seedlings. A specific polyclonal antiserum raised against purified soybean beta-1,3-endoglucanase was used to immunoprecipitate in vitro translation products, demonstrating that ethylene induction increased translatable beta-1,3-endoglucanase mRNA. Several cDNA clones for the endoglucanase gene were obtained by antibody screening of a lambda-gt11 expression library prepared from soybean cotyledons. Hybrid-select translation experiments indicated that the cloned cDNA encoded a 36-kilodalton precursor protein product that was specifically immunoprecipitated with beta-1,3-endoglucanase antiserum. Escherichia coli cells expressing the cloned cDNA also synthesized an immunologically positive protein. Nucleotide sequence of three independent clones revealed a single uninterrupted open reading frame of 1041 nucleotides, corresponding to a polypeptide of 347 residue long. The primary amino acid sequence of beta-1,3-endoglucanase as deduced from the nucleotide sequence was confirmed by direct amino acid sequencing of trypsin digests of the glucanase. The soybean beta-1,3-endoglucanase exhibited 53% amino acid homology to a beta-1,3-glucanase cloned from cultured tobacco cells and 48% homology to a beta-(1,3-1,4)-glucanase from barley. Utilizing the largest cloned cDNA (pEG488) as a hybridization probe, it was found that the increase in translatable beta-1,3-endoglucanase mRNA seen upon ethylene treatment of soybean seedlings was due to 50- to 100-fold increase in steady state mRNA levels, indicating that ethylene regulates gene expression of this enzyme important in disease resistance at the level of gene transcription.

How Do Young Students with Different Profiles of Reading Skill Mastery, Perceived Ability, and Goal Orientation Respond to Holistic Diagnostic Feedback?

ERIC Educational Resources Information Center

Jang, Eunice Eunhee; Dunlop, Maggie; Park, Gina; van der Boom, Edith H.

2015-01-01

One critical issue with cognitive diagnostic assessment (CDA) lies in its lack of research evidence that shows how diagnostic feedback from CDA is interpreted and used by young students. This mixed methods research examined how holistic diagnostic feedback (HDF) is processed by young learners with different profiles of reading skills, goal…

EXPOSURE-DISEASE CONTINUUM FOR 2-CHLORO-2'-DEOXYADENOSINE (2-CDA), A PROTOTYPE TERATOGEN: INDUCTION OF LUMBAR HERNIA IN THE RAT AND SPECIES COMPARISON FOR THE TERATOGENIC RESPONSES

EPA Science Inventory

Abstract

The purine analog 2-chloro-2'-deoxyadenosine (2-CdA, cladribine), an anti-leukemic and immunosuppressive agent, has been found to be teratogenic in the mouse and rabbit, causing ocular and limb defects. The current study examined the teratogenic potential of th...

Drugs, Discourses and Education: A Critical Discourse Analysis of a High School Drug Education Text

ERIC Educational Resources Information Center

Tupper, Kenneth W.

2008-01-01

This paper examines a high school drug education text using critical discourse analysis (CDA) to discern its underlying ideological commitments and political dispositions. I begin with an overview of CDA and why it is a suitable methodology for my work, and then provide a brief history of drug education in North America. Next, I consider some of…

Trilateration range and range rate system. Volume 1: CDA system manual

NASA Technical Reports Server (NTRS)

1976-01-01

This document is one of a series of manuals designed to provide the information required to operate and maintain the Command and Data Acquisition (CDA) equipment of the Trilateration Range and Range Rate (TRRR) System. Information pertaining to the equipment in the Trilateration Range and Range Rate System which is designed to interface with existing NASA equipment located at Wallops Island, Virginia is presented.

'Overgrowth' mutants in barley and wheat: new alleles and phenotypes of the 'Green Revolution' DELLA gene.

PubMed

Chandler, Peter Michael; Harding, Carol Anne

2013-04-01

A suppressor screen using dwarf mutants of barley (Hordeum vulgare L.) led to the isolation of 'overgrowth' derivatives, which retained the original dwarfing gene but grew at a faster rate because of a new mutation. The new mutations were in the Slender1 (Sln1) gene (11/13 cases), which encodes the DELLA protein central to gibberellin (GA) signalling, showed 100% genetic linkage to Sln1 (1/13), or were in the Spindly1 (Spy1) gene (1/13), which encodes another protein involved in GA signalling. The overgrowth mutants were characterized by increased GA signalling, although the extent still depended on the background GA biosynthesis capacity, GA receptor function, and DELLA activity. A comparison between two GA responses, α-amylase production and leaf growth rate, revealed degrees of specificity for both the overgrowth allele and the GA response under consideration. Many overgrowth mutants were also isolated in a dwarf line of bread wheat (Triticum aestivum L.) and 19 new alleles were identified in the Rht-B1 gene, one of the 'Green Revolution' semi-dwarfing genes and the orthologue of Sln1. The sites of amino acid substitutions in the DELLA proteins of both species provide insight into DELLA function, and included examples where identical but independent substitutions were observed. In both species, the starting lines were too dwarfed to be directly useful in breeding programmes, but new overgrowth derivatives with semidwarf heights have now been characterized. The variation they exhibit in GA-influenced traits identifies novel alleles with perfect markers that are of potential use in breeding.

Lateralized delay period activity marks the focus of spatial attention in working memory: evidence from somatosensory event-related brain potentials.

PubMed

Katus, Tobias; Eimer, Martin

2015-04-29

The short-term retention of sensory information in working memory (WM) is known to be associated with a sustained enhancement of neural activity. What remains controversial is whether this neural trace indicates the sustained storage of information or the allocation of attention. To evaluate the storage and attention accounts, we examined sustained tactile contralateral delay activity (tCDA component) of the event-related potential. The tCDA manifests over somatosensory cortex contralateral to task-relevant tactile information during stimulus retention. Two tactile sample sets (S1, S2) were presented sequentially, separated by 1.5 s. Each set comprised two stimuli, one per hand. Human participants memorized the location of one task-relevant stimulus per sample set and judged whether one of these locations was stimulated again at memory test. The two relevant pulses were unpredictably located on the same hand (stay trials) or on different hands (shift trials). Initially, tCDA components emerged contralateral to the relevant S1 pulse. Sequential loading of WM enhanced the tCDA after S2 was presented on stay trials. On shift trials, the tCDA's polarity reversed after S2 presentation, resulting in delay activity that was now contralateral to the task-relevant S2 pulse. The disappearance of a lateralized neural trace for the relevant S1 pulse did not impair memory accuracy for this stimulus on shift trials. These results contradict the storage account and suggest that delay period activity indicates the sustained engagement of an attention-based rehearsal mechanism. In conclusion, somatosensory delay period activity marks the current focus of attention in tactile WM. Copyright © 2015 the authors 0270-6474/15/356689-07$15.00/0.

Automated Cell Detection and Morphometry on Growth Plate Images of Mouse Bone

PubMed Central

Ascenzi, Maria-Grazia; Du, Xia; Harding, James I; Beylerian, Emily N; de Silva, Brian M; Gross, Ben J; Kastein, Hannah K; Wang, Weiguang; Lyons, Karen M; Schaeffer, Hayden

2014-01-01

Microscopy imaging of mouse growth plates is extensively used in biology to understand the effect of specific molecules on various stages of normal bone development and on bone disease. Until now, such image analysis has been conducted by manual detection. In fact, when existing automated detection techniques were applied, morphological variations across the growth plate and heterogeneity of image background color, including the faint presence of cells (chondrocytes) located deeper in tissue away from the image’s plane of focus, and lack of cell-specific features, interfered with identification of cell. We propose the first method of automated detection and morphometry applicable to images of cells in the growth plate of long bone. Through ad hoc sequential application of the Retinex method, anisotropic diffusion and thresholding, our new cell detection algorithm (CDA) addresses these challenges on bright-field microscopy images of mouse growth plates. Five parameters, chosen by the user in respect of image characteristics, regulate our CDA. Our results demonstrate effectiveness of the proposed numerical method relative to manual methods. Our CDA confirms previously established results regarding chondrocytes’ number, area, orientation, height and shape of normal growth plates. Our CDA also confirms differences previously found between the genetic mutated mouse Smad1/5CKO and its control mouse on fluorescence images. The CDA aims to aid biomedical research by increasing efficiency and consistency of data collection regarding arrangement and characteristics of chondrocytes. Our results suggest that automated extraction of data from microscopy imaging of growth plates can assist in unlocking information on normal and pathological development, key to the underlying biological mechanisms of bone growth. PMID:25525552

Personalized-detailed clinical model for data interoperability among clinical standards.

PubMed

Khan, Wajahat Ali; Hussain, Maqbool; Afzal, Muhammad; Amin, Muhammad Bilal; Saleem, Muhammad Aamir; Lee, Sungyoung

2013-08-01

Data interoperability among health information exchange (HIE) systems is a major concern for healthcare practitioners to enable provisioning of telemedicine-related services. Heterogeneity exists in these systems not only at the data level but also among different heterogeneous healthcare standards with which these are compliant. The relationship between healthcare organization data and different heterogeneous standards is necessary to achieve the goal of data level interoperability. We propose a personalized-detailed clinical model (P-DCM) approach for the generation of customized mappings that creates the necessary linkage between organization-conformed healthcare standards concepts and clinical model concepts to ensure data interoperability among HIE systems. We consider electronic health record (EHR) standards, openEHR, and HL7 CDA instances transformation using P-DCM. P-DCM concepts associated with openEHR and HL7 CDA help in transformation of instances among these standards. We investigated two datasets: (1) data of 100 diabetic patients, including 50 each of type 1 and type 2, from a local hospital in Korea and (2) data of a single Alzheimer's disease patient. P-DCMs were created for both scenarios, which provided the basis for deriving instances for HL7 CDA and openEHR standards. For proof of concept, we present case studies of encounter information for type 2 diabetes mellitus patients and monitoring of daily routine activities of an Alzheimer's disease patient. These reflect P-DCM-based customized mappings generation with openEHR and HL7 CDA standards. Customized mappings are generated based on the relationship of P-DCM concepts with CDA and openEHR concepts. The objective of this work is to achieve semantic data interoperability among heterogeneous standards. This would lead to effective utilization of resources and allow timely information exchange among healthcare systems.

Personalized-Detailed Clinical Model for Data Interoperability Among Clinical Standards

PubMed Central

Khan, Wajahat Ali; Hussain, Maqbool; Afzal, Muhammad; Amin, Muhammad Bilal; Saleem, Muhammad Aamir

2013-01-01

Abstract Objective: Data interoperability among health information exchange (HIE) systems is a major concern for healthcare practitioners to enable provisioning of telemedicine-related services. Heterogeneity exists in these systems not only at the data level but also among different heterogeneous healthcare standards with which these are compliant. The relationship between healthcare organization data and different heterogeneous standards is necessary to achieve the goal of data level interoperability. We propose a personalized-detailed clinical model (P-DCM) approach for the generation of customized mappings that creates the necessary linkage between organization-conformed healthcare standards concepts and clinical model concepts to ensure data interoperability among HIE systems. Materials and Methods: We consider electronic health record (EHR) standards, openEHR, and HL7 CDA instances transformation using P-DCM. P-DCM concepts associated with openEHR and HL7 CDA help in transformation of instances among these standards. We investigated two datasets: (1) data of 100 diabetic patients, including 50 each of type 1 and type 2, from a local hospital in Korea and (2) data of a single Alzheimer's disease patient. P-DCMs were created for both scenarios, which provided the basis for deriving instances for HL7 CDA and openEHR standards. Results: For proof of concept, we present case studies of encounter information for type 2 diabetes mellitus patients and monitoring of daily routine activities of an Alzheimer's disease patient. These reflect P-DCM-based customized mappings generation with openEHR and HL7 CDA standards. Customized mappings are generated based on the relationship of P-DCM concepts with CDA and openEHR concepts. Conclusions: The objective of this work is to achieve semantic data interoperability among heterogeneous standards. This would lead to effective utilization of resources and allow timely information exchange among healthcare systems. PMID:23875730

Genome sequence of a cluster A13 mycobacteriophage detected in Mycobacterium phlei over a half century ago.

PubMed

Marton, Szilvia; Fehér, Enikő; Horváth, Balázs; Háber, Katalin; Somogyi, Pál; Minárovits, János; Bányai, Krisztián

2016-01-01

A phage infecting Mycobacterium phlei was isolated in 1958 from a soil sample in Hungary. Some physicochemical and biological properties of the virus were described in independent studies over the years. Here, we report the genome sequence of this early mycobacteriophage isolate. The Phlei phage genome measured 50,418 bp, had a GC content of 60.1 % and was predicted to encode 81 proteins and three tRNAs. Phylogeny of the tape measure protein revealed genetic relatedness to other early isolates of mycobacteriophages within subcluster A2. The genomic organization and genetic relationships to other strains showed that the Phlei phage belongs to a novel genetic cluster, designated A13.

Canine distemper virus in the Serengeti ecosystem: molecular adaptation to different carnivore species.

PubMed

Nikolin, Veljko M; Olarte-Castillo, Ximena A; Osterrieder, Nikolaus; Hofer, Heribert; Dubovi, Edward; Mazzoni, Camila J; Brunner, Edgar; Goller, Katja V; Fyumagwa, Robert D; Moehlman, Patricia D; Thierer, Dagmar; East, Marion L

2017-04-01

Was the 1993/1994 fatal canine distemper virus (CDV) epidemic in lions and spotted hyaenas in the Serengeti ecosystem caused by the recent spillover of a virulent domestic dog strain or one well adapted to these noncanids? We examine this question using sequence data from 13 'Serengeti' strains including five complete genomes obtained between 1993 and 2011. Phylogenetic and haplotype network analyses reveal that strains from noncanids during the epidemic were more closely related to each other than to those from domestic or wild canids. All noncanid 'Serengeti' strains during the epidemic encoded: (1) one novel substitution G134S in the CDV-V protein; and (2) the rare amino acid combination 519I/549H at two sites under positive selection in the region of the CDV-H protein that binds to SLAM (CD 150) host cell receptors. Worldwide, only a few noncanid strains in the America II lineage encode CDV-H 519I/549H. All canid 'Serengeti' strains during the epidemic coded CDV-V 134G, and CDV-H 519R/549Y, or 519R/549H. A functional assay of cell entry revealed the highest performance by CDV-H proteins encoding 519I/549H in cells expressing lion SLAM receptors, and the highest performance by proteins encoding 519R/549Y, typical of dog strains worldwide, in cells expressing dog SLAM receptors. Our findings are consistent with an epidemic in lions and hyaenas caused by CDV variants better adapted to noncanids than canids, but not with the recent spillover of a dog strain. Our study reveals a greater complexity of CDV molecular epidemiology in multihost environments than previously thought. © 2016 John Wiley & Sons Ltd.

Characterization of the complete mitochondrial genomes of Nematodirus oiratianus and Nematodirus spathiger of small ruminants

PubMed Central

2014-01-01

Background Nematodirus spp. are among the most common nematodes of ruminants worldwide. N. oiratianus and N. spathiger are distributed worldwide as highly prevalent gastrointestinal nematodes, which cause emerging health problems and economic losses. Accurate identification of Nematodirus species is essential to develop effective control strategies for Nematodirus infection in ruminants. Mitochondrial DNA (mtDNA) could provide powerful genetic markers for identifying these closely related species and resolving phylogenetic relationships at different taxonomic levels. Methods In the present study, the complete mitochondrial (mt) genomes of N. oiratianus and N. spathiger from small ruminants in China were obtained using Long-range PCR and sequencing. Results The complete mt genomes of N. oiratianus and N. spathiger were 13,765 bp and 13,519 bp in length, respectively. Both mt genomes were circular and consisted of 36 genes, including 12 genes encoding proteins, 2 genes encoding rRNA, and 22 genes encoding tRNA. Phylogenetic analyses based on the concatenated amino acid sequence data of all 12 protein-coding genes by Bayesian inference (BI), Maximum likelihood (ML) and Maximum parsimony (MP) showed that the two Nematodirus species (Molineidae) were closely related to Dictyocaulidae. Conclusions The availability of the complete mtDNA sequences of N. oiratianus and N. spathiger not only provides new mtDNA sources for a better understanding of nematode mt genomics and phylogeny, but also provides novel and useful genetic markers for studying diagnosis, population genetics and molecular epidemiology of Nematodirus spp. in small ruminants. PMID:25015379

Characterization of the complete mitochondrial genomes of Nematodirus oiratianus and Nematodirus spathiger of small ruminants.

PubMed

Zhao, Guang-Hui; Jia, Yan-Qing; Cheng, Wen-Yu; Zhao, Wen; Bian, Qing-Qing; Liu, Guo-Hua

2014-07-11

Nematodirus spp. are among the most common nematodes of ruminants worldwide. N. oiratianus and N. spathiger are distributed worldwide as highly prevalent gastrointestinal nematodes, which cause emerging health problems and economic losses. Accurate identification of Nematodirus species is essential to develop effective control strategies for Nematodirus infection in ruminants. Mitochondrial DNA (mtDNA) could provide powerful genetic markers for identifying these closely related species and resolving phylogenetic relationships at different taxonomic levels. In the present study, the complete mitochondrial (mt) genomes of N. oiratianus and N. spathiger from small ruminants in China were obtained using Long-range PCR and sequencing. The complete mt genomes of N. oiratianus and N. spathiger were 13,765 bp and 13,519 bp in length, respectively. Both mt genomes were circular and consisted of 36 genes, including 12 genes encoding proteins, 2 genes encoding rRNA, and 22 genes encoding tRNA. Phylogenetic analyses based on the concatenated amino acid sequence data of all 12 protein-coding genes by Bayesian inference (BI), Maximum likelihood (ML) and Maximum parsimony (MP) showed that the two Nematodirus species (Molineidae) were closely related to Dictyocaulidae. The availability of the complete mtDNA sequences of N. oiratianus and N. spathiger not only provides new mtDNA sources for a better understanding of nematode mt genomics and phylogeny, but also provides novel and useful genetic markers for studying diagnosis, population genetics and molecular epidemiology of Nematodirus spp. in small ruminants.

Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.

PubMed

Krishnan, Arunkumar; Mustafa, Arshi; Almén, Markus Sällman; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

2015-10-01

Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further understand the differential roles of GPCR/G protein mediated intracellular signaling system across various metazoan lineages. Copyright © 2015 Elsevier Inc. All rights reserved.

Mitochondrial genome of the blackfin tuna Thunnus atlanticus Lesson, 1831 (Perciformes, Scrombidae).

PubMed

Márquez, Edna J; Isaza, Juan P; Alzate, Juan F

2016-05-01

Blackfin tuna, Thunnus atlanticus is a widespread epipelagic oceanic species in the western Atlantic. So far the mitochondrial genome of this species remained unknown, although the mitogenomes of all congeners are known. The mitochondrial genome encodes for 13 proteins, 21 tRNAs, 2 ribosomal RNAs and the gene synteny is conserved with other previously reported mitogenomes of tunas.

Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain

PubMed Central

Wang, Wen-Jie; Cheng, Wang; Luo, Ming; Yan, Qingyu; Yu, Hong-Mei; Li, Qiong; Cao, Dong-Dong; Huang, Shengfeng; Xu, Anlong; Mariuzza, Roy A.; Chen, Yuxing; Zhou, Cong-Zhao

2015-01-01

Peptidoglycan recognition proteins (PGRPs), which have been identified in most animals, are pattern recognition molecules that involve antimicrobial defense. Resulting from extraordinary expansion of innate immune genes, the amphioxus encodes many PGRPs of diverse functions. For instance, three isoforms of PGRP encoded by Branchiostoma belcheri tsingtauense, termed BbtPGRP1~3, are fused with a chitin binding domain (CBD) at the N-terminus. Here we report the 2.7 Å crystal structure of BbtPGRP3, revealing an overall structure of an N-terminal hevein-like CBD followed by a catalytic PGRP domain. Activity assays combined with site-directed mutagenesis indicated that the individual PGRP domain exhibits amidase activity towards both DAP-type and Lys-type peptidoglycans (PGNs), the former of which is favored. The N-terminal CBD not only has the chitin-binding activity, but also enables BbtPGRP3 to gain a five-fold increase of amidase activity towards the Lys-type PGNs, leading to a significantly broadened substrate spectrum. Together, we propose that modular evolution via domain shuffling combined with gene horizontal transfer makes BbtPGRP1~3 novel PGRPs of augmented catalytic activity and broad recognition spectrum. PMID:26479246

Identification of the G13 (cAMP-response-element-binding protein-related protein) gene product related to activating transcription factor 6 as a transcriptional activator of the mammalian unfolded protein response.

PubMed

Haze, K; Okada, T; Yoshida, H; Yanagi, H; Yura, T; Negishi, M; Mori, K

2001-04-01

Eukaryotic cells control the levels of molecular chaperones and folding enzymes in the endoplasmic reticulum (ER) by a transcriptional induction process termed the unfolded protein response (UPR). The mammalian UPR is mediated by the cis-acting ER stress response element consisting of 19 nt (CCAATN(9)CCACG), the CCACG part of which is considered to provide specificity. We recently identified the basic leucine zipper (bZIP) protein ATF6 as a mammalian UPR-specific transcription factor; ATF6 is activated by ER stress-induced proteolysis and binds directly to CCACG. Here we report that eukaryotic cells express another bZIP protein closely related to ATF6 in both structure and function. This protein encoded by the G13 (cAMP response element binding protein-related protein) gene is constitutively synthesized as a type II transmembrane glycoprotein anchored in the ER membrane and processed into a soluble form upon ER stress as occurs with ATF6. The proteolytic processing of ATF6 and the G13 gene product is accompanied by their relocation from the ER to the nucleus; their basic regions seem to function as a nuclear localization signal. Overexpression of the soluble form of the G13 product constitutively activates the UPR, whereas overexpression of a mutant lacking the activation domain exhibits a strong dominant-negative effect. Furthermore, the soluble forms of ATF6 and the G13 gene product are unable to bind to several point mutants of the cis-acting ER stress response element in vitro that hardly respond to ER stress in vivo. We thus concluded that the two related bZIP proteins are crucial transcriptional regulators of the mammalian UPR, and propose calling the ATF6 gene product ATF6alpha and the G13 gene product ATF6beta.

Hydroxyethyl cellulose doped with copper(II) phthalocyanine-tetrasulfonic acid tetrasodium salt as an effective dual functional hole-blocking layer for polymer light-emitting diodes

NASA Astrophysics Data System (ADS)

Wu, Cheng-Liang; Chen, Yun

2017-07-01

We report a doping method to improve the performance of solution-processed polymer light-emitting diodes (PLEDs). Doping 12 wt% copper(II) phthalocyanine-tetrasulfonated acid tetrasodium salt (TS-CuPc) into hydroxyethyl cellulose (HEC) as a dual functional hole-blocking layer (df-HBL) of multilayer PLED (glass/ITO/PEDOT:PSS/HY-PPV/TS-CuPc-doped HEC/LiF/Al) significantly enhanced maximum luminance, maximum current and power efficiency over that without the df-HBL (10,319 cd/m2, 2.98 cd/A and 1.24 lm/W) to (29,205 cd/m2, 13.27 cd/A and 9.56 lm/W). CV measurements reveal that HEC possesses a powerful hole-blocking capability. Topography and conductivity AFM images show that doping TS-CuPc increases the interfacial contact area and interfacial conductivity, which can overcome the insulating nature of HEC and thus further facilitate electron injection. Enhancements in device performance are attributed to the improved carrier balance and recombination in the presence of df-HBL, confirmed in electron-only and hole-only devices. Moreover, apparently raised open-circuit voltages provide further evidence that enhanced electron injection is indeed realized by the df-HBL. This study demonstrates an effective approach to develop highly efficient PLEDs.

The effect of a charge control layer on the electroluminescent characteristic of blue and white organic light-emitting diodes.

PubMed

Lee, Dong Hyung; Lee, Seok Jae; Koo, Ja-Ryong; Lee, Ho Won; Shin, Hyun Su; Lee, Song Eun; Kim, Woo Young; Lee, Kum Hee; Yoon, Seung Soo; Kim, Young Kwan

2014-08-01

We investigated blue fluorescent organic light-emitting diode (OLED) with a charge control layer (CCL) to produce high efficiency and improve the half-decay lifetime. Three types of devices (device A, B, and C) were fabricated following the number of CCLs within the emitting layer (EML), maintaining the thickness of whole EML. The CCL and host material, 2-methyl-9,10-di(2-naphthyl)anthracene, which has a bipolar property, was able to control the carrier movement with ease inside the EML. Device B demonstrated a maximum luminous efficiency (LE) and external quantum efficiency (EQE) of 9.19 cd/A and 5.78%, respectively. It also showed that the enhancement of the half-decay lifetime, measured at an initial luminance of 1,000 cd/m2, was 1.5 times longer than that of the conventional structure. A hybrid white OLED (WOLED) was also fabricated using a phosphorescent red emitter, bis(2-phenylquinoline)-acetylacetonate iridium III doped in 4,4'-N,N'-dicarbazolyl-biphenyl. The property of the hybrid WOLED with CCL showed a maximum LE and an EQE of 13.46 cd/A and 8.32%, respectively. It also showed white emission with Commission International de L'Éclairage coordinates of (x = 0.41, y = 0.33) at 10 V.

Synergetic Influences of Mixed-Host Emitting Layer Structures and Hole Injection Layers on Efficiency and Lifetime of Simplified Phosphorescent Organic Light-Emitting Diodes.

PubMed

Han, Tae-Hee; Kim, Young-Hoon; Kim, Myung Hwan; Song, Wonjun; Lee, Tae-Woo

2016-03-09

We used various nondestructive analyses to investigate various host material systems in the emitting layer (EML) of simple-structured, green phosphorescent organic light-emitting diodes (OLEDs) to clarify how the host systems affect its luminous efficiency (LE) and operational stability. An OLED that has a unipolar single-host EML with conventional poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) ( PSS) showed high operating voltage, low LE (∼26.6 cd/A, 13.7 lm/W), and short lifetime (∼4.4 h @ 1000 cd/m(2)). However, the combined use of a gradient mixed-host EML and a molecularly controlled HIL that has increased surface work function (WF) remarkably decreased operating voltage and improved LE (∼68.7 cd/A, 77.0 lm/W) and lifetime (∼70.7 h @ 1000 cd/m(2)). Accumulated charges at the injecting interfaces and formation of a narrow recombination zone close to the interfaces are the major factors that accelerate degradation of charge injection/transport and electroluminescent properties of OLEDs, so achievement of simple-structured OLEDs with high efficiency and long lifetime requires facilitating charge injection and balanced transport into the EML and distributing charge carriers and excitons in EML.

Inhibition and dispersal of Agrobacterium tumefaciens biofilms by a small diffusible Pseudomonas aeruginosa exoproduct(s).

PubMed

Hibbing, Michael E; Fuqua, Clay

2012-06-01

Environmental biofilms often contain mixed populations of different species. In these dense communities, competition between biofilm residents for limited nutrients such as iron can be fierce, leading to the evolution of competitive factors that affect the ability of competitors to grow or form biofilms. We have discovered a compound(s) present in the conditioned culture fluids of Pseudomonas aeruginosa that disperses and inhibits the formation of biofilms produced by the facultative plant pathogen Agrobacterium tumefaciens. The inhibitory activity is strongly induced when P. aeruginosa is cultivated in iron-limited conditions, but it does not function through iron sequestration. In addition, the production of the biofilm inhibitory activity is not regulated by the global iron regulatory protein Fur, the iron-responsive extracytoplasmic function σ factor PvdS, or three of the recognized P. aeruginosa quorum-sensing systems. In addition, the compound(s) responsible for the inhibition and dispersal of A. tumefaciens biofilm formation is likely distinct from the recently identified P. aeruginosa dispersal factor, cis-2-decenoic acid (CDA), as dialysis of the culture fluids showed that the inhibitory compound was larger than CDA and culture fluids that dispersed and inhibited biofilm formation by A. tumefaciens had no effect on biofilm formation by P. aeruginosa.

Inhibition and dispersal of Agrobacterium tumefaciens biofilms by a small diffusible Pseudomonas aeruginosa exoproduct(s)

PubMed Central

Hibbing, Michael E.; Fuqua, Clay

2013-01-01

Environmental biofilms often contain mixed populations of different species. In these dense communities, competition between biofilm residents for limited nutrients such as iron, can be fierce, leading to the evolution of competitive factors that affect the ability of competitors to grow or form biofilms. We have discovered a compound(s) present in the conditioned culture fluids of Pseudomonas aeruginosa that disperses and inhibits the formation of biofilms produced by the facultative plant pathogen Agrobacterium tumefaciens. The inhibitory activity is strongly induced when P. aeruginosa is cultivated in iron-limited conditions, but it does not function through iron sequestration. In addition, the production of the inhibitory activity is not regulated by the global iron regulatory protein Fur, the iron-responsive extra-cytoplasmic function (ECF) σ factor PvdS, or three of the recognized P. aeruginosa quorum sensing systems. In addition, the compound(s) responsible for the inhibition and dispersal of A. tumefaciens biofilm formation is likely distinct from the recently identified P. aeruginosa dispersal factor, cis-2-decenoic acid (CDA), as dialysis of the culture fluids showed that the inhibitory compound was larger than CDA and culture fluids that dispersed and inhibited biofilm formation by A. tumefaciens had no effect on biofilm formation by P. aeruginosa. PMID:22105093

The complete chloroplast genome sequence of Dianthus superbus var. longicalycinus.

PubMed

Gurusamy, Raman; Lee, Do-Hyung; Park, SeonJoo

2016-05-01

The complete chloroplast genome (cpDNA) sequence of Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicine was reported and characterized. The cpDNA of Dianthus superbus var. longicalycinus is 149,539 bp, with 36.3% GC content. A pair of inverted repeats (IRs) of 24,803 bp is separated by a large single-copy region (LSC, 82,805 bp) and a small single-copy region (SSC, 17,128 bp). It encodes 85 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Of 129 individual genes, 13 genes encoded one intron and three genes have two introns.

Biocompatible and Biomimetic Self-Assembly of Functional

DTIC Science & Technology

2007-10-03

rearrangement of the lipid/silica matrix to create a bio/nano interface quite similar to that formed by direct CDA. This approach has several advantages over CDA...precursors with a biologically compatible surfactant, glycerol monooleate ( GMO ) via dip-coating, spin-coating, drop-casting, or aerosol deposition...with water and remains in a semi-solid state. Upon exposure to UV/ozone, the GMO begins to photodecompose and the silanol precursors become more

Young swimmers' classification based on kinematics, hydrodynamics, and anthropometrics.

PubMed

Barbosa, Tiago M; Morais, Jorge E; Costa, Mário J; Goncalves, José; Marinho, Daniel A; Silva, António J

2014-04-01

The aim of this article has been to classify swimmers based on kinematics, hydrodynamics, and anthropometrics. Sixty-seven young swimmers made a maximal 25 m front-crawl to measure with a speedometer the swimming velocity (v), speed-fluctuation (dv) and dv normalized to v (dv/v). Another two 25 m bouts with and without carrying a perturbation device were made to estimate active drag coefficient (CDa). Trunk transverse surface area (S) was measured with photogrammetric technique on land and in the hydrodynamic position. Cluster 1 was related to swimmers with a high speed fluctuation (ie, dv and dv/v), cluster 2 with anthropometrics (ie, S) and cluster 3 with a high hydrodynamic profile (ie, CDa). The variable that seems to discriminate better the clusters was the dv/v (F=53.680; P<.001), followed by the dv (F=28.506; P<.001), CDa (F=21.025; P<.001), S (F=6.297; P<.01) and v (F=5.375; P=.01). Stepwise discriminant analysis extracted 2 functions: Function 1 was mainly defined by dv/v and S (74.3% of variance), whereas function 2 was mainly defined by CDa (25.7% of variance). It can be concluded that kinematics, hydrodynamics and anthropometrics are determinant domains in which to classify and characterize young swimmers' profiles.

Multiple foci of spatial attention in multimodal working memory.

PubMed

Katus, Tobias; Eimer, Martin

2016-11-15

The maintenance of sensory information in working memory (WM) is mediated by the attentional activation of stimulus representations that are stored in perceptual brain regions. Using event-related potentials (ERPs), we measured tactile and visual contralateral delay activity (tCDA/CDA components) in a bimodal WM task to concurrently track the attention-based maintenance of information stored in anatomically segregated (somatosensory and visual) brain areas. Participants received tactile and visual sample stimuli on both sides, and in different blocks, memorized these samples on the same side or on opposite sides. After a retention delay, memory was unpredictably tested for touch or vision. In the same side blocks, tCDA and CDA components simultaneously emerged over the same hemisphere, contralateral to the memorized tactile/visual sample set. In opposite side blocks, these two components emerged over different hemispheres, but had the same sizes and onset latencies as in the same side condition. Our results reveal distinct foci of tactile and visual spatial attention that were concurrently maintained on task-relevant stimulus representations in WM. The independence of spatially-specific biasing mechanisms for tactile and visual WM content suggests that multimodal information is stored in distributed perceptual brain areas that are activated through modality-specific processes that can operate simultaneously and largely independently of each other. Copyright © 2016 Elsevier Inc. All rights reserved.

The RFamide receptor DMSR-1 regulates stress-induced sleep in C. elegans.

PubMed

Iannacone, Michael J; Beets, Isabel; Lopes, Lindsey E; Churgin, Matthew A; Fang-Yen, Christopher; Nelson, Matthew D; Schoofs, Liliane; Raizen, David M

2017-01-17

In response to environments that cause cellular stress, animals engage in sleep behavior that facilitates recovery from the stress. In Caenorhabditis elegans , stress-induced sleep(SIS) is regulated by cytokine activation of the ALA neuron, which releases FLP-13 neuropeptides characterized by an amidated arginine-phenylalanine (RFamide) C-terminus motif. By performing an unbiased genetic screen for mutants that impair the somnogenic effects of FLP-13 neuropeptides, we identified the gene dmsr-1 , which encodes a G-protein coupled receptor similar to an insect RFamide receptor. DMSR-1 is activated by FLP-13 peptides in cell culture, is required for SIS in vivo , is expressed non-synaptically in several wake-promoting neurons, and likely couples to a Gi/o heterotrimeric G-protein. Our data expand our understanding of how a single neuroendocrine cell coordinates an organism-wide behavioral response, and suggest that similar signaling principles may function in other organisms to regulate sleep during sickness.

The active gene that encodes human High Mobility Group 1 protein (HMG1) contains introns and maps to chromosome 13

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

Ferrari, S.; Finelli, P.; Rocchi, M.

The human genome contains a large number of sequences related to the cDNA for High Mobility Group 1 protein (HMG1), which so far has hampered the cloning and mapping of the active HMG1 gene. We show that the human HMG1 gene contains introns, while the HMG1-related sequences do not and most likely are retrotransposed pseudogenes. We identified eight YACs from the ICI and CEPH libraries that contain the human HMG1 gene. The HMG1 gene is similar in structure to the previously characterized murine homologue and maps to human chromosome 13 and q12, as determined by in situ hybridization. The mousemore » Hmg1 gene maps to the telomeric region of murine Chromosome 5, which is syntenic to the human 13q12 band. 18 refs., 3 figs.« less

The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca).

PubMed

Peng, Rui; Zeng, Bo; Meng, Xiuxiang; Yue, Bisong; Zhang, Zhihe; Zou, Fangdong

2007-08-01

The complete mitochondrial genome sequence of the giant panda, Ailuropoda melanoleuca, was determined by the long and accurate polymerase chain reaction (LA-PCR) with conserved primers and primer walking sequence methods. The complete mitochondrial DNA is 16,805 nucleotides in length and contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and one control region. The total length of the 13 protein-coding genes is longer than the American black bear, brown bear and polar bear by 3 amino acids at the end of ND5 gene. The codon usage also followed the typical vertebrate pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 5 (ND5) gene. The molecular phylogenetic analysis was performed on the sequences of 12 concatenated heavy-strand encoded protein-coding genes, and suggested that the giant panda is most closely related to bears.

Mechanism of protein biosynthesis in mammalian mitochondria.

PubMed

Christian, Brooke E; Spremulli, Linda L

2012-01-01

Protein synthesis in mammalian mitochondria produces 13 proteins that are essential subunits of the oxidative phosphorylation complexes. This review provides a detailed outline of each phase of mitochondrial translation including initiation, elongation, termination, and ribosome recycling. The roles of essential proteins involved in each phase are described. All of the products of mitochondrial protein synthesis in mammals are inserted into the inner membrane. Several proteins that may help bind ribosomes to the membrane during translation are described, although much remains to be learned about this process. Mutations in mitochondrial or nuclear genes encoding components of the translation system often lead to severe deficiencies in oxidative phosphorylation, and a summary of these mutations is provided. This article is part of a Special Issue entitled: Mitochondrial Gene Expression. Copyright © 2011 Elsevier B.V. All rights reserved.

[Cloning and expressing of cyclophilin B gene from Schistosoma japonnicum and the analysis of immunoprotective effect].

PubMed

Peng, Jinbiao; Han, Hongxiao; Hong, Yang; Wang, Yan; Guo, Fanji; Shi, Yaojun; Fu, Zhiqiang; Liu, Jinming; Cheng, Guofeng; Lin, Jiaojiao

2010-03-01

The present study was intend to clone and express the cDNA encoding Cyclophilin B (CyPB) of Schistosoma japonicum, its preliminary biological function and further immunoprotective effect against schistosome infection in mice. RT-PCR technique was applied to amplify a full-length cDNA encoding protein Cyclophilin B (Sj CyPB) from schistosomula cDNA. The expression profiles of Sj CyPB were determined by Real-time PCR using the template cDNAs isolated from 7, 13, 18, 23, 32 and 42 days parasites. The cDNA containing the Open Reading Frame of CyPB was then subcloned into a pGEX-6P-1 vector and transformed into competent Escherichia coli BL21 for expressing. The recombinant protein was renaturated, purified and its antigenicity were detected by Western blotting, and the immunoprotective effect induced by recombinant Sj CyPB was evaluated in Balb/C mice. The cDNA containing the ORF of Sj CyPB was cloned with the length of 672 base pairs, encoding 223 amino acids. Real-time PCR analysis revealed that the gene had the highest expression in 18-day schistosomula, suggesting that Sj CyPB was schistosomula differentially expressed gene. The recombinant protein showed a good antigenicity detected by Western blotting. Animal experiment indicated that the vaccination of recombinant CyPB protein in mice led to 31.5% worm and 41.01% liver egg burden reduction, respectively, compared with those of the control. A full-length cDNA differentially expressed in schistosomula was obtained. The recombinant Sj CyPB protein could induce partial protection against schistosome infection.

Immune functions of insect βGRPs and their potential application.

PubMed

Rao, Xiang-Jun; Zhan, Ming-Yue; Pan, Yue-Min; Liu, Su; Yang, Pei-Jin; Yang, Li-Ling; Yu, Xiao-Qiang

2018-06-01

Insects rely completely on the innate immune system to sense the foreign bodies and to mount the immune responses. Germ-line encoded pattern recognition receptors play crucial roles in recognizing pathogen-associated molecular patterns. Among them, β-1,3-glucan recognition proteins (βGRPs) and gram-negative bacteria-binding proteins (GNBPs) belong to the same pattern recognition receptor family, which can recognize β-1,3-glucans. Typical insect βGRPs are comprised of a tandem carbohydrate-binding module in the N-terminal and a glucanase-like domain in the C-terminal. The former can recognize triple-helical β-1,3-glucans, whereas the latter, which normally lacks the enzymatic activity, can recruit adapter proteins to initiate the protease cascade. According to studies, insect βGRPs possess at least three types of functions. Firstly, some βGRPs cooperate with peptidoglycan recognition proteins to recognize the lysine-type peptidoglycans upstream of the Toll pathway. Secondly, some directly recognize fungal β-1,3-glucans to activate the Toll pathway and melanization. Thirdly, some form the 'attack complexes' with other immune effectors to promote the antifungal defenses. The current review will focus on the discovery of insect βGRPs, functions of some well-characterized members, structure-function studies and their potential application. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cloning of the Gene Encoding a 22-Kilodalton Cell Surface Antigen of Mycobacterium bovis BCG and Analysis of Its Potential for DNA Vaccination against Tuberculosis

PubMed Central

Lefèvre, Philippe; Denis, Olivier; De Wit, Lucas; Tanghe, Audrey; Vandenbussche, Paul; Content, Jean; Huygen, Kris

2000-01-01

Using spleen cells from mice vaccinated with live Mycobacterium bovis BCG, we previously generated three monoclonal antibodies reactive against a 22-kDa protein present in mycobacterial culture filtrate (CF) (K. Huygen et al., Infect. Immun. 61:2687–2693, 1993). These monoclonal antibodies were used to screen an M. bovis BCG genomic library made in phage λgt11. The gene encoding a 233-amino-acid (aa) protein, including a putative 26-aa signal sequence, was isolated, and sequence analysis indicated that the protein was 98% identical with the M. tuberculosis Lppx protein and that it contained a sequence 94% identical with the M. leprae 38-mer polypeptide 13B3 recognized by T cells from killed M. leprae-immunized subjects. Flow cytometry and cell fractionation demonstrated that the 22-kDa CF protein is also highly expressed in the bacterial cell wall and membrane compartment but not in the cytosol. C57BL/6, C3H, and BALB/c mice were vaccinated with plasmid DNA encoding the 22-kDa protein and analyzed for immune response and protection against intravenous M. tuberculosis challenge. Whereas DNA vaccination induced elevated antibody responses in C57BL/6 and particularly in C3H mice, Th1-type cytokine response, as measured by interleukin-2 and gamma interferon secretion, was only modest, and no protection against intravenous M. tuberculosis challenge was observed in any of the three mouse strains tested. Therefore, the 22-kDa antigen seems to have little potential for a DNA vaccine against tuberculosis, but it may be a good candidate for a mycobacterial antigen detection test. PMID:10678905

Activation of Pathogenesis-related Genes by the Rhizobacterium, Bacillus sp. JS, Which Induces Systemic Resistance in Tobacco Plants.

PubMed

Kim, Ji-Seong; Lee, Jeongeun; Lee, Chan-Hui; Woo, Su Young; Kang, Hoduck; Seo, Sang-Gyu; Kim, Sun-Hyung

2015-06-01

Plant growth promoting rhizobacteria (PGPR) are known to confer disease resistance to plants. Bacillus sp. JS demonstrated antifungal activities against five fungal pathogens in in vitro assays. To verify whether the volatiles of Bacillus sp. JS confer disease resistance, tobacco leaves pre-treated with the volatiles were damaged by the fungal pathogen, Rhizoctonia solani and oomycete Phytophthora nicotianae. Pre-treated tobacco leaves had smaller lesion than the control plant leaves. In pathogenesis-related (PR) gene expression analysis, volatiles of Bacillus sp. JS caused the up-regulation of PR-2 encoding β-1,3-glucanase and acidic PR-3 encoding chitinase. Expression of acidic PR-4 encoding chitinase and acidic PR-9 encoding peroxidase increased gradually after exposure of the volatiles to Bacillus sp. JS. Basic PR-14 encoding lipid transfer protein was also increased. However, PR-1 genes, as markers of salicylic acid (SA) induced resistance, were not expressed. These results suggested that the volatiles of Bacillus sp. JS confer disease resistance against fungal and oomycete pathogens through PR genes expression.

AKAP13 Rho-GEF and PKD-Binding Domain Deficient Mice Develop Normally but Have an Abnormal Response to β-Adrenergic-Induced Cardiac Hypertrophy

PubMed Central

Spindler, Matthew J.; Burmeister, Brian T.; Huang, Yu; Hsiao, Edward C.; Salomonis, Nathan; Scott, Mark J.; Srivastava, Deepak; Carnegie, Graeme K.; Conklin, Bruce R.

2013-01-01

Background A-kinase anchoring proteins (AKAPs) are scaffolding molecules that coordinate and integrate G-protein signaling events to regulate development, physiology, and disease. One family member, AKAP13, encodes for multiple protein isoforms that contain binding sites for protein kinase A (PKA) and D (PKD) and an active Rho-guanine nucleotide exchange factor (Rho-GEF) domain. In mice, AKAP13 is required for development as null embryos die by embryonic day 10.5 with cardiovascular phenotypes. Additionally, the AKAP13 Rho-GEF and PKD-binding domains mediate cardiomyocyte hypertrophy in cell culture. However, the requirements for the Rho-GEF and PKD-binding domains during development and cardiac hypertrophy are unknown. Methodology/Principal Findings To determine if these AKAP13 protein domains are required for development, we used gene-trap events to create mutant mice that lacked the Rho-GEF and/or the protein kinase D-binding domains. Surprisingly, heterozygous matings produced mutant mice at Mendelian ratios that had normal viability and fertility. The adult mutant mice also had normal cardiac structure and electrocardiograms. To determine the role of these domains during β-adrenergic-induced cardiac hypertrophy, we stressed the mice with isoproterenol. We found that heart size was increased similarly in mice lacking the Rho-GEF and PKD-binding domains and wild-type controls. However, the mutant hearts had abnormal cardiac contractility as measured by fractional shortening and ejection fraction. Conclusions These results indicate that the Rho-GEF and PKD-binding domains of AKAP13 are not required for mouse development, normal cardiac architecture, or β-adrenergic-induced cardiac hypertrophic remodeling. However, these domains regulate aspects of β-adrenergic-induced cardiac hypertrophy. PMID:23658642

Data Warehouse Design from HL7 Clinical Document Architecture Schema.

PubMed

Pecoraro, Fabrizio; Luzi, Daniela; Ricci, Fabrizio L

2015-01-01

This paper proposes a semi-automatic approach to extract clinical information structured in a HL7 Clinical Document Architecture (CDA) and transform it in a data warehouse dimensional model schema. It is based on a conceptual framework published in a previous work that maps the dimensional model primitives with CDA elements. Its feasibility is demonstrated providing a case study based on the analysis of vital signs gathered during laboratory tests.

Efficient non-doped phosphorescent orange, blue and white organic light-emitting devices

NASA Astrophysics Data System (ADS)

Yin, Yongming; Yu, Jing; Cao, Hongtao; Zhang, Letian; Sun, Haizhu; Xie, Wenfa

2014-10-01

Efficient phosphorescent orange, blue and white organic light-emitting devices (OLEDs) with non-doped emissive layers were successfully fabricated. Conventional blue phosphorescent emitters bis [4,6-di-fluorophenyl]-pyridinato-N,C2'] picolinate (Firpic) and Bis(2,4-difluorophenylpyridinato) (Fir6) were adopted to fabricate non-doped blue OLEDs, which exhibited maximum current efficiency of 7.6 and 4.6 cd/A for Firpic and Fir6 based devices, respectively. Non-doped orange OLED was fabricated utilizing the newly reported phosphorescent material iridium (III) (pbi)2Ir(biq), of which manifested maximum current and power efficiency of 8.2 cd/A and 7.8 lm/W. The non-doped white OLEDs were achieved by simply combining Firpic or Fir6 with a 2-nm (pbi)2Ir(biq). The maximum current and power efficiency of the Firpic and (pbi)2Ir(biq) based white OLED were 14.8 cd/A and 17.9 lm/W.

De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder.

PubMed

Snijders Blok, Lot; Hiatt, Susan M; Bowling, Kevin M; Prokop, Jeremy W; Engel, Krysta L; Cochran, J Nicholas; Bebin, E Martina; Bijlsma, Emilia K; Ruivenkamp, Claudia A L; Terhal, Paulien; Simon, Marleen E H; Smith, Rosemarie; Hurst, Jane A; McLaughlin, Heather; Person, Richard; Crunk, Amy; Wangler, Michael F; Streff, Haley; Symonds, Joseph D; Zuberi, Sameer M; Elliott, Katherine S; Sanders, Victoria R; Masunga, Abigail; Hopkin, Robert J; Dubbs, Holly A; Ortiz-Gonzalez, Xilma R; Pfundt, Rolph; Brunner, Han G; Fisher, Simon E; Kleefstra, Tjitske; Cooper, Gregory M

2018-05-08

Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders. Other features that were reported in two or more patients include autism spectrum disorder, attention deficit hyperactivity disorder, optic nerve abnormalities, Duane anomaly, hypotonia, mild congenital heart abnormalities, and dysmorphisms. Six affected individuals had mutations that are predicted to truncate the MED13 protein, six had missense mutations, and one had an in-frame-deletion of one amino acid. Out of the seven non-truncating mutations, six clustered in two specific locations of the MED13 protein: an N-terminal and C-terminal region. The four N-terminal clustering mutations affect two adjacent amino acids that are known to be involved in MED13 ubiquitination and degradation, p.Thr326 and p.Pro327. MED13 is a component of the CDK8-kinase module that can reversibly bind Mediator, a multi-protein complex that is required for Polymerase II transcription initiation. Mutations in several other genes encoding subunits of Mediator have been previously shown to associate with DD/ID, including MED13L, a paralog of MED13. Thus, our findings add MED13 to the group of CDK8-kinase module-associated disease genes.

Avirulence Effector Discovery in a Plant Galling and Plant Parasitic Arthropod, the Hessian Fly (Mayetiola destructor)

PubMed Central

Aggarwal, Rajat; Subramanyam, Subhashree; Zhao, Chaoyang; Chen, Ming-Shun; Harris, Marion O.; Stuart, Jeff J.

2014-01-01

Highly specialized obligate plant-parasites exist within several groups of arthropods (insects and mites). Many of these are important pests, but the molecular basis of their parasitism and its evolution are poorly understood. One hypothesis is that plant parasitic arthropods use effector proteins to defeat basal plant immunity and modulate plant growth. Because avirulence (Avr) gene discovery is a reliable method of effector identification, we tested this hypothesis using high-resolution molecular genetic mapping of an Avr gene (vH13) in the Hessian fly (HF, Mayetiola destructor), an important gall midge pest of wheat (Triticum spp.). Chromosome walking resolved the position of vH13, and revealed alleles that determine whether HF larvae are virulent (survive) or avirulent (die) on wheat seedlings carrying the wheat H13 resistance gene. Association mapping found three independent insertions in vH13 that appear to be responsible for H13-virulence in field populations. We observed vH13 transcription in H13-avirulent larvae and the salivary glands of H13-avirulent larvae, but not in H13-virulent larvae. RNA-interference-knockdown of vH13 transcripts allowed some H13-avirulent larvae to escape H13-directed resistance. vH13 is the first Avr gene identified in an arthropod. It encodes a small modular protein with no sequence similarities to other proteins in GenBank. These data clearly support the hypothesis that an effector-based strategy has evolved in multiple lineages of plant parasites, including arthropods. PMID:24964065

P53 protein in proliferation, repair and apoptosis of cells.

PubMed

Wawryk-Gawda, Ewelina; Chylińska-Wrzos, Patrycja; Lis-Sochocka, Marta; Chłapek, Katarzyna; Bulak, Kamila; Jędrych, Marian; Jodłowska-Jędrych, Barbara

2014-05-01

The p53 protein is an important factor of many intra- and extracellular processes. This protein regulates the repair of cellular DNA and induces apoptosis. It is also responsible for the regulation of the senescence and the cell entering the subsequent stages of the cellular cycle. The protein p53 is also involved in inhibiting angiogenesis and the induction of oxidative shock. In our study, we examined the activity of p53 protein in the uterine epithelial cells in rats treated with cladribine. Its action is mainly based on apoptosis induction. We compared the activity of p53 protein in cells with a high apoptosis index and in cells with active repair mechanisms and high proliferation index. We observed stronger p53 protein expression in the epithelial cells of the materials taken 24 h after the last dose of 2-CdA associated with the active process of apoptosis and inhibition of proliferation. After 4 weeks from the last dose of cladribine, the stronger expression of p53 protein was associated with both the existing changes in the cell's genome, the effects of the ongoing repair mechanisms, as well as the high proliferation activity.

Cloning and characterization of the ddc homolog encoding L-2,4-diaminobutyrate decarboxylase in Enterobacter aerogenes.

PubMed

Yamamoto, S; Mutoh, N; Tsuzuki, D; Ikai, H; Nakao, H; Shinoda, S; Narimatsu, S; Miyoshi, S I

2000-05-01

L-2,4-diaminobutyrate decarboxylase (DABA DC) catalyzes the formation of 1,3-diaminopropane (DAP) from DABA. In the present study, the ddc gene encoding DABA DC from Enterobacter aerogenes ATCC 13048 was cloned and characterized. Determination of the nucleotide sequence revealed an open reading frame of 1470 bp encoding a 53659-Da protein of 490 amino acids, whose deduced NH2-terminal sequence was identical to that of purified DABA DC from E. aerogenes. The deduced amino acid sequence was highly similar to those of Acinetobacter baumannii and Haemophilus influenzae DABA DCs encoded by the ddc genes. The lysine-307 of the E. aerogenes DABA DC was identified as the pyridoxal 5'-phosphate binding residue by site-directed mutagenesis. Furthermore, PCR analysis revealed the distribution of E. aerogenes ddc homologs in some other species of Enterobacteriaceae. Such a relatively wide occurrence of the ddc homologs implies biological significance of DABA DC and its product DAP.

Structural characterization of the FKHR gene and its rearrangement in alveolar rhabdomyosarcoma.

PubMed

Davis, R J; Bennicelli, J L; Macina, R A; Nycum, L M; Biegel, J A; Barr, F G

1995-12-01

The FKHR gene, which contains a forkhead DNA-binding motif, is fused to either PAX3 or PAX7 by the t(2;13) or t(1;13) translocation in alveolar rhabdomyosarcoma,respectively. These tumors express chimeric transcripts encoding the N-terminal portion of either PAX protein fused to the C-terminal portion of FKHR. To understand the structural basis and functional consequences of these translocations, we characterized the wild-type FKHR gene and its rearrangement in alveolar rhabdomyosarcomas. By isolating and analyzing phage, cosmid and YAC clones, we determined that FKHR consists of three exons spanning 140 kb and that several highly similar loci are present in other genomic regions. Exon 1 encodes the N-terminus of the forkhead domain and is embedded within demethylated CpG island. RNA analyses reveal FKHR transcripts initiate from a TATA-less promoter within this island. Exon 2 encodes the C-terminus of the forkhead domain and a transcription activation domain, whereas exon 3 encodes a large 3' untranslated region. The intron 1-exon 2 boundary precisely matches the FHKR fusion point in the chimeric transcripts found in alveolar rhabdomyosarcomas. Using pulsed-field and fluorescence in situ hybridization analyses, we demonstrate that the 130kb FKHR intron 1 is rearranged in t(2;13)-containing alveolar rhabdomyosarcomas. Our findings indicate that FKHR intron 1 provides a large target for DNA rearrangemnt. Rearrangement of this intron with PAX3 produces two important functional consequences: in-frame fusion of N-terminal PAX3 sequences to the FKHR transcriptional activation domain and disruption of the FKHR DNA binding domain.

Intracellular Localization Map of Human Herpesvirus 8 Proteins▿

PubMed Central

Sander, Gaby; Konrad, Andreas; Thurau, Mathias; Wies, Effi; Leubert, Rene; Kremmer, Elisabeth; Dinkel, Holger; Schulz, Thomas; Neipel, Frank; Stürzl, Michael

2008-01-01

Human herpesvirus 8 (HHV-8) is the etiological agent of Kaposi's sarcoma. We present a localization map of 85 HHV-8-encoded proteins in mammalian cells. Viral open reading frames were cloned with a Myc tag in expression plasmids, confirmed by full-length sequencing, and expressed in HeLa cells. Protein localizations were analyzed by immunofluorescence microscopy. Fifty-one percent of all proteins were localized in the cytoplasm, 22% were in the nucleus, and 27% were found in both compartments. Surprisingly, we detected viral FLIP (v-FLIP) in the nucleus and in the cytoplasm, whereas cellular FLIPs are generally localized exclusively in the cytoplasm. This suggested that v-FLIP may exert additional or alternative functions compared to cellular FLIPs. In addition, it has been shown recently that the K10 protein can bind to at least 15 different HHV-8 proteins. We noticed that K10 and only five of its 15 putative binding factors were localized in the nucleus when the proteins were expressed in HeLa cells individually. Interestingly, in coexpression experiments K10 colocalized with 87% (13 of 15) of its putative binding partners. Colocalization was induced by translocation of either K10 alone or both proteins. These results indicate active intracellular translocation processes in virus-infected cells. Specifically in this framework, the localization map may provide a useful reference to further elucidate the function of HHV-8-encoded genes in human diseases. PMID:18077714

Isolation and characterization of the pea cytochrome c oxidase Vb gene.

PubMed

Kubo, Nakao; Arimura, Shin-Ichi; Tsutsumi, Nobuhiro; Kadowaki, Koh-Ichi; Hirai, Masashi

2006-11-01

Three copies of the gene that encodes cytochrome c oxidase subunit Vb were isolated from the pea (PscoxVb-1, PscoxVb-2, and PscoxVb-3). Northern Blot and reverse transcriptase-PCR analyses suggest that all 3 genes are transcribed in the pea. Each pea coxVb gene has an N-terminal extended sequence that can encode a mitochondrial targeting signal, called a presequence. The localization of green fluorescent proteins fused with the presequence strongly suggests the targeting of pea COXVb proteins to mitochondria. Each pea coxVb gene has 5 intron sites within the coding region. These are similar to Arabidopsis and rice, although the intron lengths vary greatly. A phylogenetic analysis of coxVb suggests the occurrence of gene duplication events during angiosperm evolution. In particular, 2 duplication events might have occurred in legumes, grasses, and Solanaceae. A comparison of amino acid sequences in COXVb or its counterpart shows the conservation of several amino acids within a zinc finger motif. Interestingly, a homology search analysis showed that bacterial protein COG4391 and a mitochondrial complex I 13 kDa subunit also have similar amino acid compositions around this motif. Such similarity might reflect evolutionary relationships among the 3 proteins.

Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes

PubMed Central

Dhar, Alok; Polev, Dmitrii E.; Masharsky, Alexey E.; Rogozin, Igor B.; Pavlov, Youri I.

2015-01-01

Mutations in genomes of species are frequently distributed non-randomly, resulting in mutation clusters, including recently discovered kataegis in tumors. DNA editing deaminases play the prominent role in the etiology of these mutations. To gain insight into the enigmatic mechanisms of localized hypermutagenesis that lead to cluster formation, we analyzed the mutational single nucleotide variations (SNV) data obtained by whole-genome sequencing of drug-resistant mutants induced in yeast diploids by AID/APOBEC deaminase and base analog 6-HAP. Deaminase from sea lamprey, PmCDA1, induced robust clusters, while 6-HAP induced a few weak ones. We found that PmCDA1, AID, and APOBEC1 deaminases preferentially mutate the beginning of the actively transcribed genes. Inactivation of transcription initiation factor Sub1 strongly reduced deaminase-induced can1 mutation frequency, but, surprisingly, did not decrease the total SNV load in genomes. However, the SNVs in the genomes of the sub1 clones were re-distributed, and the effect of mutation clustering in the regions of transcription initiation was even more pronounced. At the same time, the mutation density in the protein-coding regions was reduced, resulting in the decrease of phenotypically detected mutants. We propose that the induction of clustered mutations by deaminases involves: a) the exposure of ssDNA strands during transcription and loss of protection of ssDNA due to the depletion of ssDNA-binding proteins, such as Sub1, and b) attainment of conditions favorable for APOBEC action in subpopulation of cells, leading to enzymatic deamination within the currently expressed genes. This model is applicable to both the initial and the later stages of oncogenic transformation and explains variations in the distribution of mutations and kataegis events in different tumor cells. PMID:25941824

Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

PubMed Central

Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P.

2016-01-01

Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

Endo-β-1,3-Glucanase GLU1, from the Fruiting Body of Lentinula edodes, Belongs to a New Glycoside Hydrolase Family ▿ †

PubMed Central

Sakamoto, Yuichi; Nakade, Keiko; Konno, Naotake

2011-01-01

The cell wall of the fruiting body of the mushroom Lentinula edodes is degraded after harvesting by enzymes such as β-1,3-glucanase. In this study, a novel endo-type β-1,3-glucanase, GLU1, was purified from L. edodes fruiting bodies after harvesting. The gene encoding it, glu1, was isolated by rapid amplification of cDNA ends (RACE)-PCR using primers designed from the N-terminal amino acid sequence of GLU1. The putative amino acid sequence of the mature protein contained 247 amino acid residues with a molecular mass of 26 kDa and a pI of 3.87, and recombinant GLU1 expressed in Pichia pastoris exhibited β-1,3-glucanase activity. GLU1 catalyzed depolymerization of glucans composed of β-1,3-linked main chains, and reaction product analysis by thin-layer chromatography (TLC) clearly indicated that the enzyme had an endolytic mode. However, the amino acid sequence of GLU1 showed no significant similarity to known glycoside hydrolases. GLU1 has similarity to several hypothetical proteins in fungi, and GLU1 and highly similar proteins should be classified as a novel glycoside hydrolase family (GH128). PMID:21965406

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

PubMed Central

Zivanovic, Yvan; Confalonieri, Fabrice; Ponchon, Luc; Lurz, Rudi; Chami, Mohamed; Flayhan, Ali; Renouard, Madalena; Huet, Alexis; Decottignies, Paulette; Davidson, Alan R.; Breyton, Cécile

2014-01-01

Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm. PMID:24198424

Tissue-specific and pathogen-induced regulation of a Nicotiana plumbaginifolia beta-1,3-glucanase gene.

PubMed Central

Castresana, C; de Carvalho, F; Gheysen, G; Habets, M; Inzé, D; Van Montagu, M

1990-01-01

The Nicotiana plumbaginifolia gn1 gene encoding a beta-1,3-glucanase isoform has been characterized. The gn1 product represents an isoform distinct from the previously identified tobacco beta-1,3-glucanases. By expressing gn1 in Escherichia coli, we have determined directly that the encoded protein does, indeed, correspond to a beta-1,3-glucanase. In N. plumbaginifolia, gn1 was found to be expressed in roots and older leaves. Transgenic tobacco plants containing the 5'-noncoding region of gn1 fused to the beta-glucuronidase (GUS) reporter gene also showed maximum levels of GUS activity in roots and older leaves. No detectable activity was present in the upper part of the transgenic plants with the exception of stem cells at the bases of emerging shoots. The expression conferred by the gn1 promoter was differentially induced in response to specific plant stress treatments. Studies of three plant-bacteria interactions showed high levels of GUS activity when infection resulted in a hypersensitive reaction. Increased gene expression was confined to cells surrounding the necrotic lesions. The observed expression pattern suggests that the characterized beta-1,3-glucanase plays a role both in plant development and in the defense response against pathogen infection. PMID:2152158

Arabidopsis F-box protein containing a Nictaba-related lectin domain interacts with N-acetyllactosamine structures.

PubMed

Stefanowicz, Karolina; Lannoo, Nausicaä; Proost, Paul; Van Damme, Els J M

2012-01-01

The Arabidopsis thaliana genome contains a small group of bipartite F-box proteins, consisting of an N-terminal F-box domain and a C-terminal domain sharing sequence similarity with Nictaba, the jasmonate-induced glycan-binding protein (lectin) from tobacco. Based on the high sequence similarity between the C-terminal domain of these proteins and Nictaba, the hypothesis was put forward that the so-called F-box-Nictaba proteins possess carbohydrate-binding activity and accordingly can be considered functional homologs of the mammalian sugar-binding F-box or Fbs proteins which are involved in proteasomal degradation of glycoproteins. To obtain experimental evidence for the carbohydrate-binding activity and specificity of the A. thaliana F-box-Nictaba proteins, both the complete F-box-Nictaba sequence of one selected Arabidopsis F-box protein (in casu At2g02360) as well as the Nictaba-like domain only were expressed in Pichia pastoris and analyzed by affinity chromatography, agglutination assays and glycan micro-array binding assays. These results demonstrated that the C-terminal Nictaba-like domain provides the F-box-protein with a carbohydrate-binding activity that is specifically directed against N- and O-glycans containing N-acetyllactosamine (Galβ1-3GlcNAc and Galβ1-4GlcNAc) and poly-N-acetyllactosamine ([Galβ1-4GlcNAc]n) as well as Lewis A (Galβ1-3(Fucα1-4)GlcNAc), Lewis X (Galβ1-4(Fucα1-3)GlcNAc, Lewis Y (Fucα1-2Galβ1-4(Fucα1-3)GlcNAc) and blood type B (Galα1-3(Fucα1-2)Galβ1-3GlcNAc) motifs. Based on these findings one can reasonably conclude that at least the A. thaliana F-box-Nictaba protein encoded by At2g02360 can act as a carbohydrate-binding protein. The results from the glycan array assays revealed differences in sugar-binding specificity between the F-box protein and Nictaba, indicating that the same carbohydrate-binding motif can accommodate unrelated oligosaccharides.

Adaptive Evolution of Mitochondrial Energy Metabolism Genes Associated with Increased Energy Demand in Flying Insects

PubMed Central

Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

2014-01-01

Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects. PMID:24918926

Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects.

PubMed

Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

2014-01-01

Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects.

Acute Liver Failure in a Pediatric Patient with Congenital Dysery-Thropoietic Anemia Type I Treated with Deferasirox.

PubMed

Ling, Galina; Pinsk, Vered; Golan-Tripto, Inbal; Ling, Eduard

2015-09-23

Congenital dyserythropoietic anemias (CDA) represent a heterogeneous group of disorders characterized by morphological abnormalities of erythroid precursor cells and various degrees of hemolysis. Iron overload is a result of continuous hemolysis and recurrent transfusions. It is treated with iron chelators, including deferasirox. We present here a case of acute liver failure in a 12 years old girl with CDA type I treated with deferasirox and discuss the approach to treatment.

Fulminant 2-chlorodeoxyadenosine-related peripheral neuropathy in a patient with paraneoplastic neurological syndrome associated with lymphoma.

PubMed

Warzocha, K; Krykowksi, E; Góra-Tybor, J; Fronczak, A; Robak, T

1996-04-01

2-chlorodeoxyadenosine (2-CdA) has been demonstrated to be a neurotoxic agent when used at significantly greater doses than currently recommended for clinical use. In this report we describe a case of a 37-years-old man lymphoplasmacytoid malignant lymphoma and pre-existing paraneoplastic neurological syndrome who died of an apparent rapidly progressive sensorimotor peripheral neuropathy after completing treatment with two courses of low-doses of 2-CdA.

Virtual Observatory Interfaces to the Chandra Data Archive

NASA Astrophysics Data System (ADS)

Tibbetts, M.; Harbo, P.; Van Stone, D.; Zografou, P.

2014-05-01

The Chandra Data Archive (CDA) plays a central role in the operation of the Chandra X-ray Center (CXC) by providing access to Chandra data. Proprietary interfaces have been the backbone of the CDA throughout the Chandra mission. While these interfaces continue to provide the depth and breadth of mission specific access Chandra users expect, the CXC has been adding Virtual Observatory (VO) interfaces to the Chandra proposal catalog and observation catalog. VO interfaces provide standards-based access to Chandra data through simple positional queries or more complex queries using the Astronomical Data Query Language. Recent development at the CDA has generalized our existing VO services to create a suite of services that can be configured to provide VO interfaces to any dataset. This approach uses a thin web service layer for the individual VO interfaces, a middle-tier query component which is shared among the VO interfaces for parsing, scheduling, and executing queries, and existing web services for file and data access. The CXC VO services provide Simple Cone Search (SCS), Simple Image Access (SIA), and Table Access Protocol (TAP) implementations for both the Chandra proposal and observation catalogs within the existing archive architecture. Our work with the Chandra proposal and observation catalogs, as well as additional datasets beyond the CDA, illustrates how we can provide configurable VO services to extend core archive functionality.

The role of porcine reproductive and respiratory syndrome (PRRS) virus structural and non-structural proteins in virus pathogenesis.

PubMed

Music, Nedzad; Gagnon, Carl A

2010-12-01

Porcine reproductive and respiratory syndrome (PRRS) is an economically devastating viral disease affecting the swine industry worldwide. The etiological agent, PRRS virus (PRRSV), possesses a RNA viral genome with nine open reading frames (ORFs). The ORF1a and ORF1b replicase-associated genes encode the polyproteins pp1a and pp1ab, respectively. The pp1a is processed in nine non-structural proteins (nsps): nsp1α, nsp1β, and nsp2 to nsp8. Proteolytic cleavage of pp1ab generates products nsp9 to nsp12. The proteolytic pp1a cleavage products process and cleave pp1a and pp1ab into nsp products. The nsp9 to nsp12 are involved in virus genome transcription and replication. The 3' end of the viral genome encodes four minor and three major structural proteins. The GP(2a), GP₃ and GP₄ (encoded by ORF2a, 3 and 4), are glycosylated membrane associated minor structural proteins. The fourth minor structural protein, the E protein (encoded by ORF2b), is an unglycosylated membrane associated protein. The viral envelope contains two major structural proteins: a glycosylated major envelope protein GP₅ (encoded by ORF5) and an unglycosylated membrane M protein (encoded by ORF6). The third major structural protein is the nucleocapsid N protein (encoded by ORF7). All PRRSV non-structural and structural proteins are essential for virus replication, and PRRSV infectivity is relatively intolerant to subtle changes within the structural proteins. PRRSV virulence is multigenic and resides in both the non-structural and structural viral proteins. This review discusses the molecular characteristics, biological and immunological functions of the PRRSV structural and nsps and their involvement in the virus pathogenesis.

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

PubMed Central

Quiroz, Felipe García; Chilkoti, Ashutosh

2015-01-01

Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level. PMID:26390327

The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs.

PubMed

Root-Bernstein, Robert; Root-Bernstein, Meredith

2016-05-21

We have proposed that the ribosome may represent a missing link between prebiotic chemistries and the first cells. One of the predictions that follows from this hypothesis, which we test here, is that ribosomal RNA (rRNA) must have encoded the proteins necessary for ribosomal function. In other words, the rRNA also functioned pre-biotically as mRNA. Since these ribosome-binding proteins (rb-proteins) must bind to the rRNA, but the rRNA also functioned as mRNA, it follows that rb-proteins should bind to their own mRNA as well. This hypothesis can be contrasted to a "null" hypothesis in which rb-proteins evolved independently of the rRNA sequences and therefore there should be no necessary similarity between the rRNA to which rb-proteins bind and the mRNA that encodes the rb-protein. Five types of evidence reported here support the plausibility of the hypothesis that the mRNA encoding rb-proteins evolved from rRNA: (1) the ubiquity of rb-protein binding to their own mRNAs and autogenous control of their own translation; (2) the higher-than-expected incidence of Arginine-rich modules associated with RNA binding that occurs in rRNA-encoded proteins; (3) the fact that rRNA-binding regions of rb-proteins are homologous to their mRNA binding regions; (4) the higher than expected incidence of rb-protein sequences encoded in rRNA that are of a high degree of homology to their mRNA as compared with a random selection of other proteins; and (5) rRNA in modern prokaryotes and eukaryotes encodes functional proteins. None of these results can be explained by the null hypothesis that assumes independent evolution of rRNA and the mRNAs encoding ribosomal proteins. Also noteworthy is that very few proteins bind their own mRNAs that are not associated with ribosome function. Further tests of the hypothesis are suggested: (1) experimental testing of whether rRNA-encoded proteins bind to rRNA at their coding sites; (2) whether tRNA synthetases, which are also known to bind to their own mRNAs, are encoded by the tRNA sequences themselves; (3) and the prediction that archaeal and prokaryotic (DNA-based) genomes were built around rRNA "genes" so that rRNA-related sequences will be found to make up an unexpectedly high proportion of these genomes. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

The RNA-binding protein Spo5 promotes meiosis II by regulating cyclin Cdc13 in fission yeast.

PubMed

Arata, Mayumi; Sato, Masamitsu; Yamashita, Akira; Yamamoto, Masayuki

2014-03-01

Meiosis comprises two consecutive nuclear divisions, meiosis I and II. Despite this unique progression through the cell cycle, little is known about the mechanisms controlling the sequential divisions. In this study, we carried out a genetic screen to identify factors that regulate the initiation of meiosis II in the fission yeast Schizosaccharomyces pombe. We identified mutants deficient in meiosis II progression and repeatedly isolated mutants defective in spo5, which encodes an RNA-binding protein. Using fluorescence microscopy to visualize YFP-tagged protein, we found that spo5 mutant cells precociously lost Cdc13, the major B-type cyclin in fission yeast, before meiosis II. Importantly, the defect in meiosis II was rescued by increasing CDK activity. In wild-type cells, cdc13 transcripts increased during meiosis II, but this increase in cdc13 expression was weaker in spo5 mutants. Thus, Spo5 is a novel regulator of meiosis II that controls the level of cdc13 expression and promotes de novo synthesis of Cdc13. We previously reported that inhibition of Cdc13 degradation is necessary to initiate meiosis II; together with the previous information, the current findings indicate that the dual control of Cdc13 by de novo synthesis and suppression of proteolysis ensures the progression of meiosis II. © 2014 The Authors Genes to Cells © 2014 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

Evolutionary Characteristics of Missing Proteins: Insights into the Evolution of Human Chromosomes Related to Missing-Protein-Encoding Genes.

PubMed

Xu, Aishi; Li, Guang; Yang, Dong; Wu, Songfeng; Ouyang, Hongsheng; Xu, Ping; He, Fuchu

2015-12-04

Although the "missing protein" is a temporary concept in C-HPP, the biological information for their "missing" could be an important clue in evolutionary studies. Here we classified missing-protein-encoding genes into two groups, the genes encoding PE2 proteins (with transcript evidence) and the genes encoding PE3/4 proteins (with no transcript evidence). These missing-protein-encoding genes distribute unevenly among different chromosomes, chromosomal regions, or gene clusters. In the view of evolutionary features, PE3/4 genes tend to be young, spreading at the nonhomology chromosomal regions and evolving at higher rates. Interestingly, there is a higher proportion of singletons in PE3/4 genes than the proportion of singletons in all genes (background) and OTCSGs (organ, tissue, cell type-specific genes). More importantly, most of the paralogous PE3/4 genes belong to the newly duplicated members of the paralogous gene groups, which mainly contribute to special biological functions, such as "smell perception". These functions are heavily restricted into specific type of cells, tissues, or specific developmental stages, acting as the new functional requirements that facilitated the emergence of the missing-protein-encoding genes during evolution. In addition, the criteria for the extremely special physical-chemical proteins were first set up based on the properties of PE2 proteins, and the evolutionary characteristics of those proteins were explored. Overall, the evolutionary analyses of missing-protein-encoding genes are expected to be highly instructive for proteomics and functional studies in the future.

Digital Map of Surficial Geology, Wetlands, and Deepwater Habitats, Coeur d'Alene River Valley, Idaho

USGS Publications Warehouse

Bookstrom, Arthur A.; Box, Stephen E.; Jackson, Berne L.; Brandt, Theodore R.; Derkey, Pamela D.; Munts, Steven R.

1999-01-01

The Coeur d'Alene (CdA) River channel and its floodplain in north Idaho are mostly covered by metal-enriched sediments, partially derived from upstream mining, milling and smelting wastes. Relative to uncontaminated sediments of the region, metal-enriched sediments are highly enriched in silver, lead, zinc, arsenic, antimony and mercury, copper, cadmium, manganese, and iron. Widespread distribution of metal-enriched sediments has resulted from over a century of mining in the CdA mining district (upstream), poor mine-waste containment practices during the first 80 years of mining, and an ongoing series of over-bank floods. Previously deposited metal-enriched sediments continue to be eroded and transported down-valley and onto the floodplain during floods. The centerpiece of this report is a Digital Map Surficial Geology, Wetlands and Deepwater Habitats of the Coeur d'Alene (CdA) River valley (sheets 1 and 2). The map covers the river, its floodplain, and adjacent hills, from the confluence of the North and South Forks of the CdA River to its mouth and delta front on CdA Lake, 43 linear km (26 mi) to the southwest (river distance 58 km or 36 mi). Also included are the following derivative theme maps: 1. Wetland System Map; 2. Wetland Class Map; 3. Wetland Subclass Map; 4. Floodplain Map; 5. Water Regime Map; 6. Sediment-Type Map; 7. Redox Map; 8. pH Map; and 9. Agricultural Land Map. The CdA River is braided and has a cobble-gravel bottom from the confluence to Cataldo Flats, 8 linear km (5 mi) down-valley. Erosional remnants of up to four alluvial terraces are present locally, and all are within the floodplain, as defined by the area flooded in February of 1996. High-water (overflow) channels and partly filled channel scars braid across some alluvial terraces, toward down-valley marshes and (or) oxbow ponds, which drain back to the river. Near Cataldo Flats, the river gradient flattens, and the river coalesces into a single channel with a large friction-dominated central sand bar at Cataldo Landing. Metal-enriched sediments that were dredged from the central sand bar were deposited on Cataldo Flats, to form extensive dredge-spoil deposits. From the central sand bar to CdA Lake, thick deposits of metal-enriched sand partially fill the middle of the pre-mining-era channel along straight reaches, and form point-bars along the inside margins of meander bends. Metal-enriched sand and silt form oxidized bank-wedge deposits along riverside margins of pre-mining-era levees of gray silty mud. Metal-enriched levee sand deposits extend across bank wedges and natural levees, generally thinning and fining away from the river, toward lateral marshes and lakes, where dark gray metal-enriched silt and mud overlie silty peat, deposited before the mining era. Distributary streams and man-made canals locally diverge from the river, connecting it to lateral marshes and lakes, and metal-enriched sand splays locally fan out across the floodplain. At the mouth of the river, a bouyancy-dominated river-mouth bar crests beyond the ends of the emergent levees. Thick delta-front deposits of metal-enriched sand slope from the river-mouth bar to the bottom of CdA Lake.

Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes

PubMed Central

Minic, Zoran; Jamet, Elisabeth; San-Clemente, Hélène; Pelletier, Sandra; Renou, Jean-Pierre; Rihouey, Christophe; Okinyo, Denis PO; Proux, Caroline; Lerouge, Patrice; Jouanin, Lise

2009-01-01

Background Different strategies (genetics, biochemistry, and proteomics) can be used to study proteins involved in cell biogenesis. The availability of the complete sequences of several plant genomes allowed the development of transcriptomic studies. Although the expression patterns of some Arabidopsis thaliana genes involved in cell wall biogenesis were identified at different physiological stages, detailed microarray analysis of plant cell wall genes has not been performed on any plant tissues. Using transcriptomic and bioinformatic tools, we studied the regulation of cell wall genes in Arabidopsis stems, i.e. genes encoding proteins involved in cell wall biogenesis and genes encoding secreted proteins. Results Transcriptomic analyses of stems were performed at three different developmental stages, i.e., young stems, intermediate stage, and mature stems. Many genes involved in the synthesis of cell wall components such as polysaccharides and monolignols were identified. A total of 345 genes encoding predicted secreted proteins with moderate or high level of transcripts were analyzed in details. The encoded proteins were distributed into 8 classes, based on the presence of predicted functional domains. Proteins acting on carbohydrates and proteins of unknown function constituted the two most abundant classes. Other proteins were proteases, oxido-reductases, proteins with interacting domains, proteins involved in signalling, and structural proteins. Particularly high levels of expression were established for genes encoding pectin methylesterases, germin-like proteins, arabinogalactan proteins, fasciclin-like arabinogalactan proteins, and structural proteins. Finally, the results of this transcriptomic analyses were compared with those obtained through a cell wall proteomic analysis from the same material. Only a small proportion of genes identified by previous proteomic analyses were identified by transcriptomics. Conversely, only a few proteins encoded by genes having moderate or high level of transcripts were identified by proteomics. Conclusion Analysis of the genes predicted to encode cell wall proteins revealed that about 345 genes had moderate or high levels of transcripts. Among them, we identified many new genes possibly involved in cell wall biogenesis. The discrepancies observed between results of this transcriptomic study and a previous proteomic study on the same material revealed post-transcriptional mechanisms of regulation of expression of genes encoding cell wall proteins. PMID:19149885

Bypass of a 5',8-cyclopurine-2'-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks.

PubMed

Jiang, Zhongliang; Xu, Meng; Lai, Yanhao; Laverde, Eduardo E; Terzidis, Michael A; Masi, Annalisa; Chatgilialoglu, Chryssostomos; Liu, Yuan

2015-09-01

5',8-Cyclopurine-2'-deoxynucleosides including 5',8-cyclo-dA (cdA) and 5',8-cyclo-dG (cdG) are induced by hydroxyl radicals resulting from oxidative stress such as ionizing radiation. 5',8-cyclopurine-2'-deoxynucleoside lesions are repaired by nucleotide excision repair with low efficiency, thereby leading to their accumulation in the human genome and lesion bypass by DNA polymerases during DNA replication and base excision repair (BER). In this study, for the first time, we discovered that DNA polymerase β (pol β) efficiently bypassed a 5'R-cdA, but inefficiently bypassed a 5'S-cdA during DNA replication and BER. We found that cell extracts from pol β wild-type mouse embryonic fibroblasts exhibited significant DNA synthesis activity in bypassing a cdA lesion located in replication and BER intermediates. However, pol β knock-out cell extracts exhibited little DNA synthesis to bypass the lesion. This indicates that pol β plays an important role in bypassing a cdA lesion during DNA replication and BER. Furthermore, we demonstrated that pol β inserted both a correct and incorrect nucleotide to bypass a cdA at a low concentration. Nucleotide misinsertion was significantly stimulated by a high concentration of pol β, indicating a mutagenic effect induced by pol β lesion bypass synthesis of a 5',8-cyclopurine-2'-deoxynucleoside. Moreover, we found that bypass of a 5'S-cdA by pol β generated an intermediate that failed to be extended by pol β, resulting in accumulation of single-strand DNA breaks. Our study provides the first evidence that pol β plays an important role in bypassing a 5',8-cyclo-dA during DNA replication and repair, as well as new insight into mutagenic effects and genome instability resulting from pol β bypassing of a cdA lesion. Copyright © 2015 Elsevier B.V. All rights reserved.

In situ dust measurements by the Cassini Cosmic Dust Analyzer in 2014 and beyond

NASA Astrophysics Data System (ADS)

Srama, R.

2015-10-01

Today, the German-lead Cosmic Dust Analyser (CDA) is operated continuously for 11 years in orbit around Saturn. Many discoveries like the Saturn nanodust streams or the large extended Ering were achieved. CDA provided unique results regarding Enceladus, his plume and the liquid water below the icy crust. In 2014 and 2015 CDA focuses on extended inclination and equatorial scans of the ring particle densities. Furthermore, scans are performed of the Pallene and Helene regions. Special attention is also given to the search of the dust cloud around Dione and to the Titan region. Long integration times are needed in order to characterize the flux and composition of exogenous dust (including interstellar dust) or possible retrograde dust particles. Finally, dedicated observation campaigns focus on the coupling of nanodust streams to Saturn's magnetosphere and the search of possible periodicities in the stream data. Saturn's rotation frequency was identified in the impact rate of nanodust particles at a Saturn distance of 40 Saturn radii. A special geometry in 2014-065 lead to an occultation of the dust stream by the moon Titan and its atmosphere when Titan crossed the line-of-sight between Saturn and Cassini. Here, CDA pointed towards Saturn for the measurement of stream particles. Around closest approach when Cassini was behind Titan, the flux of stream particles went down to zero (Fig. 1). This "dust occultation" is a new method to analyse the properties of the stream particles (speed, composition, mass) or the properties of Titans atmosphere (density). Furthermore, the particle trajectories can be constrained for a better analysis of their origin. In the final three years CDA performs exogenous and interstellar dust campaigns, studies of the composition and origin of Saturn's main rings by unique ring ejecta measurements, long-duration nano-dust stream observations, high-resolution maps of small moon orbit crossings, studies of the dust cloud around Dione and studies of the E-ring interaction with the large moon Titan.

Targeted Quantitative Screening of Chromosome 18 Encoded Proteome in Plasma Samples of Astronaut Candidates.

PubMed

Kopylov, Artur T; Ilgisonis, Ekaterina V; Moysa, Alexander A; Tikhonova, Olga V; Zavialova, Maria G; Novikova, Svetlana E; Lisitsa, Andrey V; Ponomarenko, Elena A; Moshkovskii, Sergei A; Markin, Andrey A; Grigoriev, Anatoly I; Zgoda, Victor G; Archakov, Alexander I

2016-11-04

This work was aimed at estimating the concentrations of proteins encoded by human chromosome 18 (Chr 18) in plasma samples of 54 healthy male volunteers (aged 20-47). These young persons have been certified by the medical evaluation board as healthy subjects ready for space flight training. Over 260 stable isotope-labeled peptide standards (SIS) were synthesized to perform the measurements of proteins encoded by Chr 18. Selected reaction monitoring (SRM) with SIS allowed an estimate of the levels of 84 of 276 proteins encoded by Chr 18. These proteins were quantified in whole and depleted plasma samples. Concentration of the proteins detected varied from 10 -6 M (transthyretin, P02766) to 10 -11 M (P4-ATPase, O43861). A minor part of the proteins (mostly representing intracellular proteins) was characterized by extremely high inter individual variations. The results provide a background for studies of a potential biomarker in plasma among proteins encoded by Chr 18. The SRM raw data are available in ProteomeXchange repository (PXD004374).

Malonyl-CoA Synthetase, Encoded by ACYL ACTIVATING ENZYME13, Is Essential for Growth and Development of Arabidopsis[C][W][OA

PubMed Central

Chen, Hui; Kim, Hyun Uk; Weng, Hua; Browse, John

2011-01-01

Malonyl-CoA is the precursor for fatty acid synthesis and elongation. It is also one of the building blocks for the biosynthesis of some phytoalexins, flavonoids, and many malonylated compounds. In plants as well as in animals, malonyl-CoA is almost exclusively derived from acetyl-CoA by acetyl-CoA carboxylase (EC 6.4.1.2). However, previous studies have suggested that malonyl-CoA may also be made directly from malonic acid by malonyl-CoA synthetase (EC 6.2.1.14). Here, we report the cloning of a eukaryotic malonyl-CoA synthetase gene, Acyl Activating Enzyme13 (AAE13; At3g16170), from Arabidopsis thaliana. Recombinant AAE13 protein showed high activity against malonic acid (Km = 529.4 ± 98.5 μM; Vm = 24.0 ± 2.7 μmol/mg/min) but little or no activity against other dicarboxylic or fatty acids tested. Exogenous malonic acid was toxic to Arabidopsis seedlings and caused accumulation of malonic and succinic acids in the seedlings. aae13 null mutants also grew poorly and accumulated malonic and succinic acids. These defects were complemented by an AAE13 transgene or by a bacterial malonyl-CoA synthetase gene under control of the AAE13 promoter. Our results demonstrate that the malonyl-CoA synthetase encoded by AAE13 is essential for healthy growth and development, probably because it is required for the detoxification of malonate. PMID:21642549

Loss of virulence in Ustilago maydis by Umchs6 gene disruption.

PubMed

Garcerá-Teruel, Ana; Xoconostle-Cázares, Beatriz; Rosas-Quijano, Raymundo; Ortiz, Lucila; León-Ramírez, Claudia; Specht, Charles A; Sentandreu, Rafael; Ruiz-Herrera, José

2004-03-01

A gene encoding a sixth chitin synthase (Umchs6, sequence GenBank accession No. ) from the plant pathogenic hemibasidiomycete Ustilago maydis (DC.) Cda. was isolated and characterized. The predicted protein is 1103 amino acids in length with a calculated molecular mass of 123.5 kDa. a2b2 null mutants were obtained by substitution of a central fragment of the Umchs6 gene with the hygromycin resistance cassette, and a1b1 null mutants were obtained by genetic recombination in plants of an a2b2deltach6 and a wild-type a1b1 strain. The mutation had no effect on the dimorphic transition in vitro or on mating, and growth rate of the mutants was only slightly reduced. On the other hand, they displayed important alterations in cell morphology, particularly at the mycelial stage, and in the staining pattern with calcofluor white. Levels of chitin synthase activity in vitro and chitin content were reduced. The most noticeable characteristic of the mutants was their almost complete loss of virulence to maize (Zea mays L.). This was a recessive character. Microscopic observations during the infectious process suggest that chitin synthase 6 activity is very important for growth of the fungus into the plant. Transformation of a2b2deltach6 mutants with an autonomous replicating plasmid carrying the full Umchs6 gene restored their normal morphological phenotype and virulence. These results are evidence that the mutation in the Umchs6 gene was solely responsible for the phenotypic alterations observed.

A loss of profilin-1 in late-stage oral squamous cell carcinoma.

PubMed

Adami, Guy R; O'Callaghan, Thomas N; Kolokythas, Antonia; Cabay, Robert J; Zhou, Yalu; Schwartz, Joel L

2017-08-01

The genes for PFN1 and TMSB4 are both highly expressed in oral tissue and both encode actin monomer binding proteins thought to play a role in cell motility and possibly other crucial parts of tumor progression. Oral brush cytology of epithelium from oral squamous cell carcinoma (OSCC) was used to measure PFN1 and TMSB4 mRNA in OSCC, while immunohistochemical analysis of tissue was used to check protein levels. High but variable expression of mRNAs encoding these two proteins was observed suggesting they may contribute to tumor characteristics in a subset of OSCCs. Both proteins were highly expressed in normal appearing basal epithelium, in the cytoplasm, and perinuclear area, while expression was minimal in upper epithelial layers. In OSCCs, expression of these proteins varied. In tumors classified as later stage, based on size and/or lymph node involvement, PFN1 levels were lower in tumor epithelium. A control gene, KRT13, showed expression in normal differentiated basal and suprabasal oral mucosa epithelial cells and as reported was lost in OSCC cells. Loss of PFN1 in tumor cells has been associated with lymph node invasion and metastasis in other tumor types, strengthening the argument that the protein has the potential to be a tumor suppressor in late-stage OSCC. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Gene Expression Profiling in Pachyonychia Congenita Skin

PubMed Central

Cao, Yu-An; Hickerson, Robyn P.; Seegmiller, Brandon L.; Grapov, Dmitry; Gross, Maren M.; Bessette, Marc R.; Phinney, Brett S.; Flores, Manuel A.; Speaker, Tycho J.; Vermeulen, Annaleen; Bravo, Albert A.; Bruckner, Anna L.; Milstone, Leonard M.; Schwartz, Mary E.; Rice, Robert H.; Kaspar, Roger L.

2015-01-01

Background Pachyonychia congenita (PC) is a skin disorder resulting from mutations in keratin (K) proteins including K6a, K6b, K16, and K17. One of the major symptoms is painful plantar keratoderma. The pathogenic sequelae resulting from the keratin mutations remain unclear. Objective To better understand PC pathogenesis. Methods RNA profiling was performed on biopsies taken from PC-involved and uninvolved plantar skin of seven genotyped PC patients (two K6a, one K6b, three K16, and one K17) as well as from control volunteers. Protein profiling was generated from tape-stripping samples. Results A comparison of PC-involved skin biopsies to adjacent uninvolved plantar skin identified 112 differentially-expressed mRNAs common to patient groups harboring K6 (i.e., both K6a and K6b) and K16 mutations. Among these mRNAs, 25 encode structural proteins including keratins, small proline-rich and late cornified envelope proteins, 20 are related to metabolism and 16 encode proteases, peptidases, and their inhibitors including kallikrein-related peptidases (KLKs), and serine protease inhibitors (SERPINs). mRNAs were also identified to be differentially expressed only in K6 (81) or K16 (141) patient samples. Furthermore, 13 mRNAs were identified that may be involved in pain including nociception and neuropathy. Protein profiling, comparing three K6a plantar tape-stripping samples to non-PC controls, showed changes in the PC corneocytes similar, but not identical, to the mRNA analysis. Conclusion Many differentially-expressed genes identified in PC-involved skin encode components critical for skin barrier homeostasis including keratinocyte proliferation, differentiation, cornification, and desquamation. The profiling data provide a foundation for unraveling the pathogenesis of PC and identifying targets for developing effective PC therapeutics. PMID:25656049

An ABC Transporter System of Yersinia pestis Allows Utilization of Chelated Iron by Escherichia coli SAB11

PubMed Central

Bearden, Scott W.; Staggs, Teanna M.; Perry, Robert D.

1998-01-01

The acquisition of iron is an essential component in the pathogenesis of Yersinia pestis, the agent of bubonic and pneumonic plague. A cosmid library derived from the genomic DNA of Y. pestis KIM6+ was used for transduction of an Escherichia coli mutant (SAB11) defective in the biosynthesis of the siderophore enterobactin. Recombinant plasmids which had a common 13-kb BamHI fragment were isolated from SAB11 transductants in which growth but not enterobactin synthesis was restored on media containing the iron chelator EDDA [ethylenediamine-di(o-hydroxyphenyl acetic acid)]. Subcloning and transposon mutagenesis revealed a 5.6-kb region, designated yfe, essential for SAB11 growth stimulation. In vitro transcription-translation analysis identified polypeptides of 18, 29.5, 32, and 33 kDa encoded by the yfe locus. Sequence analysis shows this locus to be comprised of five genes in two separate operons which have potential Fur-binding sequences in both promoters. A putative polycistronic operon, yfeABCD, is Fur regulated and responds to iron and manganese. A functional Fur protein is required for the observed manganese repression of this operon. This operon encodes polypeptides which have strong similarity to the ATP-binding cassette (ABC) family of transporters and include a periplasmic binding protein (YfeA), an ATP-binding protein (YfeB), and two integral membrane proteins (YfeC and -D), which likely function in the acquisition of inorganic iron and possibly other ions. The ∼21-kDa protein encoded by the separately transcribed yfeE gene may be located in the cell envelope, since a yfeE::TnphoA fusion is PhoA+. Mutations in this gene abrogate growth of SAB11 on iron-chelated media. PMID:9495751

An ABC transporter system of Yersinia pestis allows utilization of chelated iron by Escherichia coli SAB11.

PubMed

Bearden, S W; Staggs, T M; Perry, R D

1998-03-01

The acquisition of iron is an essential component in the pathogenesis of Yersinia pestis, the agent of bubonic and pneumonic plague. A cosmid library derived from the genomic DNA of Y. pestis KIM6+ was used for transduction of an Escherichia coli mutant (SAB11) defective in the biosynthesis of the siderophore enterobactin. Recombinant plasmids which had a common 13-kb BamHI fragment were isolated from SAB11 transductants in which growth but not enterobactin synthesis was restored on media containing the iron chelator EDDA [ethylenediamine-di(o-hydroxyphenyl acetic acid)]. Subcloning and transposon mutagenesis revealed a 5.6-kb region, designated yfe, essential for SAB11 growth stimulation. In vitro transcription-translation analysis identified polypeptides of 18, 29.5, 32, and 33 kDa encoded by the yfe locus. Sequence analysis shows this locus to be comprised of five genes in two separate operons which have potential Fur-binding sequences in both promoters. A putative polycistronic operon, yfeABCD, is Fur regulated and responds to iron and manganese. A functional Fur protein is required for the observed manganese repression of this operon. This operon encodes polypeptides which have strong similarity to the ATP-binding cassette (ABC) family of transporters and include a periplasmic binding protein (YfeA), an ATP-binding protein (YfeB), and two integral membrane proteins (YfeC and -D), which likely function in the acquisition of inorganic iron and possibly other ions. The approximately 21-kDa protein encoded by the separately transcribed yfeE gene may be located in the cell envelope, since a yfeE::TnphoA fusion is PhoA+. Mutations in this gene abrogate growth of SAB11 on iron-chelated media.

Identification of Two Candidate Tumor Suppressor Genes on Chromosome 17p13.3: Assessment of Their Roles in Breast and Ovarian Carcinogenesis

DTIC Science & Technology

1997-07-01

minimum region of allelic loss on chromosome 17p 13.3, between polymorphic markers D17S5 and D17S28, in genomic DNA from breast and ovarian tumors (Figure 1...encode proteins of 443 and 227 amino acids, with no known functional motifs. Comparison of genomic and cDNA sequences showed that the genes overlap...is tissue specific (Figure 4). When zoo blots comprised of EcoRI fragments of genomic DNA from various species were probed with the unique exon 1 of

A Document-Based EHR System That Controls the Disclosure of Clinical Documents Using an Access Control List File Based on the HL7 CDA Header.

PubMed

Takeda, Toshihiro; Ueda, Kanayo; Nakagawa, Akito; Manabe, Shirou; Okada, Katsuki; Mihara, Naoki; Matsumura, Yasushi

2017-01-01

Electronic health record (EHR) systems are necessary for the sharing of medical information between care delivery organizations (CDOs). We developed a document-based EHR system in which all of the PDF documents that are stored in our electronic medical record system can be disclosed to selected target CDOs. An access control list (ACL) file was designed based on the HL7 CDA header to manage the information that is disclosed.

Sec13 safeguards the integrity of the endoplasmic reticulum and organogenesis of the digestive system in zebrafish.

PubMed

Niu, Xubo; Gao, Chuan; Jan Lo, Li; Luo, Yue; Meng, Chunmei; Hong, Jian; Hong, Wanjin; Peng, Jinrong

2012-07-15

The Sec13-Sec31 heterotetramer serves as the outer coat in the COPII complex, which mediates protein trafficking from the endoplasmic reticulum (ER) to the Golgi apparatus. Although it has been studied in depth in yeast and cultured cells, the role of COPII in organogenesis in a multicellular organism has not. We report here that a zebrafish sec13(sq198) mutant, which exhibits a phenotype of hypoplastic digestive organs, has a mutation in the sec13 gene. The mutant gene encodes a carboxyl-terminus-truncated Sec13 that loses its affinity to Sec31a, which leads to disintegration of the ER structure in various differentiated cells in sec13(sq198), including chondrocytes, intestinal epithelial cells and hepatocytes. Disruption of the ER structure activates an unfolded protein response that eventually causes the cells to undergo cell-cycle arrest and cell apoptosis, which arrest the growth of developing digestive organs in the mutant. Our data provide the first direct genetic evidence that COPII function is essential for the organogenesis of the digestive system. Copyright © 2012 Elsevier Inc. All rights reserved.

Extraordinary Structured Noncoding RNAs Revealed by Bacterial Metagenome Analysis

PubMed Central

Weinberg, Zasha; Perreault, Jonathan; Meyer, Michelle M.; Breaker, Ronald R.

2012-01-01

Estimates of the total number of bacterial species1-3 suggest that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins4 and RNAs5. Bioinformatics searches6-10 of genomic DNA from bacteria commonly identify novel noncoding RNAs (ncRNAs)10-12 such as riboswitches13,14. In rare instances, RNAs that exhibit more extensive sequence and structural conservation across a wide range of bacteria are encountered15,16. Given that large structured RNAs are known to carry out complex biochemical functions such as protein synthesis and RNA processing reactions, identifying more RNAs of great size and intricate structure is likely to reveal additional biochemical functions that can be achieved by RNA. We applied an updated computational pipeline17 to discover ncRNAs that rival the known large ribozymes in size and structural complexity or that are among the most abundant RNAs in bacteria that encode them. These RNAs would have been difficult or impossible to detect without examining environmental DNA sequences, suggesting that numerous RNAs with extraordinary size, structural complexity, or other exceptional characteristics remain to be discovered in unexplored sequence space. PMID:19956260

Characterization of signatures from organic compounds in CDA mass spectra of ice particles in Saturn's E-ring

NASA Astrophysics Data System (ADS)

Khawaja, Nozair; Postberg, Frank; Reviol, Rene; Srama, Ralf

2015-04-01

The major source of ice particles in Saturn's E-ring is Enceladus - a geological active moon of Saturn. Enceladus is emanating ice particles from its fractured south polar terrain (SPT), the so-called "Tiger Stripes". The source of Enceladus activity and many of the ice particles is a subsurface ocean. The Cosmic Dust Analyzer (CDA) onboard the Cassini spacecraft is sampling these icy particles and producing TOF mass spectra of cations of impinging particles [1]. Three compositional types of ice particles have been identified from CDA-mass spectra: (i) pure water ice (Type-1) (ii) organic rich (Type-2) (iii) salt rich (Type-3) [2][3]. These organic rich (Type-2) spectra are particularly abundant in the icy jets of Enceladus as we found out during the Cassini's Enceladus flybys (E17 and E18) in 2012 [4]. We present a compositional analysis of the CDA spectra of these organic rich icy grains sampled in the E ring. We have characterized hundreds of Type-2 spectra of impinging ice particles. These were recorded at different impact velocities causing different molecular fragmentation patterns observed in the mass spectra. We defined 3 typical impact speed intervals: (i) 4-7 km/s (ii) 8-11 km/s and (iii) 12-16km/s. Organic features best observed at slow (4-7 km/s) or at intermediate (8-11 km/s) impact velocity ranges. Several classes of organic rich spectra are identified. Classifying Type-2 spectra are according to their characteristic mass lines of possible organic species. We try to infer the composition of each class of organic rich spectra is inferred by using an experimental setup (IR-FL-MALDI) to simulate the CDA spectra of different compositional types. In the laboratory we have used infrared laser to disperse a micro-beam of a water solution [5]. The laser energy is adjusted to simulate different impact velocities of ice particles on the CDA. Four families of organic compounds including alcohols, fatty acids, amines and aromatic, with varying number of carbon atoms, have been measured and compared with the CDA Type-2 spectra. References [1] Srama, R. et.al.: The Cassini Cosmic Dust Analyzer, SSR, Vol. 114, 465 -- 518, 2004. [2] Postberg, F. et.al.: The E-ring in the vicinity of Enceladus II. Probing the moon's interior -- The composition of E-ring particles, Icarus, Vol. 193, 438 -- 454, 2008. [3] Postberg, F. et.al.: Sodium salts in E-ring ice grains from an ocean below the surface of Enceladus, Nature, Vol. 459, 1098 - 1101, 2009. [4] Khawaja, N. et.al.: Compositional differentiation of Enceladus' plume, EPSC, Vol. 9, 2014. [5] Reviol, R. et.al.: Simulation of TOF spectra from cosmic ice particles in the Laboratory by IR-FL-MALDI, EPSC, Vol. 7, 2012.

Heterologous mitochondrial targeting sequences can deliver functional proteins into mitochondria.

PubMed

Marcus, Dana; Lichtenstein, Michal; Cohen, Natali; Hadad, Rita; Erlich-Hadad, Tal; Greif, Hagar; Lorberboum-Galski, Haya

2016-12-01

Mitochondrial Targeting Sequences (MTSs) are responsible for trafficking nuclear-encoded proteins into mitochondria. Once entering the mitochondria, the MTS is recognized and cleaved off. Some MTSs are long and undergo two-step processing, as in the case of the human frataxin (FXN) protein (80aa), implicated in Friedreich's ataxia (FA). Therefore, we chose the FXN protein to examine whether nuclear-encoded mitochondrial proteins can efficiently be targeted via a heterologous MTS (hMTS) and deliver a functional protein into mitochondria. We examined three hMTSs; that of citrate synthase (cs), lipoamide deydrogenase (LAD) and C6ORF66 (ORF), as classically MTS sequences, known to be removed by one-step processing, to deliver FXN into mitochondria, in the form of fusion proteins. We demonstrate that using hMTSs for delivering FXN results in the production of 4-5-fold larger amounts of the fusion proteins, and at 4-5-fold higher concentrations. Moreover, hMTSs delivered a functional FXN protein into the mitochondria even more efficiently than the native MTSfxn, as evidenced by the rescue of FA patients' cells from oxidative stress; demonstrating a 18%-54% increase in cell survival; and a 13%-33% increase in ATP levels, as compared to the fusion protein carrying the native MTS. One fusion protein with MTScs increased aconitase activity within patients' cells, by 400-fold. The implications form our studies are of vast importance for both basic and translational research of mitochondrial proteins as any mitochondrial protein can be delivered efficiently by an hMTS. Moreover, effective targeting of functional proteins is important for restoration of mitochondrial function and treatment of related disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular mechanisms for protein-encoded inheritance

PubMed Central

Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

2013-01-01

Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

Thionin-D4E1 chimeric protein protects plants against bacterial infections

DOEpatents

Stover, Eddie W; Gupta, Goutam; Hao, Guixia

2017-08-08

The generation of a chimeric protein containing a first domain encoding either a pro-thionon or thionin, a second domain encoding D4E1 or pro-D4E1, and a third domain encoding a peptide linker located between the first domain and second domain is described. Either the first domain or the second domain is located at the amino terminal of the chimeric protein and the other domain (second domain or first domain, respectively) is located at the carboxyl terminal. The chimeric protein has antibacterial activity. Genetically altered plants and their progeny expressing a polynucleotide encoding the chimeric protein resist diseases caused by bacteria.

Glycoside hydrolase family 13 α-glucosidases encoded by Bifidobacterium breve UCC2003; A comparative analysis of function, structure and phylogeny.

PubMed

Kelly, Emer D; Bottacini, Francesca; O'Callaghan, John; Motherway, Mary O'Connell; O'Connell, Kerry Joan; Stanton, Catherine; van Sinderen, Douwe

2016-05-02

Bifidobacterium breve is a noted inhabitant and one of the first colonizers of the human gastro intestinal tract (GIT). The ability of this bacterium to persist in the GIT is reflected by the abundance of carbohydrate-active enzymes that are encoded by its genome. One such family of enzymes is represented by the α-glucosidases, of which three, Agl1, Agl2 and MelD, have previously been identified and characterized in the prototype B. breve strain UCC2003. In this report, we describe an additional B. breve UCC2003-encoded α-glucosidase, along with a B. breve UCC2003-encoded α-glucosidase-like protein, designated here as Agl3 and Agl4, respectively, which together with the three previously described enzymes belong to glycoside hydrolase (GH) family 13. Agl3 was shown to exhibit hydrolytic specificity towards the α-(1→6) linkage present in palatinose; the α-(1→3) linkage present in turanose; the α-(1→4) linkages found in maltotriose and maltose; and to a lesser degree, the α-(1→2) linkage found in sucrose and kojibiose; and the α-(1→5) linkage found in leucrose. Surprisingly, based on the substrates analyzed, Agl4 did not exhibit biologically relevant α-glucosidic activity. With the presence of four functionally active GH13 α-glucosidases, B. breve UCC2003 is capable of hydrolyzing all α-glucosidic linkages that can be expected in glycan substrates in the lower GIT. This abundance of α-glucosidases provides B. breve UCC2003 with an adaptive ability and metabolic versatility befitting the transient nature of growth substrates in the GIT. Copyright © 2016 Elsevier B.V. All rights reserved.

Highly Efficient White Organic Light Emitting Diodes Using New Blue Fluorescence Emitter.

PubMed

Kim, Seungho; Kim, Beomjin; Lee, Jaehyun; Yu, Young-Jun; Park, Jongwook

2015-07-01

Two different emitting compounds, 1-[1,1';3',1"]Terphenyl-5'-yl-6-(10-[1,1';3',1"]terpheny-5'-yl- anthracen-9-yl)-pyrene (TP-AP-TP) and Poly-phenylene vinylene derivative (PDY 132) were used to white OLED device. By incorporating adjacent blue and yellow emitting layers in a multi-layered structure, highly efficient white emission has been attained. The device was fabricated with a hybrid configuration structure: ITO/PEDOT (40 nm)/PDY-132 (8-50 nm)/ NPB (10 nm)/TP-AP-TP (30 nm)/Alq3 (20 nm)/LiF (1 nm)/Al (200 nm). After fixing TP-AP-TP thickness of 30 nm by evaporation, PDY-132 thickness varied with 8, 15, 35, and 50 nm by spin coating in device. The luminance efficiency of the white devices at 10 mA/cm2 were 2.93 cd/A-6.55 cd/A. One of white devices showed 6.55 cd/A and white color of (0.290, 0.331).

Multilayer polymer light-emitting diodes by blade coating method

NASA Astrophysics Data System (ADS)

Tseng, Shin-Rong; Meng, Hsin-Fei; Lee, Kuan-Chen; Horng, Sheng-Fu

2008-10-01

Multilayer polymer light-emitting diodes fabricated by blade coating are presented. Multilayer of polymers can be easily deposited by blade coating on a hot plate. The multilayer structure is confirmed by the total thickness and the cross section view in the scanning electron microscope. The film thickness variation is only 3.3% in 10cm scale and the film roughness is about 0.3nm in the micron scale. The efficiency of single layer poly(para-phenylene vinylene) copolymer Super Yellow and poly(9,9-dioctylfluorene) (PFO, deep blue) devices are 9 and 1.7cd/A, respectively, by blade coating. The efficiency of the PFO device is raised to 2.9cd/A with a 2-(4-tert-butylphenyl)-5-(4-biphenylyl)-1,3,4-oxadiazole (PBD) hole-blocking layer and to 2.3cd/A with a poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-(4,4'-(N-(4-sec-butylphenyl))diphenylamine)] elec-tron-blocking layer added by blade coating.

DNA bases thymine and adenine in bio-organic light emitting diodes.

PubMed

Gomez, Eliot F; Venkatraman, Vishak; Grote, James G; Steckl, Andrew J

2014-11-24

We report on the use of nucleic acid bases (NBs) in organic light emitting diodes (OLEDs). NBs are small molecules that are the basic building blocks of the larger DNA polymer. NBs readily thermally evaporate and integrate well into the vacuum deposited OLED fabrication. Adenine (A) and thymine (T) were deposited as electron-blocking/hole-transport layers (EBL/HTL) that resulted in increases in performance over the reference OLED containing the standard EBL material NPB. A-based OLEDs reached a peak current efficiency and luminance performance of 48 cd/A and 93,000 cd/m(2), respectively, while T-based OLEDs had a maximum of 76 cd/A and 132,000 cd/m(2). By comparison, the reference OLED yielded 37 cd/A and 113,000 cd/m(2). The enhanced performance of T-based devices is attributed to a combination of energy levels and structured surface morphology that causes more efficient and controlled hole current transport to the emitting layer.

The yeast vps class E mutants: the beginning of the molecular genetic analysis of multivesicular body biogenesis.

PubMed

Coonrod, Emily M; Stevens, Tom H

2010-12-01

In 1992, Raymond et al. published a compilation of the 41 yeast vacuolar protein sorting (vps) mutant groups and described a large class of mutants (class E vps mutants) that accumulated an exaggerated prevacuolar endosome-like compartment. Further analysis revealed that this "class E compartment" contained soluble vacuolar hydrolases, vacuolar membrane proteins, and Golgi membrane proteins unable to recycle back to the Golgi complex, yet these class E vps mutants had what seemed to be normal vacuoles. The 13 class E VPS genes were later shown to encode the proteins that make up the complexes required for formation of intralumenal vesicles in late endosomal compartments called multivesicular bodies, and for the sorting of ubiquitinated cargo proteins into these internal vesicles for eventual delivery to the vacuole or lysosome.

The rice blast resistance gene Ptr encodes an atypical protein required for broad spectrum disease resistance

USDA-ARS?s Scientific Manuscript database

Plant resistance (R) genes typically encode proteins with nucleotide binding site-leucine rich repeat (NLR) domains. We identified a novel, broad-spectrum rice blast R gene, Ptr, encoding a non-NLR protein with four Armadillo repeats. Ptr was originally identified by fast neutron mutagenesis as a ...

Alternative intronic promoters in development and disease.

PubMed

Vacik, Tomas; Raska, Ivan

2017-05-01

Approximately 20,000 mammalian genes are estimated to encode between 250 thousand and 1 million different proteins. This enormous diversity of the mammalian proteome is caused by the ability of a single-gene locus to encode multiple protein isoforms. Protein isoforms encoded by one gene locus can be functionally distinct, and they can even have antagonistic functions. One of the mechanisms involved in creating this proteome complexity is alternative promoter usage. Alternative intronic promoters are located downstream from their canonical counterparts and drive the expression of alternative RNA isoforms that lack upstream exons. These upstream exons can encode some important functional domains, and proteins encoded by alternative mRNA isoforms can be thus functionally distinct from the full-length protein encoded by canonical mRNA isoforms. Since any misbalance of functionally distinct protein isoforms is likely to have detrimental consequences for the cell and the whole organism, their expression must be precisely regulated. Misregulation of alternative intronic promoters is frequently associated with various developmental defects and diseases including cancer, and it is becoming increasingly clear that this phenomenon deserves more attention.

Cloning, molecular characterization and heterologous expression of AMY1, an alpha-amylase gene from Cryptococcus flavus.

PubMed

Galdino, Alexsandro S; Ulhoa, Cirano J; Moraes, Lídia Maria P; Prates, Maura V; Bloch, Carlos; Torres, Fernando A G

2008-03-01

A Cryptococcus flavus gene (AMY1) encoding an extracellular alpha-amylase has been cloned. The nucleotide sequence of the cDNA revealed an ORF of 1896 bp encoding for a 631 amino acid polypeptide with high sequence identity with a homologous protein isolated from Cryptococcus sp. S-2. The presence of four conserved signature regions, (I) (144)DVVVNH(149), (II) (235)GLRIDSLQQ(243), (III) (263)GEVFN(267), (IV) (327)FLENQD(332), placed the enzyme in the GH13 alpha-amylase family. Furthermore, sequence comparison suggests that the C. flavusalpha-amylase has a C-terminal starch-binding domain characteristic of the CBM20 family. AMY1 was successfully expressed in Saccharomyces cerevisiae. The time course of amylase secretion in S. cerevisiae resulted in a maximal extracellular amylolytic activity (3.93 U mL(-1)) at 60 h of incubation. The recombinant protein had an apparent molecular mass similar to the native enzyme (c. 67 kDa), part of which was due to N-glycosylation.

Impact of Myopia on Corneal Biomechanics in Glaucoma and Nonglaucoma Patients.

PubMed

Chansangpetch, Sunee; Panpruk, Rawiphan; Manassakorn, Anita; Tantisevi, Visanee; Rojanapongpun, Prin; Hurst, Cameron P; Lin, Shan C

2017-10-01

We evaluated the impact of myopia on corneal biomechanical properties in primary open-angle glaucoma (POAG) and nonglaucoma patients, and the effect of modification of glaucoma on myopic eyes. This cross-sectional study included 66 POAG eyes (33 myopia, 33 nonmyopia) and 66 normal eyes (33 myopia, 33 nonmyopia). Seven corneal biomechanical parameters were measured by ultra-high-speed Scheimpflug imaging, including corneal deformation amplitude (CDA), inward/outward corneal applanation length (ICA, OCA), inward/outward corneal velocity (ICV, OCV), radius, and peak distance (PD). Mean age (SD) of the 65 male (49%) and 67 female (51%) patients was 59 (9.82) years. Myopia was associated with significantly higher CDA (adjusted effect = 0.104, P = 0.001) and lower OCV (adjusted effect = -0.105, P < 0.001) in the POAG group. Within the nonglaucoma group, myopic eyes had a significantly lower OCV (adjusted effect = -0.086, P < 0.001) and higher CDA (adjusted effect = 0.079, P = 0.001). All parameters except PD suggested that glaucoma modified the effect of myopia on corneal biomechanics. Percentage differences in the adjusted myopic effect between POAG and nonglaucoma patients was 31.65, 27.27, 31.65, 50.00, 22.09, and 60.49 for CDA, ICA, OCA, ICV, OCV, and radius, respectively. Myopia had a significant impact on corneal biomechanical properties in the POAG and nonglaucoma groups. The differences in corneal biomechanical parameters suggest that myopia is correlated with significantly lower ocular rigidity. POAG may enhance the effects of myopia on most of these parameters.

Standardized exchange of clinical documents--towards a shared care paradigm in glaucoma treatment.

PubMed

Gerdsen, F; Müller, S; Jablonski, S; Prokosch, H-U

2006-01-01

The exchange of medical data from research and clinical routine across institutional borders is essential to establish an integrated healthcare platform. In this project we want to realize the standardized exchange of medical data between different healthcare institutions to implement an integrated and interoperable information system supporting clinical treatment and research of glaucoma. The central point of our concept is a standardized communication model based on the Clinical Document Architecture (CDA). Further, a communication concept between different health care institutions applying the developed document model has been defined. With our project we have been able to prove that standardized communication between an Electronic Medical Record (EMR), an Electronic Health Record (EHR) and the Erlanger Glaucoma Register (EGR) based on the established conceptual models, which rely on CDA rel.1 level 1 and SCIPHOX, could be implemented. The HL7-tool-based deduction of a suitable CDA rel.2 compliant schema showed significant differences when compared with the manually created schema. Finally fundamental requirements, which have to be implemented for an integrated health care platform, have been identified. An interoperable information system can enhance both clinical treatment and research projects. By automatically transferring screening findings from a glaucoma research project to the electronic medical record of our ophthalmology clinic, clinicians could benefit from the availability of a longitudinal patient record. The CDA as a standard for exchanging clinical documents has demonstrated its potential to enhance interoperability within a future shared care paradigm.

The RFamide receptor DMSR-1 regulates stress-induced sleep in C. elegans

PubMed Central

Iannacone, Michael J; Beets, Isabel; Lopes, Lindsey E; Churgin, Matthew A; Fang-Yen, Christopher; Nelson, Matthew D; Schoofs, Liliane; Raizen, David M

2017-01-01

In response to environments that cause cellular stress, animals engage in sleep behavior that facilitates recovery from the stress. In Caenorhabditis elegans, stress-induced sleep(SIS) is regulated by cytokine activation of the ALA neuron, which releases FLP-13 neuropeptides characterized by an amidated arginine-phenylalanine (RFamide) C-terminus motif. By performing an unbiased genetic screen for mutants that impair the somnogenic effects of FLP-13 neuropeptides, we identified the gene dmsr-1, which encodes a G-protein coupled receptor similar to an insect RFamide receptor. DMSR-1 is activated by FLP-13 peptides in cell culture, is required for SIS in vivo, is expressed non-synaptically in several wake-promoting neurons, and likely couples to a Gi/o heterotrimeric G-protein. Our data expand our understanding of how a single neuroendocrine cell coordinates an organism-wide behavioral response, and suggest that similar signaling principles may function in other organisms to regulate sleep during sickness. DOI: http://dx.doi.org/10.7554/eLife.19837.001 PMID:28094002

The complete mitochondrial genome of Sika deer Cervus nippon hortulorum (Artiodactyla: Cervidae) and phylogenetic studies.

PubMed

Liu, Yan-Hua; Liu, Xin-Xin; Zhang, Ming-Hai

2016-07-01

Sika deer (Cervus nippon Temminck 1836) are classified in the order Artiodactyla, family Cervidae, subfamily Cervinae. At present, the phylogenetic studies of C. nippon are problematic. In this study, we first determined and described the complete mitochondrial sequence of the wild C. nippon hortulorum. The complete mitogenome sequence is 16 566 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR) and a light-strand replication origin (OL). The overall base composition was 33.4% A, 28.6% T, 24.5% C, 13.5% G, with a 62.0% AT bias. The 13 protein-coding genes encode 3782 amino acids in total. To further validate the new determined sequences and phylogeny of Sika deer, phylogenetic trees involving 15 most closely related species available in GenBank database were constructed. These results are expected to provide useful molecular data for deer species identification and further phylogenetic studies of Artiodactyla.

The primary structure of L37--a rat ribosomal protein with a zinc finger-like motif.

PubMed

Chan, Y L; Paz, V; Olvera, J; Wool, I G

1993-04-30

The amino acid sequence of the rat 60S ribosomal subunit protein L37 was deduced from the sequence of nucleotides in a recombinant cDNA. Ribosomal protein L37 has 96 amino acids, the NH2-terminal methionine is removed after translation of the mRNA, and has a molecular weight of 10,939. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 13 or 14 copies of the L37 gene. The mRNA for the protein is about 500 nucleotides in length. Rat L37 is related to Saccharomyces cerevisiae ribosomal protein YL35 and to Caenorhabditis elegans L37. We have identified in the data base a DNA sequence that encodes the chicken homolog of rat L37.

The Peripheral Olfactory Repertoire of the Lightbrown Apple Moth, Epiphyas postvittana

PubMed Central

Thrimawithana, Amali H.; Crowhurst, Ross N.; Newcomb, Richard D.

2015-01-01

The lightbrown apple moth, Epiphyas postvittana is an increasingly global pest of horticultural crops. Like other moths, E. postvittana relies on olfactory cues to locate mates and oviposition sites. To detect these cues, moths have evolved families of genes encoding elements of the peripheral olfactory reception system, including odor carriers, receptors and degrading enzymes. Here we undertake a transcriptomic approach to identify members of these families expressed in the adult antennae of E. postvittana, describing open reading frames encoding 34 odorant binding proteins, 13 chemosensory proteins, 70 odorant receptors, 19 ionotropic receptors, nine gustatory receptors, two sensory neuron membrane proteins, 27 carboxylesterases, 20 glutathione-S-transferases, 49 cytochrome p450s and 18 takeout proteins. For the odorant receptors, quantitative RT-PCR corroborated RNAseq count data on steady state transcript levels. Of the eight odorant receptors that group phylogenetically with pheromone receptors from other moths, two displayed significant male-biased expression patterns, one displayed significant female-biased expression pattern and five were expressed equally in the antennae of both sexes. In addition, we found two male-biased odorant receptors that did not group with previously described pheromone receptors. This suite of olfaction-related genes provides a substantial resource for the functional characterization of this signal transduction system and the development of odor-mediated control strategies for horticultural pests. PMID:26017144

Mitochondrial genome of the endangered marine gastropod Strombus gigas Linnaeus, 1758 (Mollusca: Gastropoda).

PubMed

Márquez, Edna J; Castro, Erick R; Alzate, Juan F

2016-01-01

The queen conch Strombus gigas is an endangered marine gastropod of significant economic importance across the Greater Caribbean region. This work reports for the first time the complete mitochondrial genome of S. gigas, obtained by FLX 454 pyrosequencing. The mtDNA genome encodes for 13 proteins, 22 tRNAs and 2 ribosomal RNAs. In addition, the coding sequences and gene synteny were similar to other previously reported mitogenomes of gastropods.

Encoding of contextual fear memory requires de novo proteins in the prelimbic cortex

PubMed Central

Rizzo, Valerio; Touzani, Khalid; Raveendra, Bindu L.; Swarnkar, Supriya; Lora, Joan; Kadakkuzha, Beena M.; Liu, Xin-An; Zhang, Chao; Betel, Doron; Stackman, Robert W.; Puthanveettil, Sathyanarayanan V.

2016-01-01

Background Despite our understanding of the significance of the prefrontal cortex in the consolidation of long-term memories (LTM), its role in the encoding of LTM remains elusive. Here we investigated the role of new protein synthesis in the mouse medial prefrontal cortex (mPFC) in encoding contextual fear memory. Methods Because a change in the association of mRNAs to polyribosomes is an indicator of new protein synthesis, we assessed the changes in polyribosome-associated mRNAs in the mPFC following contextual fear conditioning (CFC) in the mouse. Differential gene expression in mPFC was identified by polyribosome profiling (n = 18). The role of new protein synthesis in mPFC was determined by focal inhibition of protein synthesis (n = 131) and by intra-prelimbic cortex manipulation (n = 56) of Homer 3, a candidate identified from polyribosome profiling. Results We identified several mRNAs that are differentially and temporally recruited to polyribosomes in the mPFC following CFC. Inhibition of protein synthesis in the prelimbic (PL), but not in the anterior cingulate cortex (ACC) region of the mPFC immediately after CFC disrupted encoding of contextual fear memory. Intriguingly, inhibition of new protein synthesis in the PL 6 hours after CFC did not impair encoding. Furthermore, expression of Homer 3, an mRNA enriched in polyribosomes following CFC, in the PL constrained encoding of contextual fear memory. Conclusions Our studies identify several molecular substrates of new protein synthesis in the mPFC and establish that encoding of contextual fear memories require new protein synthesis in PL subregion of mPFC. PMID:28503670

Gene Expression Profiling of the Cephalothorax and Eyestalk in Penaeus Monodon during Ovarian Maturation

PubMed Central

Brady, Philip; Elizur, Abigail; Williams, Richard; Cummins, Scott F.; Knibb, Wayne

2012-01-01

In crustaceans, a range of physiological processes involved in ovarian maturation occurs in organs of the cephalothorax including the hepatopancrease, mandibular and Y-organ. Additionally, reproduction is regulated by neuropeptide hormones and other proteins released from secretory sites within the eyestalk. Reproductive dysfunction in captive-reared prawns, Penaeus monodon, is believed to be due to deficiencies in these factors. In this study, we investigated the expression of gene transcripts in the cephalothorax and eyestalk from wild-caught and captive-reared animals throughout ovarian maturation using custom oligonucleotide microarray screening. We have isolated numerous transcripts that appear to be differentially expressed throughout ovarian maturation and between wild-caught and captive-reared animals. In the cephalothorax, differentially expressed genes included the 1,3-β-D-glucan-binding high-density lipoprotein, 2/3-oxoacyl-CoA thiolase and vitellogenin. In the eyestalk, these include gene transcripts that encode a protein that modulates G-protein coupled receptor activity and another that encodes an architectural transcription factor. Each may regulate the expression of reproductive neuropeptides, such as the crustacean hyperglycaemic hormone and molt-inhibiting hormone. We could not identify differentially expressed transcripts encoding known reproductive neuropeptides in the eyestalk of either wild-caught or captive-reared prawns at any ovarian maturation stage, however, this result may be attributed to low relative expression levels of these transcripts. In summary, this study provides a foundation for the study of target genes involved in regulating penaeid reproduction. PMID:22355268

Molecular Determinants of Human T-lymphotropic Virus Type 1 Transmission and Spread

PubMed Central

Lairmore, Michael D.; Anupam, Rajaneesh; Bowden, Nadine; Haines, Robyn; Haynes, Rashade A. H.; Ratner, Lee; Green, Patrick L.

2011-01-01

Human T-lymphotrophic virus type-1 (HTLV-1) infects approximately 15 to 20 million people worldwide, with endemic areas in Japan, the Caribbean, and Africa. The virus is spread through contact with bodily fluids containing infected cells, most often from mother to child through breast milk or via blood transfusion. After prolonged latency periods, approximately 3 to 5% of HTLV-1 infected individuals will develop either adult T-cell leukemia/lymphoma (ATL), or other lymphocyte-mediated disorders such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The genome of this complex retrovirus contains typical gag, pol, and env genes, but also unique nonstructural proteins encoded from the pX region. These nonstructural genes encode the Tax and Rex regulatory proteins, as well as novel proteins essential for viral spread in vivo such as, p30, p12, p13 and the antisense encoded HBZ. While progress has been made in the understanding of viral determinants of cell transformation and host immune responses, host and viral determinants of HTLV-1 transmission and spread during the early phases of infection are unclear. Improvements in the molecular tools to test these viral determinants in cellular and animal models have provided new insights into the early events of HTLV-1 infection. This review will focus on studies that test HTLV-1 determinants in context to full length infectious clones of the virus providing insights into the mechanisms of transmission and spread of HTLV-1. PMID:21994774

Burkholderia Mallei tssM Encodes a Secreted Deubiquitinase that is Expressed Inside Infected RAW 264.7 Murine Macrophages

DTIC Science & Technology

2008-10-13

Furthermore, the encoded protein of this gene is only 30 kDa. A potential GTG start codon at position 625 also encodes a protein that is too small...horizontal bar and putative alternate translation initiation sites (ATG, GTG , and TTG) are indicated. The sizes and locations of the proteins encoded... gray line with rounded rectangles showing sequence features and motifs, including the Ala- and Pro-rich N-terminal region and the C-terminal Cys and

Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs.

PubMed

Hsu, Jack C-C; Reid, David W; Hoffman, Alyson M; Sarkar, Devanand; Nicchitta, Christopher V

2018-05-01

Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs. Cluster mapping of the AEG-1/RNA interaction sites demonstrated a normalized rank order interaction of coding sequence >5' untranslated region, with 3' untranslated region interactions only weakly represented. Intriguingly, AEG-1/membrane protein mRNA interaction sites clustered downstream from encoded transmembrane domains, suggestive of a role in membrane protein biogenesis. Secretory and cytosolic protein-encoding mRNAs were also represented in the AEG-1 RNA interactome, with the latter category notably enriched in genes functioning in mRNA localization, translational regulation, and RNA quality control. Bioinformatic analyses of RNA-binding motifs and predicted secondary structure characteristics indicate that AEG-1 lacks established RNA-binding sites though shares the property of high intrinsic disorder commonly seen in RBPs. These data implicate AEG-1 in the localization and regulation of secretory and membrane protein-encoding mRNAs and provide a framework for understanding AEG-1 function in health and disease. © 2018 Hsu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Solenopsis invicta virus 3: mapping of structural proteins, ribosomal frameshifting, and similarities to Acyrthosiphon pisum virus and Kelp fly virus.

PubMed

Valles, Steven M; Bell, Susanne; Firth, Andrew E

2014-01-01

Solenopsis invicta virus 3 (SINV-3) is a positive-sense single-stranded RNA virus that infects the red imported fire ant, Solenopsis invicta. We show that the second open reading frame (ORF) of the dicistronic genome is expressed via a frameshifting mechanism and that the sequences encoding the structural proteins map to both ORF2 and the 3' end of ORF1, downstream of the sequence that encodes the RNA-dependent RNA polymerase. The genome organization and structural protein expression strategy resemble those of Acyrthosiphon pisum virus (APV), an aphid virus. The capsid protein that is encoded by the 3' end of ORF1 in SINV-3 and APV is predicted to have a jelly-roll fold similar to the capsid proteins of picornaviruses and caliciviruses. The capsid-extension protein that is produced by frameshifting, includes the jelly-roll fold domain encoded by ORF1 as its N-terminus, while the C-terminus encoded by the 5' half of ORF2 has no clear homology with other viral structural proteins. A third protein, encoded by the 3' half of ORF2, is associated with purified virions at sub-stoichiometric ratios. Although the structural proteins can be translated from the genomic RNA, we show that SINV-3 also produces a subgenomic RNA encoding the structural proteins. Circumstantial evidence suggests that APV may also produce such a subgenomic RNA. Both SINV-3 and APV are unclassified picorna-like viruses distantly related to members of the order Picornavirales and the family Caliciviridae. Within this grouping, features of the genome organization and capsid domain structure of SINV-3 and APV appear more similar to caliciviruses, perhaps suggesting the basis for a "Calicivirales" order.

Dissociation and recombination of positive holes in minerals

NASA Technical Reports Server (NTRS)

Freund, Friedemann; Batllo, Francois; Freund, Minoru M.

1990-01-01

The formation mechanisms are described of positive holes - electronic defects in the O2 sublattice - with attention given to detecting the positive surface charge of minerals with these holes. Charge distribution analysis (CDA) is presented which measures dielectric polarization in an inhomogeneous field. CDA can be applied to the detection of the peroxide/superoxide functionality caused by positive holes on the surface. It is demonstrated with obsidian that the measurements provide data on O(-) mobility as a function of surface-charge carrier density and on O(-) generation as a function of temperature.

27 CFR 21.151 - List of denaturants authorized for denatured spirits.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Denatured Rum (S.D.R.) Acetaldehyde S.D.A. 29. Acetone, U.S.P S.D.A. 23-A, 23-H. Acetaldol C.D.A. 18. Almond... alcohol S.D.A. 39, 39-A, 39-B, 40, 40-A, 40-B, 40-C. Camphor, U.S.P S.D.A. 27, 27-A, 38-B. Caustic soda.... Formaldehyde solution, U.S.P S.D.A. 22, 38-C, 38-D. Gasoline C.D.A. 18, 19; S.D.A. 28-A. Gasoline, unleaded C.D...

27 CFR 21.151 - List of denaturants authorized for denatured spirits.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Denatured Rum (S.D.R.) Acetaldehyde S.D.A. 29. Acetone, U.S.P S.D.A. 23-A, 23-H. Acetaldol C.D.A. 18. Almond... alcohol S.D.A. 39, 39-A, 39-B, 40, 40-A, 40-B, 40-C. Camphor, U.S.P S.D.A. 27, 27-A, 38-B. Caustic soda.... Formaldehyde solution, U.S.P S.D.A. 22, 38-C, 38-D. Gasoline C.D.A. 18, 19; S.D.A. 28-A. Gasoline, unleaded C.D...

Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins.

PubMed

Plant, Ewan P; Rakauskaite, Rasa; Taylor, Deborah R; Dinman, Jonathan D

2010-05-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

1984 CRC (Coordinating Research Council) Octane Number Requirement Survey.

DTIC Science & Technology

1985-12-01

Knocking IAE 230A3/LAE 230A3 14 13 5 38.5 (Knock Sensor, Max. [high]) NAR F25A3/HAR F25A3/ IAR F25A3/LAR F25A3 12 11 8 72.7 NAX 228A3/HAX 228A3 13 10 6...102 -- 14 86 91.4 10.6 103 -- 5 95 92.6 10.4 7 C- 3 TABLE C-111 -" - 44. SENSITIVITIES OF 1984 AND 1983 FBRU AND FBRSU FUELS FBRU FBRSJ Research...c CA LA V) - I- 00 co =I CJ 9 Lo a, INN wo. I"L co 0 I- J o󈧄A ON m ~ al c m M. CDj CDa *l 14 00 1 I0 ff Ln tD1 00 ON Q𔃾.036 P-04 -, LOJ L- %% W D m

Protein synthesis in sperm: dialog between mitochondria and cytoplasm.

PubMed

Gur, Yael; Breitbart, Haim

2008-01-30

Ejaculated sperm are capable of using mRNAs transcripts for protein translation during the final maturation steps before fertilization. In a capacitation-dependent process, nuclear-encoded mRNAs are translated by mitochondrial-type ribosomes while the cytoplasmic translation machinery is not involved. Our findings suggest that new proteins are synthesized to replace degraded proteins while swimming and waiting in the female reproductive tract before fertilization, or produced due to the specific needs of the capacitating spermatozoa. In addition, a growing number of articles have reported evidence for the correlation of nuclear-encoded mRNA and protein synthesis in somatic mitochondria. It is known that all of the proteins necessary for the replication, transcription and translation of the genes encoded in mtDNA are now encoded in the nuclear genome. This genetic investment is far out of proportion to the number of proteins involved, as there have been multiple movements and duplications of genes. However, the evolutionary retention (or secondary uptake) of the mitochondrial machinery for translation of nuclear-encoded mRNAs may shed light on this paradox.

Human AZU-1 gene, variants thereof and expressed gene products

DOEpatents

Chen, Huei-Mei; Bissell, Mina

2004-06-22

A human AZU-1 gene, mutants, variants and fragments thereof. Protein products encoded by the AZU-1 gene and homologs encoded by the variants of AZU-1 gene acting as tumor suppressors or markers of malignancy progression and tumorigenicity reversion. Identification, isolation and characterization of AZU-1 and AZU-2 genes localized to a tumor suppressive locus at chromosome 10q26, highly expressed in nonmalignant and premalignant cells derived from a human breast tumor progression model. A recombinant full length protein sequences encoded by the AZU-1 gene and nucleotide sequences of AZU-1 and AZU-2 genes and variant and fragments thereof. Monoclonal or polyclonal antibodies specific to AZU-1, AZU-2 encoded protein and to AZU-1, or AZU-2 encoded protein homologs.

The Bean pod mottle virus RNA2-encoded 58-kilodalton protein P58 is required in cis for RNA2 accumulation

USDA-ARS?s Scientific Manuscript database

Bean pod mottle virus (BPMV) is a bipartite, positive sense (+) RNA plant virus in the Secoviridae family. Its RNA1 encodes proteins required for genome replication, whereas RNA2 primarily encodes proteins needed for virion assembly and cell-to-cell movement. However, the function of a 58 kilo-dalto...

Characterization of the 5’- and 3’-terminal subgenomic RNAs produced by a capillovirus: evidence for a CP subgenomic RNA

USDA-ARS?s Scientific Manuscript database

The members of Capillovirus genus encode two overlapping open reading frames (ORFs): ORF1 encodes a large polyprotein containing the domains of replication-associated proteins plus a coat protein (CP), and ORF2 encodes a movement protein, located within ORF1 in a different reading frame. Organizatio...

Protection of Mice from Fatal Measles Encephalitis by Vaccination with Vaccinia Virus Recombinants Encoding Either the Hemagglutinin or the Fusion Protein

NASA Astrophysics Data System (ADS)

Drillien, Robert; Spehner, Daniele; Kirn, Andre; Giraudon, Pascale; Buckland, Robin; Wild, Fabian; Lecocq, Jean-Pierre

1988-02-01

Vaccinia virus recombinants encoding the hemagglutinin or fusion protein of measles virus have been constructed. Infection of cell cultures with the recombinants led to the synthesis of authentic measles proteins as judged by their electrophoretic mobility, recognition by antibodies, glycosylation, proteolytic cleavage, and presentation on the cell surface. Mice vaccinated with a single dose of the recombinant encoding the hemagglutinin protein developed antibodies capable of both inhibiting hemagglutination activity and neutralizing measles virus, whereas animals vaccinated with the recombinant encoding the fusion protein developed measles neutralizing antibodies. Mice vaccinated with either of the recombinants resisted a normally lethal intracerebral inoculation of a cell-associated measles virus subacute sclerosing panencephalitis strain.

Identification of a maize nucleic acid-binding protein (NBP) belonging to a family of nuclear-encoded chloroplast proteins.

PubMed Central

Cook, W B; Walker, J C

1992-01-01

A cDNA encoding a nuclear-encoded chloroplast nucleic acid-binding protein (NBP) has been isolated from maize. Identified as an in vitro DNA-binding activity, NBP belongs to a family of nuclear-encoded chloroplast proteins which share a common domain structure and are thought to be involved in posttranscriptional regulation of chloroplast gene expression. NBP contains an N-terminal chloroplast transit peptide, a highly acidic domain and a pair of ribonucleoprotein consensus sequence domains. NBP is expressed in a light-dependent, organ-specific manner which is consistent with its involvement in chloroplast biogenesis. The relationship of NBP to the other members of this protein family and their possible regulatory functions are discussed. Images PMID:1346929

Genome of turbot rhabdovirus exhibits unusual non-coding regions and an additional ORF that could be expressed in fish cell.

PubMed

Zhu, Ruo-Lin; Lei, Xiao-Ying; Ke, Fei; Yuan, Xiu-Ping; Zhang, Qi-Ya

2011-02-01

Genomic sequence of Scophthalmus maximus rhabdovirus (SMRV) isolated from diseased turbot has been characterized. The complete genome of SMRV comprises 11,492 nucleotides and encodes five typical rhabdovirus genes N, P, M, G and L. In addition, two open reading frames (ORF) are predicted overlapping with P gene, one upstream of P and smaller than P (temporarily called Ps), and another in P gene which may encodes a protein similar to the vesicular stomatitis virus C protein. The C ORF is contained within the P ORF. The five typical proteins share the highest sequence identities (48.9%) with the corresponding proteins of rhabdoviruses in genus Vesiculovirus. Phylogenetic analysis of partial L protein sequence indicates that SMRV is close to genus Vesiculovirus. The first 13 nucleotides at the ends of the SMRV genome are absolutely inverse complementarity. The gene junctions between the five genes show conserved polyadenylation signal (CATGA(7)) and intergenic dinucleotide (CT) followed by putative transcription initiation sequence A(A/G)(C/G)A(A/G/T), which are different from known rhabdoviruses. The entire Ps ORF was cloned and expressed, and used to generate polyclonal antibody in mice. One obvious band could be detected in SMRV-infected carp leucocyte cells (CLCs) by anti-Ps/C serum via Western blot, and the subcellular localization of Ps-GFP fusion protein exhibited cytoplasm distribution as multiple punctuate or doughnut shaped foci of uneven size. Copyright © 2010 Elsevier B.V. All rights reserved.

Constitutive activation of NF-kappa B and secretion of interleukin-8 induced by the G protein-coupled receptor of Kaposi's sarcoma-associated herpesvirus involve G alpha(13) and RhoA.

PubMed

Shepard, L W; Yang, M; Xie, P; Browning, D D; Voyno-Yasenetskaya, T; Kozasa, T; Ye, R D

2001-12-07

The Kaposi's sarcoma herpesvirus (KSHV) open reading frame 74 encodes a G protein-coupled receptor (GPCR) for chemokines. Exogenous expression of this constitutively active GPCR leads to cell transformation and vascular overgrowth characteristic of Kaposi's sarcoma. We show here that expression of KSHV-GPCR in transfected cells results in constitutive transactivation of nuclear factor kappa B (NF-kappa B) and secretion of interleukin-8, and this response involves activation of G alpha(13) and RhoA. The induced expression of a NF-kappa B luciferase reporter was partially reduced by pertussis toxin and the G beta gamma scavenger transducin, and enhanced by co-expression of G alpha(13) and to a lesser extent, G alpha(q). These results indicate coupling of KSHV-GPCR to multiple G proteins for NF-kappa B activation. Expression of KSHV-GPCR led to stress fiber formation in NIH 3T3 cells. To examine the involvement of the G alpha(13)-RhoA pathway in KSHV-GPCR-mediated NF-kappa B activation, HeLa cells were transfected with KSHV-GPCR alone and in combination with the regulator of G protein signaling (RGS) from p115RhoGEF or a dominant negative RhoA(T19N). Both constructs, as well as the C3 exoenzyme from Clostritium botulinum, partially reduced NF-kappa B activation by KSHV-GPCR, and by a constitutively active G alpha(13)(Q226L). KSHV-GPCR-induced NF-kappa B activation is accompanied by increased secretion of IL-8, a function mimicked by the activated G alpha(13) but not by an activated G alpha(q)(Q209L). These results suggest coupling of KSHV-GPCR to the G alpha(13)-RhoA pathway in addition to other G proteins.

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

Caberoy, Nora B.; Zhou, Yixiong; Alvarado, Gabriela

To efficiently elucidate the biological roles of phosphatidylserine (PS), we developed open-reading-frame (ORF) phage display to identify PS-binding proteins. The procedure of phage panning was optimized with a phage clone expressing MFG-E8, a well-known PS-binding protein. Three rounds of phage panning with ORF phage display cDNA library resulted in {approx}300-fold enrichment in PS-binding activity. A total of 17 PS-binding phage clones were identified. Unlike phage display with conventional cDNA libraries, all 17 PS-binding clones were ORFs encoding 13 real proteins. Sequence analysis revealed that all identified PS-specific phage clones had dimeric basic amino acid residues. GST fusion proteins were expressedmore » for 3 PS-binding proteins and verified for their binding activity to PS liposomes, but not phosphatidylcholine liposomes. These results elucidated previously unknown PS-binding proteins and demonstrated that ORF phage display is a versatile technology capable of efficiently identifying binding proteins for non-protein molecules like PS.« less

Cytochrome b5 gene and protein of Candida tropicalis and methods relating thereto

DOEpatents

Craft, David L.; Madduri, Krishna M.; Loper, John C.

2003-01-01

A novel gene has been isolated which encodes cytochrome b5 (CYTb5) protein of the .omega.-hydroxylase complex of C. tropicalis 20336. Vectors including this gene, and transformed host cells are provided. Methods of increasing the production of a CYTb5 protein are also provided which involve transforming a host cell with a gene encoding this protein and culturing the cells. Methods of increasing the production of a dicarboxylic acid are also provided which involve increasing in the host cell the number of genes encoding this protein.

Common Variants in the MKL1 Gene Confer Risk of Schizophrenia

PubMed Central

Luo, Xiong-jian; Huang, Liang; van den Oord, Edwin J.; Aberg, Karolina A.; Gan, Lin; Zhao, Zhongming; Yao, Yong-Gang

2015-01-01

Genome-wide association studies (GWAS) of schizophrenia have identified multiple risk variants with robust association signals for schizophrenia. However, these variants could explain only a small proportion of schizophrenia heritability. Furthermore, the effect size of these risk variants is relatively small (eg, most of them had an OR less than 1.2), suggesting that additional risk variants may be detected when increasing sample size in analysis. Here, we report the identification of a genome-wide significant schizophrenia risk locus at 22q13.1 by combining 2 large-scale schizophrenia cohort studies. Our meta-analysis revealed that 7 single nucleotide polymorphism (SNPs) on chromosome 22q13.1 reached the genome-wide significance level (P < 5.0×10–8) in the combined samples (a total of 38441 individuals). Among them, SNP rs6001946 had the most significant association with schizophrenia (P = 2.04×10–8). Interestingly, all 7 SNPs are in high linkage disequilibrium and located in the MKL1 gene. Expression analysis showed that MKL1 is highly expressed in human and mouse brains. We further investigated functional links between MKL1 and proteins encoded by other schizophrenia susceptibility genes in the whole human protein interaction network. We found that MKL1 physically interacts with GSK3B, a protein encoded by a well-characterized schizophrenia susceptibility gene. Collectively, our results revealed that genetic variants in MKL1 might confer risk to schizophrenia. Further investigation of the roles of MKL1 in the pathogenesis of schizophrenia is warranted. PMID:25380769

Rotor-generated unsteady aerodynamic interactions in a 1½ stage compressor

NASA Astrophysics Data System (ADS)

Papalia, John J.

Because High Cycle Fatigue (HCF) remains the predominant surprise failure mode in gas turbine engines, HCF avoidance design systems are utilized to identify possible failures early in the engine development process. A key requirement of these analyses is accurate determination of the aerodynamic forcing function and corresponding airfoil unsteady response. The current study expands the limited experimental database of blade row interactions necessary for calibration of predictive HCF analyses, with transonic axial-flow compressors of particular interest due to the presence of rotor leading edge shocks. The majority of HCF failures in aircraft engines occur at off-design operating conditions. Therefore, experiments focused on rotor-IGV interactions at off-design are conducted in the Purdue Transonic Research Compressor. The rotor-generated IGV unsteady aerodynamics are quantified when the IGV reset angle causes the vane trailing edge to be nearly aligned with the rotor leading edge shocks. A significant vane response to the impulsive static pressure perturbation associated with a shock is evident in the point measurements at 90% span, with details of this complex interaction revealed in the corresponding time-variant vane-to-vane flow field data. Industry wide implementation of Controlled Diffusion Airfoils (CDA) in modern compressors motivated an investigation of upstream propagating CDA rotor-generated forcing functions. Whole field velocity measurements in the reconfigured Purdue Transonic Research Compressor along the design speedline reveal steady loading had a considerable effect on the rotor shock structure. A detached rotor leading edge shock exists at low loading, with an attached leading edge and mid-chord suction surface normal shock present at nominal loading. These CDA forcing functions are 3--4 times smaller than those generated by the baseline NACA 65 rotor at their respective operating points. However, the IGV unsteady aerodynamic response to the CDA forcing functions remains significant. The intra-vane transport of NACA 65 and CDA rotor wakes is also observed within the time-variant passage velocity data. In general, the wake width and decay rate increase with rotor speed and compressor steady loading respectively.

The Madden-Julian Oscillation in the NCAR Community Earth System Model Coupled Data Assimilation System

NASA Astrophysics Data System (ADS)

Chatterjee, A.; Anderson, J. L.; Moncrieff, M.; Collins, N.; Danabasoglu, G.; Hoar, T.; Karspeck, A. R.; Neale, R. B.; Raeder, K.; Tribbia, J. J.

2014-12-01

We present a quantitative evaluation of the simulated MJO in analyses produced with a coupled data assimilation (CDA) framework developed at the National Center for Atmosphere Research. This system is based on the Community Earth System Model (CESM; previously known as the Community Climate System Model -CCSM) interfaced to a community facility for ensemble data assimilation (Data Assimilation Research Testbed - DART). The system (multi-component CDA) assimilates data into each of the respective ocean/atmosphere/land model components during the assimilation step followed by an exchange of information between the model components during the forecast step. Note that this is an advancement over many existing prototypes of coupled data assimilation systems, which typically assimilate observations only in one of the model components (i.e., single-component CDA). The more realistic treatment of air-sea interactions and improvements to the model mean state in the multi-component CDA recover many aspects of MJO representation, from its space-time structure and propagation (see Figure 1) to the governing relationships between precipitation and sea surface temperature on intra-seasonal scales. Standard qualitative and process-based diagnostics identified by the MJO Task Force (currently under the auspices of the Working Group on Numerical Experimentation) have been used to detect the MJO signals across a suite of coupled model experiments involving both multi-component and single-component DA experiments as well as a free run of the coupled CESM model (i.e., CMIP5 style without data assimilation). Short predictability experiments during the boreal winter are used to demonstrate that the decay rates of the MJO convective anomalies are slower in the multi-component CDA system, which allows it to retain the MJO dynamics for a longer period. We anticipate that the knowledge gained through this study will enhance our understanding of the MJO feedback mechanisms across the air-sea interface, especially regarding ocean impacts on the MJO as well as highlight the capability of coupled data assimilation systems for related tropical intraseasonal variability predictions.

Pathogenic Leptospira species express surface-exposed proteins belonging to the bacterial immunoglobulin superfamily

PubMed Central

Matsunaga, James; Barocchi, Michele A.; Croda, Julio; Young, Tracy A.; Sanchez, Yolanda; Siqueira, Isadora; Bolin, Carole A.; Reis, Mitermayer G.; Riley, Lee W.; Haake, David A.; Ko, Albert I.

2005-01-01

Summary Proteins with bacterial immunoglobulin-like (Big) domains, such as the Yersinia pseudotuberculosis invasin and Escherichia coli intimin, are surface-expressed proteins that mediate host mammalian cell invasion or attachment. Here, we report the identification and characterization of a new family of Big domain proteins, referred to as Lig (leptospiral Ig-like) proteins, in pathogenic Leptospira. Screening of L. interrogans and L. kirschneri expression libraries with sera from leptospirosis patients identified 13 lambda phage clones that encode tandem repeats of the 90 amino acid Big domain. Two lig genes, designated ligA and ligB, and one pseudo-gene, ligC, were identified. The ligA and ligB genes encode amino-terminal lipoprotein signal peptides followed by 10 or 11 Big domain repeats and, in the case of ligB, a unique carboxy-terminal non-repeat domain. The organization of ligC is similar to that of ligB but contains mutations that disrupt the reading frame. The lig sequences are present in pathogenic but not saprophytic Leptospira species. LigA and LigB are expressed by a variety of virulent leptospiral strains. Loss of Lig protein and RNA transcript expression is correlated with the observed loss of virulence during culture attenuation of pathogenic strains. High-pressure freeze substitution followed by immunocytochemical electron microscopy confirmed that the Lig proteins were localized to the bacterial surface. Immunoblot studies with patient sera found that the Lig proteins are a major antigen recognized during the acute host infection. These observations demonstrate that the Lig proteins are a newly identified surface protein of pathogenic Leptospira, which by analogy to other bacterial immunoglobulin superfamily virulence factors, may play a role in host cell attachment and invasion during leptospiral pathogenesis. PMID:12890019

Pathogenic Leptospira species express surface-exposed proteins belonging to the bacterial immunoglobulin superfamily.

PubMed

Matsunaga, James; Barocchi, Michele A; Croda, Julio; Young, Tracy A; Sanchez, Yolanda; Siqueira, Isadora; Bolin, Carole A; Reis, Mitermayer G; Riley, Lee W; Haake, David A; Ko, Albert I

2003-08-01

Proteins with bacterial immunoglobulin-like (Big) domains, such as the Yersinia pseudotuberculosis invasin and Escherichia coli intimin, are surface-expressed proteins that mediate host mammalian cell invasion or attachment. Here, we report the identification and characterization of a new family of Big domain proteins, referred to as Lig (leptospiral Ig-like) proteins, in pathogenic Leptospira. Screening of L. interrogans and L. kirschneri expression libraries with sera from leptospirosis patients identified 13 lambda phage clones that encode tandem repeats of the 90 amino acid Big domain. Two lig genes, designated ligA and ligB, and one pseudogene, ligC, were identified. The ligA and ligB genes encode amino-terminal lipoprotein signal peptides followed by 10 or 11 Big domain repeats and, in the case of ligB, a unique carboxy-terminal non-repeat domain. The organization of ligC is similar to that of ligB but contains mutations that disrupt the reading frame. The lig sequences are present in pathogenic but not saprophytic Leptospira species. LigA and LigB are expressed by a variety of virulent leptospiral strains. Loss of Lig protein and RNA transcript expression is correlated with the observed loss of virulence during culture attenuation of pathogenic strains. High-pressure freeze substitution followed by immunocytochemical electron microscopy confirmed that the Lig proteins were localized to the bacterial surface. Immunoblot studies with patient sera found that the Lig proteins are a major antigen recognized during the acute host infection. These observations demonstrate that the Lig proteins are a newly identified surface protein of pathogenic Leptospira, which by analogy to other bacterial immunoglobulin superfamily virulence factors, may play a role in host cell attachment and invasion during leptospiral pathogenesis.

1,3,4-Oxadiazole containing silanes as novel hosts for blue phosphorescent organic light emitting diodes.

PubMed

Leung, Man-kit; Yang, Wan-Hsi; Chuang, Ching-Nan; Lee, Jiun-Haw; Lin, Chi-Feng; Wei, Mao-Kuo; Liu, Yu-Hao

2012-10-05

Five rigid oxadiazole (OXD) containing silanes, denoted 1-5, have been developed with high morphological stability. Disruption of the π-aromatic conjugation by introduction of Si atoms leads to a large band gap and high triplet energy. Among the OXDs we studied, 2,5-bis(triphenylsilylphenyl)-1,3,4-oxadiazole 5 is the best host for FIrpic, with a phosphorescent organic light emitting diode (PHOLED) turn-on voltage of 6.9 V, maximum luminance of 5124 cd/m(2), current efficiency of 39.9 cd/A, and external quantum efficiency of 13.1%. Special molecular stacking in the single crystal of 5 was discussed.

Identification of the Mamestra configurata (Lepidoptera: Noctuidae) peritrophic matrix proteins and enzymes involved in peritrophic matrix chitin metabolism.

PubMed

Toprak, Umut; Erlandson, Martin; Baldwin, Doug; Karcz, Steve; Wan, Lianglu; Coutu, Cathy; Gillott, Cedric; Hegedus, Dwayne D

2016-10-01

The peritrophic matrix (PM) is essential for insect digestive system physiology as it protects the midgut epithelium from damage by food particles, pathogens, and toxins. The PM is also an attractive target for development of new pest control strategies due to its per os accessibility. To understand how the PM performs these functions, the molecular architecture of the PM was examined using genomic and proteomic approaches in Mamestra configurata (Lepidoptera: Noctuidae), a major pest of cruciferous oilseed crops in North America. Liquid chromatography-tandem mass spectrometry analyses of the PM identified 82 proteins classified as: (i) peritrophins, including a new class with a CBDIII domain; (ii) enzymes involved in chitin modification (chitin deacetylases), digestion (serine proteases, aminopeptidases, carboxypeptidases, lipases and α-amylase) or other reactions (β-1,3-glucanase, alkaline phosphatase, dsRNase, astacin, pantetheinase); (iii) a heterogenous group consisting of polycalin, REPATs, serpin, C-Type lectin and Lsti99/Lsti201 and 3 novel proteins without known orthologs. The genes encoding PM proteins were expressed predominantly in the midgut. cDNAs encoding chitin synthase-2 (McCHS-2), chitinase (McCHI), and β-N-acetylglucosaminidase (McNAG) enzymes, involved in PM chitin metabolism, were also identified. McCHS-2 expression was specific to the midgut indicating that it is responsible for chitin synthesis in the PM, the only chitinous material in the midgut. In contrast, the genes encoding the chitinolytic enzymes were expressed in multiple tissues. McCHS-2, McCHI, and McNAG were expressed in the midgut of feeding larvae, and NAG activity was present in the PM. This information was used to generate an updated model of the lepidopteran PM architecture. © 2015 Institute of Zoology, Chinese Academy of Sciences.

Rpl13a small nucleolar RNAs regulate systemic glucose metabolism

PubMed Central

Lee, Jiyeon; Harris, Alexis N.; Holley, Christopher L.; Mahadevan, Jana; Pyles, Kelly D.; Lavagnino, Zeno; Scherrer, David E.; Fujiwara, Hideji; Sidhu, Rohini; Zhang, Jessie; Huang, Stanley Ching-Cheng; Piston, David W.; Remedi, Maria S.; Urano, Fumihiko; Ory, Daniel S.

2016-01-01

Small nucleolar RNAs (snoRNAs) are non-coding RNAs that form ribonucleoproteins to guide covalent modifications of ribosomal and small nuclear RNAs in the nucleus. Recent studies have also uncovered additional non-canonical roles for snoRNAs. However, the physiological contributions of these small RNAs are largely unknown. Here, we selectively deleted four snoRNAs encoded within the introns of the ribosomal protein L13a (Rpl13a) locus in a mouse model. Loss of Rpl13a snoRNAs altered mitochondrial metabolism and lowered reactive oxygen species tone, leading to increased glucose-stimulated insulin secretion from pancreatic islets and enhanced systemic glucose tolerance. Islets from mice lacking Rpl13a snoRNAs demonstrated blunted oxidative stress responses. Furthermore, these mice were protected against diabetogenic stimuli that cause oxidative stress damage to islets. Our study illuminates a previously unrecognized role for snoRNAs in metabolic regulation. PMID:27820699

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

Molecular characterization and expression of the M6 gene of grass carp hemorrhage virus (GCHV), an aquareovirus.

PubMed

Qiu, T; Lu, R H; Zhang, J; Zhu, Z Y

2001-07-01

The complete nucleotide sequence of M6 gene of grass carp hemorrhage virus (GCHV) was determined. It is 2039 nucleotides in length and contains a single large open reading frame that could encode a protein of 648 amino acids with predicted molecular mass of 68.7 kDa. Amino acid sequence comparison revealed that the protein encoded by GCHV M6 is closely related to the protein mu1 of mammalian reovirus. The M6 gene, encoding the major outer-capsid protein, was expressed using the pET fusion protein vector in Escherichia coli and detected by Western blotting using chicken anti-GCHV immunoglobulin (IgY). The result indicates that the protein encoded by M6 may share a putative Asn-42-Pro-43 proteolytic cleavage site with mu1.

Two-dimensional over-all neutronics analysis of the ITER device

NASA Astrophysics Data System (ADS)

Zimin, S.; Takatsu, Hideyuki; Mori, Seiji; Seki, Yasushi; Satoh, Satoshi; Tada, Eisuke; Maki, Koichi

1993-07-01

The present work attempts to carry out a comprehensive neutronics analysis of the International Thermonuclear Experimental Reactor (ITER) developed during the Conceptual Design Activities (CDA). The two-dimensional cylindrical over-all calculational models of ITER CDA device including the first wall, blanket, shield, vacuum vessel, magnets, cryostat and support structures were developed for this purpose with a help of the DOGII code. Two dimensional DOT 3.5 code with the FUSION-40 nuclear data library was employed for transport calculations of neutron and gamma ray fluxes, tritium breeding ratio (TBR), and nuclear heating in reactor components. The induced activity calculational code CINAC was employed for the calculations of exposure dose rate after reactor shutdown around the ITER CDA device. The two-dimensional over-all calculational model includes the design specifics such as the pebble bed Li2O/Be layered blanket, the thin double wall vacuum vessel, the concrete cryostat integrated with the over-all ITER design, the top maintenance shield plug, the additional ring biological shield placed under the top cryostat lid around the above-mentioned top maintenance shield plug etc. All the above-mentioned design specifics were included in the employed calculational models. Some alternative design options, such as the water-rich shielding blanket instead of lithium-bearing one, the additional biological shield plug at the top zone between the poloidal field (PF) coil No. 5, and the maintenance shield plug, were calculated as well. Much efforts have been focused on analyses of obtained results. These analyses aimed to obtain necessary recommendations on improving the ITER CDA design.

Impact of Myopia on Corneal Biomechanics in Glaucoma and Nonglaucoma Patients

PubMed Central

Panpruk, Rawiphan; Manassakorn, Anita; Tantisevi, Visanee; Rojanapongpun, Prin; Hurst, Cameron P.; Lin, Shan C.

2017-01-01

Purpose We evaluated the impact of myopia on corneal biomechanical properties in primary open-angle glaucoma (POAG) and nonglaucoma patients, and the effect of modification of glaucoma on myopic eyes. Methods This cross-sectional study included 66 POAG eyes (33 myopia, 33 nonmyopia) and 66 normal eyes (33 myopia, 33 nonmyopia). Seven corneal biomechanical parameters were measured by ultra-high-speed Scheimpflug imaging, including corneal deformation amplitude (CDA), inward/outward corneal applanation length (ICA, OCA), inward/outward corneal velocity (ICV, OCV), radius, and peak distance (PD). Results Mean age (SD) of the 65 male (49%) and 67 female (51%) patients was 59 (9.82) years. Myopia was associated with significantly higher CDA (adjusted effect = 0.104, P = 0.001) and lower OCV (adjusted effect = −0.105, P < 0.001) in the POAG group. Within the nonglaucoma group, myopic eyes had a significantly lower OCV (adjusted effect = −0.086, P < 0.001) and higher CDA (adjusted effect = 0.079, P = 0.001). All parameters except PD suggested that glaucoma modified the effect of myopia on corneal biomechanics. Percentage differences in the adjusted myopic effect between POAG and nonglaucoma patients was 31.65, 27.27, 31.65, 50.00, 22.09, and 60.49 for CDA, ICA, OCA, ICV, OCV, and radius, respectively. Conclusions Myopia had a significant impact on corneal biomechanical properties in the POAG and nonglaucoma groups. The differences in corneal biomechanical parameters suggest that myopia is correlated with significantly lower ocular rigidity. POAG may enhance the effects of myopia on most of these parameters. PMID:28979996

Contralateral delay activity tracks the influence of Gestalt grouping principles on active visual working memory representations.

PubMed

Peterson, Dwight J; Gözenman, Filiz; Arciniega, Hector; Berryhill, Marian E

2015-10-01

Recent studies have demonstrated that factors influencing perception, such as Gestalt grouping cues, can influence the storage of information in visual working memory (VWM). In some cases, stationary cues, such as stimulus similarity, lead to superior VWM performance. However, the neural correlates underlying these benefits to VWM performance remain unclear. One neural index, the contralateral delay activity (CDA), is an event-related potential that shows increased amplitude according to the number of items held in VWM and asymptotes at an individual's VWM capacity limit. Here, we applied the CDA to determine whether previously reported behavioral benefits supplied by similarity, proximity, and uniform connectedness were reflected as a neural savings such that the CDA amplitude was reduced when these cues were present. We implemented VWM change-detection tasks with arrays including similarity and proximity (Experiment 1); uniform connectedness (Experiments 2a and 2b); and similarity/proximity and uniform connectedness (Experiment 3). The results indicated that when there was a behavioral benefit to VWM, this was echoed by a reduction in CDA amplitude, which suggests more efficient processing. However, not all perceptual grouping cues provided a VWM benefit in the same measure (e.g., accuracy) or of the same magnitude. We also found unexpected interactions between cues. We observed a mixed bag of effects, suggesting that these powerful perceptual grouping benefits are not as predictable in VWM. The current findings indicate that when grouping cues produce behavioral benefits, there is a parallel reduction in the neural resources required to maintain grouped items within VWM.

Contralateral delay activity tracks the influence of Gestalt grouping principles on active visual working memory representations

PubMed Central

Peterson, Dwight J.; Gözenman, Filiz; Arciniega, Hector; Berryhill, Marian E.

2015-01-01

Recent studies have demonstrated that factors influencing perception, such as Gestalt grouping cues, can influence the storage of information in visual working memory (VWM). In some cases, stationary cues such as stimulus similarity lead to superior VWM performance. However, the neural correlates underlying these benefits to VWM performance remain unclear. One neural index, the contralateral delay activity (CDA) is an event-related potential that shows increased amplitude according to the number of items held in VWM and asymptotes at an individual’s VWM capacity limit. Here, we applied the CDA to determine whether previously reported behavioral benefits supplied by similarity, proximity and uniform connectedness were reflected as a neural savings such that the CDA amplitude was reduced when these cues were present. We implemented VWM change detection tasks with arrays including similarity and proximity (Experiment 1); uniform connectedness (Experiments 2a and 2b); similarity/proximity and uniform connectedness (Experiment 3). The results indicated that when there was a behavioral benefit to VWM, this was echoed by a reduction in CDA amplitude, which suggests more efficient processing. However, not all perceptual grouping cues provided a VWM benefit in the same measure (e.g., accuracy) or of the same magnitude. We also found unexpected interactions between cues. We observed a mixed bag of effects, suggesting that these powerful perceptual grouping benefits are not as predictable in VWM. The current findings indicate that, when grouping cues produce behavioral benefits, there is a parallel reduction in the neural resources required to maintain grouped items within VWM. PMID:26018644

DNA encoding a DNA repair protein

DOEpatents

Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

2006-08-15

An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

Rgs13 constrains early B cell responses and limits germinal center sizes.

PubMed

Hwang, Il-Young; Hwang, Kyung-Sun; Park, Chung; Harrison, Kathleen A; Kehrl, John H

2013-01-01

Germinal centers (GCs) are microanatomic structures that develop in secondary lymphoid organs in response to antigenic stimulation. Within GCs B cells clonally expand and their immunoglobulin genes undergo class switch recombination and somatic hypermutation. Transcriptional profiling has identified a number of genes that are prominently expressed in GC B cells. Among them is Rgs13, which encodes an RGS protein with a dual function. Its canonical function is to accelerate the intrinsic GTPase activity of heterotrimeric G-protein α subunits at the plasma membrane, thereby limiting heterotrimeric G-protein signaling. A unique, non-canonical function of RGS13 occurs following translocation to the nucleus, where it represses CREB transcriptional activity. The functional role of RGS13 in GC B cells is unknown. To create a surrogate marker for Rgs13 expression and a loss of function mutation, we inserted a GFP coding region into the Rgs13 genomic locus. Following immunization GFP expression rapidly increased in activated B cells, persisted in GC B cells, but declined in newly generated memory B and plasma cells. Intravital microscopy of the inguinal lymph node (LN) of immunized mice revealed the rapid appearance of GFP(+) cells at LN interfollicular regions and along the T/B cell borders, and eventually within GCs. Analysis of WT, knock-in, and mixed chimeric mice indicated that RGS13 constrains extra-follicular plasma cell generation, GC size, and GC B cell numbers. Analysis of select cell cycle and GC specific genes disclosed an aberrant gene expression profile in the Rgs13 deficient GC B cells. These results indicate that RGS13, likely acting at cell membranes and in nuclei, helps coordinate key decision points during the expansion and differentiation of naive B cells.

Automatic Preocessing of Impact Ionization Mass Spectra Obtained by Cassini CDA

NASA Astrophysics Data System (ADS)

Villeneuve, M.

2015-12-01

Since Cassini's arrival at Saturn in 2004, the Comic Dust Analyzer (CDA) has recorded nearly 200,000 mass spectra of dust particles. A majority of this data has been collected in Saturn's diffuse E ring where sodium salts embedded in water ice particles indicate that many particles are in fact frozen droplets from Enceladus' subsurface ocean that have been expelled from cracks in the icy crust. So far only a small fraction of the obtained spectra have been processed because the steps in processing the spectra require human manipulation. We developed an automatic processing pipeline for CDA mass spectra which will consistently analyze this data. The preprocessing steps are to de-noise the spectra, determine and remove the baseline, calculate the correct stretch parameter, and finally to identify elements and compounds in the spectra. With the E ring constantly evolving due to embedded active moons, this data will provide valuable information about the source of the E ring, the subsurface of Saturn's ice moon Enceladus, as well as about the dynamics of the ring itself.

Ultrahigh-efficiency solution-processed simplified small-molecule organic light-emitting diodes using universal host materials

PubMed Central

Han, Tae-Hee; Choi, Mi-Ri; Jeon, Chan-Woo; Kim, Yun-Hi; Kwon, Soon-Ki; Lee, Tae-Woo

2016-01-01

Although solution processing of small-molecule organic light-emitting diodes (OLEDs) has been considered as a promising alternative to standard vacuum deposition requiring high material and processing cost, the devices have suffered from low luminous efficiency and difficulty of multilayer solution processing. Therefore, high efficiency should be achieved in simple-structured small-molecule OLEDs fabricated using a solution process. We report very efficient solution-processed simple-structured small-molecule OLEDs that use novel universal electron-transporting host materials based on tetraphenylsilane with pyridine moieties. These materials have wide band gaps, high triplet energy levels, and good solution processabilities; they provide balanced charge transport in a mixed-host emitting layer. Orange-red (~97.5 cd/A, ~35.5% photons per electron), green (~101.5 cd/A, ~29.0% photons per electron), and white (~74.2 cd/A, ~28.5% photons per electron) phosphorescent OLEDs exhibited the highest recorded electroluminescent efficiencies of solution-processed OLEDs reported to date. We also demonstrate a solution-processed flexible solid-state lighting device as a potential application of our devices. PMID:27819053

Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis

DOE PAGES

Plett, Jonathan M.; Yin, Hengfu; Mewalal, Ritesh; ...

2017-03-23

During symbiosis, organisms use a range of metabolic and protein-based signals to communicate. Of these protein signals, one class is defined as ‘effectors’, i.e., small secreted proteins (SSPs) that cause phenotypical and physiological changes in another organism. To date, protein-based effectors have been described in aphids, nematodes, fungi and bacteria. Using RNA sequencing of Populus trichocarpa roots in mutualistic symbiosis with the ectomycorrhizal fungus Laccaria bicolor, we sought to determine if host plants also contain genes encoding effector-like proteins. We identified 417 plant-encoded putative SSPs that were significantly regulated during this interaction, including 161 SSPs specific to P. trichocarpa andmore » 15 SSPs exhibiting expansion in Populus and closely related lineages. We demonstrate that a subset of these SSPs can enter L. bicolor hyphae, localize to the nucleus and affect hyphal growth and morphology. Finally, we conclude that plants encode proteins that appear to function as effector proteins that may regulate symbiotic associations.« less

Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis

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

Plett, Jonathan M.; Yin, Hengfu; Mewalal, Ritesh

During symbiosis, organisms use a range of metabolic and protein-based signals to communicate. Of these protein signals, one class is defined as ‘effectors’, i.e., small secreted proteins (SSPs) that cause phenotypical and physiological changes in another organism. To date, protein-based effectors have been described in aphids, nematodes, fungi and bacteria. Using RNA sequencing of Populus trichocarpa roots in mutualistic symbiosis with the ectomycorrhizal fungus Laccaria bicolor, we sought to determine if host plants also contain genes encoding effector-like proteins. We identified 417 plant-encoded putative SSPs that were significantly regulated during this interaction, including 161 SSPs specific to P. trichocarpa andmore » 15 SSPs exhibiting expansion in Populus and closely related lineages. We demonstrate that a subset of these SSPs can enter L. bicolor hyphae, localize to the nucleus and affect hyphal growth and morphology. Finally, we conclude that plants encode proteins that appear to function as effector proteins that may regulate symbiotic associations.« less

Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages.

PubMed Central

Vasala, A; Dupont, L; Baumann, M; Ritzenthaler, P; Alatossava, T

1993-01-01

Virulent phage LL-H and temperate phage mv4 are two related bacteriophages of Lactobacillus delbrueckii. The gene clusters encoding structural proteins of these two phages have been sequenced and further analyzed. Six open reading frames (ORF-1 to ORF-6) were detected. Protein sequencing and Western immunoblotting experiments confirmed that ORF-3 (g34) encoded the main capsid protein Gp34. The presence of a putative late promoter in front of the phage LL-H g34 gene was suggested by primer extension experiments. Comparative sequence analysis between phage LL-H and phage mv4 revealed striking similarities in the structure and organization of this gene cluster, suggesting that the genes encoding phage structural proteins belong to a highly conservative module. Images PMID:8497043

Three copies of a single protein II-encoding sequence in the genome of Neisseria gonorrhoeae JS3: evidence for gene conversion and gene duplication.

PubMed

van der Ley, P

1988-11-01

Gonococci express a family of related outer membrane proteins designated protein II (P.II). These surface proteins are subject to both phase variation and antigenic variation. The P.II gene repertoire of Neisseria gonorrhoeae strain JS3 was found to consist of at least ten genes, eight of which were cloned. Sequence analysis and DNA hybridization studies revealed that one particular P.II-encoding sequence is present in three distinct, but almost identical, copies in the JS3 genome. These genes encode the P.II protein that was previously identified as P.IIc. Comparison of their sequences shows that the multiple copies of this P.IIc-encoding gene might have been generated by both gene conversion and gene duplication.

Comparative differential gene expression analysis of nucleus-encoded proteins for Rafflesia cantleyi against Arabidopsis thaliana

NASA Astrophysics Data System (ADS)

Ng, Siuk-Mun; Lee, Xin-Wei; Wan, Kiew-Lian; Firdaus-Raih, Mohd

2015-09-01

Regulation of functional nucleus-encoded proteins targeting the plastidial functions was comparatively studied for a plant parasite, Rafflesia cantleyi versus a photosynthetic plant, Arabidopsis thaliana. This study involved two species of different feeding modes and different developmental stages. A total of 30 nucleus-encoded proteins were found to be differentially-regulated during two stages in the parasite; whereas 17 nucleus-encoded proteins were differentially-expressed during two developmental stages in Arabidopsis thaliana. One notable finding observed for the two plants was the identification of genes involved in the regulation of photosynthesis-related processes where these processes, as expected, seem to be present only in the autotroph.

The Andes hantavirus NSs protein is expressed from the viral small mRNA by a leaky scanning mechanism.

PubMed

Vera-Otarola, Jorge; Solis, Loretto; Soto-Rifo, Ricardo; Ricci, Emiliano P; Pino, Karla; Tischler, Nicole D; Ohlmann, Théophile; Darlix, Jean-Luc; López-Lastra, Marcelo

2012-02-01

The small mRNA (SmRNA) of all Bunyaviridae encodes the nucleocapsid (N) protein. In 4 out of 5 genera in the Bunyaviridae, the smRNA encodes an additional nonstructural protein denominated NSs. In this study, we show that Andes hantavirus (ANDV) SmRNA encodes an NSs protein. Data show that the NSs protein is expressed in the context of an ANDV infection. Additionally, our results suggest that translation initiation from the NSs initiation codon is mediated by ribosomal subunits that have bypassed the upstream N protein initiation codon through a leaky scanning mechanism.

The Andes Hantavirus NSs Protein Is Expressed from the Viral Small mRNA by a Leaky Scanning Mechanism

PubMed Central

Vera-Otarola, Jorge; Solis, Loretto; Soto-Rifo, Ricardo; Ricci, Emiliano P.; Pino, Karla; Tischler, Nicole D.; Ohlmann, Théophile; Darlix, Jean-Luc

2012-01-01

The small mRNA (SmRNA) of all Bunyaviridae encodes the nucleocapsid (N) protein. In 4 out of 5 genera in the Bunyaviridae, the smRNA encodes an additional nonstructural protein denominated NSs. In this study, we show that Andes hantavirus (ANDV) SmRNA encodes an NSs protein. Data show that the NSs protein is expressed in the context of an ANDV infection. Additionally, our results suggest that translation initiation from the NSs initiation codon is mediated by ribosomal subunits that have bypassed the upstream N protein initiation codon through a leaky scanning mechanism. PMID:22156529

Solution NMR structure of hypothetical protein CV_2116 encoded by a viral prophage element in Chromobacterium violaceum.

PubMed

Yang, Yunhuang; Ramelot, Theresa A; Cort, John R; Garcia, Maite; Yee, Adelinda; Arrowsmith, Cheryl H; Kennedy, Michael A

2012-01-01

CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e(-07)) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and (13)C- and (15)N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β-sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.

Fusagene vectors: a novel strategy for the expression of multiple genes from a single cistron.

PubMed

Gäken, J; Jiang, J; Daniel, K; van Berkel, E; Hughes, C; Kuiper, M; Darling, D; Tavassoli, M; Galea-Lauri, J; Ford, K; Kemeny, M; Russell, S; Farzaneh, F

2000-12-01

Transduction of cells with multiple genes, allowing their stable and co-ordinated expression, is difficult with the available methodologies. A method has been developed for expression of multiple gene products, as fusion proteins, from a single cistron. The encoded proteins are post-synthetically cleaved and processed into each of their constituent proteins as individual, biologically active factors. Specifically, linkers encoding cleavage sites for the Golgi expressed endoprotease, furin, have been incorporated between in-frame cDNA sequences encoding different secreted or membrane bound proteins. With this strategy we have developed expression vectors encoding multiple proteins (IL-2 and B7.1, IL-4 and B7.1, IL-4 and IL-2, IL-12 p40 and p35, and IL-12 p40, p35 and IL-2 ). Transduction and analysis of over 100 individual clones, derived from murine and human tumour cell lines, demonstrate the efficient expression and biological activity of each of the encoded proteins. Fusagene vectors enable the co-ordinated expression of multiple gene products from a single, monocistronic, expression cassette.

Gene therapy-mediated delivery of targeted cytotoxins for glioma therapeutics

PubMed Central

Candolfi, Marianela; Xiong, Weidong; Yagiz, Kader; Liu, Chunyan; Muhammad, A. K. M. G.; Puntel, Mariana; Foulad, David; Zadmehr, Ali; Ahlzadeh, Gabrielle E.; Kroeger, Kurt M.; Tesarfreund, Matthew; Lee, Sharon; Debinski, Waldemar; Sareen, Dhruv; Svendsen, Clive N.; Rodriguez, Ron; Lowenstein, Pedro R.; Castro, Maria G.

2010-01-01

Restricting the cytotoxicity of anticancer agents by targeting receptors exclusively expressed on tumor cells is critical when treating infiltrative brain tumors such as glioblastoma multiforme (GBM). GBMs express an IL-13 receptor (IL13Rα2) that differs from the physiological IL4R/IL13R receptor. We developed a regulatable adenoviral vector (Ad.mhIL-4.TRE.mhIL-13-PE) encoding a mutated human IL-13 fused to Pseudomonas exotoxin (mhIL-13-PE) that specifically binds to IL13Rα2 to provide sustained expression, effective anti-GBM cytotoxicity, and minimal neurotoxicity. The therapeutic Ad also encodes mutated human IL-4 that binds to the physiological IL4R/IL13R without interacting with IL13Rα2, thus inhibiting potential binding of mhIL-13-PE to normal brain cells. Using intracranial GBM xenografts and syngeneic mouse models, we tested the Ad.mhIL-4.TRE.mhIL-13-PE and two protein formulations, hIL-13-PE used in clinical trials (Cintredekin Besudotox) and a second-generation mhIL-13-PE. Cintredekin Besudotox doubled median survival without eliciting long-term survival and caused severe neurotoxicity; mhIL-13-PE led to ∼40% long-term survival, eliciting severe neurological toxicity at the high dose tested. In contrast, Ad-mediated delivery of mhIL-13-PE led to tumor regression and long-term survival in over 70% of the animals, without causing apparent neurotoxicity. Although Cintredekin Besudotox was originally developed to target GBM, when tested in a phase III trial it failed to achieve clinical endpoints and revealed neurotoxicity. Limitations of Cintredekin Besudotox include its short half-life, which demanded frequent or continued administration, and binding to IL4R/IL13R, present in normal brain cells. These shortcomings were overcome by our therapeutic Ad, thus representing a significant advance in the development of targeted therapeutics for GBM. PMID:21030678

Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies

NASA Astrophysics Data System (ADS)

Zhang, Hao; Liu, Haijun; Blankenship, Robert E.; Gross, Michael L.

2016-01-01

We report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded "heavy" and "light" GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the "heavy" and "light" peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.

Isotope-encoded Carboxyl Group Footprinting for Mass Spectrometry-based Protein Conformational Studies

PubMed Central

Zhang, Hao; Liu, Haijun; Blankenship, Robert E.; Gross, Michael L.

2015-01-01

We report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded “heavy” and “light” GEE are used to label separately the two states of the Orange Carotenoid Protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the “heavy” and “light” peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting. PMID:26384685

Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies

DOE PAGES

Zhang, Hao; Liu, Haijun; Blankenship, Robert E.; ...

2015-09-18

Here, we report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded “heavy” and “light” GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the “heavy”more » and “light” peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.« less

Method for crater detection from digital topography data: interpolation based improvement and application to Lunar SELENE LALT data

NASA Astrophysics Data System (ADS)

Salamunićcar, Goran; Lončarić, Sven

Crater detection algorithms (CDAs) are an important subject of recent scientific research, as evident from the numerous recent publications in the field [ASR, 42 (1), 6-19]. In our previous work: (1) all the craters from the major currently available manually assembled catalogues have been merged into the catalogue with 57633 known Martian impact-craters [PSS, 56 (15), 1992-2008]; and (2) the CDA (developed to search for still uncatalogued impact-craters using 1/128° MOLA data) has been used to extend GT-57633 catalogue with 57592 additional craters resulting in GT-115225 catalog [GRS, 48 (5), in press, doi:10.1109/TGRS.2009.2037750]. On the other hand, the most complete catalog for Moon is the Morphological catalog of Lunar craters [edited by V. V. Shevchenko], which includes information on 14923 craters larger than 10km, visible on the lunar nearside and farside. This was the main motivation for application of our CDA to newly available Lunar SELENE LALT data. However, one of the main differences between MOLA and LALT data is the highest available resolution, wherein MOLA is available in 1/128° and LALT in 1/16° . The consequence is that only the largest craters can be detected using LALT dataset. However, this is still an excellent opportunity for further work on CDA in order to prepare it for forthcoming LRO LOLA data (which is expected to be in even better resolution than MOLA). The importance is in the fact that morphologically Martian and Lunar craters are not the same. Therefore, it is important to use the dataset for Moon in order to work on the CDA which is meant for detection of Lunar craters as well. In order to overcome the problem of currently available topography data in low resolution only, we particularly concentrated our work on the CDA's capability to detect very small craters relative to available dataset (up to the extreme case wherein the radius is as small as only two pixels). For this purpose, we improved the previous CDA with a new algorithm for sub-pixel interpolation of elevation samples, before subsequent computations. For elevation samples on larger distances from the crater's center, linear interpolation was used in order to speed-up the computations. For samples closer to the crater's center, the elevation value at the crater's center and relative sub-pixel distance to the selected elevation sample is additionally taken into account. The purpose is to compute the most realistic values for estimated elevation at a selected point. The results are, according to the initial visual evaluation, that numerous craters were successfully detected using SELENE LALT data.

Nopaline-type Ti plasmid of Agrobacterium encodes a VirF-like functional F-box protein.

PubMed

Lacroix, Benoît; Citovsky, Vitaly

2015-11-20

During Agrobacterium-mediated genetic transformation of plants, several bacterial virulence (Vir) proteins are translocated into the host cell to facilitate infection. One of the most important of such translocated factors is VirF, an F-box protein produced by octopine strains of Agrobacterium, which presumably facilitates proteasomal uncoating of the invading T-DNA from its associated proteins. The presence of VirF also is thought to be involved in differences in host specificity between octopine and nopaline strains of Agrobacterium, with the current dogma being that no functional VirF is encoded by nopaline strains. Here, we show that a protein with homology to octopine VirF is encoded by the Ti plasmid of the nopaline C58 strain of Agrobacterium. This protein, C58VirF, possesses the hallmarks of functional F-box proteins: it contains an active F-box domain and specifically interacts, via its F-box domain, with SKP1-like (ASK) protein components of the plant ubiquitin/proteasome system. Thus, our data suggest that nopaline strains of Agrobacterium have evolved to encode a functional F-box protein VirF.

DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315

PubMed Central

Polevoda, Bogdan; Joseph, Rebecca; Friedman, Alan E.; Bennett, Ryan P.; Greiner, Rebecca; De Zoysa, Thareendra; Stewart, Ryan A.; Smith, Harold C.

2017-01-01

APOBEC3G (A3G) belongs to the AID/APOBEC protein family of cytidine deaminases (CDA) that bind to nucleic acids. A3G mutates the HIV genome by deamination of dC to dU, leading to accumulation of virus-inactivating mutations. Binding to cellular RNAs inhibits A3G binding to substrate single-stranded (ss) DNA and CDA activity. Bulk RNA and substrate ssDNA bind to the same three A3G tryptic peptides (amino acids 181–194, 314–320, and 345–374) that form parts of a continuously exposed protein surface extending from the catalytic domain in the C terminus of A3G to its N terminus. We show here that the A3G tyrosines 181 and 315 directly cross-linked ssDNA. Binding experiments showed that a Y315A mutation alone significantly reduced A3G binding to both ssDNA and RNA, whereas Y181A and Y182A mutations only moderately affected A3G nucleic acid binding. Consistent with these findings, the Y315A mutant exhibited little to no deaminase activity in an Escherichia coli DNA mutator reporter, whereas Y181A and Y182A mutants retained ∼50% of wild-type A3G activity. The Y315A mutant also showed a markedly reduced ability to assemble into viral particles and had reduced antiviral activity. In uninfected cells, the impaired RNA-binding capacity of Y315A was evident by a shift of A3G from high-molecular-mass ribonucleoprotein complexes to low-molecular-mass complexes. We conclude that Tyr-315 is essential for coordinating ssDNA interaction with or entry to the deaminase domain and hypothesize that RNA bound to Tyr-315 may be sufficient to competitively inhibit ssDNA deaminase-dependent antiviral activity. PMID:28381554

Molecular identification of an ABC transporter complex for manganese: analysis of a cyanobacterial mutant strain impaired in the photosynthetic oxygen evolution process.

PubMed Central

Bartsevich, V V; Pakrasi, H B

1995-01-01

During photosynthesis, the photosystem II (PSII) pigment-protein complex catalyzes oxygen evolution, a reaction in which a four-manganese ensemble plays a crucial role. Using a newly developed selection scheme, we have isolated BP13, a random photosynthesis-deficient mutant strain of the cyanobacterium, Synechocystis 6803. This mutant grew slowly under photoautotrophic conditions, and had a low oxygen evolution activity. Biochemical analysis revealed that the lesion in this mutant strain had specifically affected the Mn ensemble in PSII. Interestingly, incubation of BP13 cells with micromolar levels of added Mn induced rapid recovery of oxygen evolution activity. The mutant could be complemented with a fragment of wild-type chromosomal DNA containing three closely linked genes, mntA, mntB and mntC. These gene products showed significant sequence similarities with polypeptide components of bacterial permeases that are members of the 'ABC (ATP binding cassette) superfamily' of transporter proteins. We determined that in the BP13 strain, a single nucleotide change had resulted in the replacement of an alanine by an aspartic acid residue in MntA, a soluble protein containing ATP binding motifs. These results suggest that the mntCAB gene cluster encodes polypeptide components of a Mn transporter, the first such protein complex identified in any organism. PMID:7743991

Microarray and differential display identify genes involved in jasmonate-dependent anther development.

PubMed

Mandaokar, Ajin; Kumar, V Dinesh; Amway, Matt; Browse, John

2003-07-01

Jasmonate (JA) is a signaling compound essential for anther development and pollen fertility in Arabidopsis. Mutations that block the pathway of JA synthesis result into male sterility. To understand the processes of anther and pollen maturation, we used microarray and differential display approaches to compare gene expression pattern in anthers of wild-type Arabidopsis and the male-sterile mutant, opr3. Microarray experiment revealed 25 genes that were up-regulated more than 1.8-fold in wild-type anthers as compared to mutant anthers. Experiments based on differential display identified 13 additional genes up-regulated in wild-type anthers compared to opr3 for a total of 38 differentially expressed genes. Searches of the Arabidopsis and non-redundant databases disclosed known or likely functions for 28 of the 38 genes identified, while 10 genes encode proteins of unknown function. Northern blot analysis of eight representative clones as probes confirmed low expression in opr3 anthers compared with wild-type anthers. JA responsiveness of these same genes was also investigated by northern blot analysis of anther RNA isolated from wild-type and opr3 plants, In these experiments, four genes were induced in opr3 anthers within 0.5-1 h of JA treatment while the remaining genes were up-regulated only 1-8 h after JA application. None of these genes was induced by JA in anthers of the coil mutant that is deficient in JA responsiveness. The four early-induced genes in opr3 encode lipoxygenase, a putative bHLH transcription factor, epithiospecifier protein and an unknown protein. We propose that these and other early components may be involved in JA signaling and in the initiation of developmental processes. The four late genes encode an extensin-like protein, a peptide transporter and two unknown proteins, which may represent components required later in anther and pollen maturation. Transcript profiling has provided a successful approach to identify genes involved in anther and pollen maturation in Arabidopsis.

The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

PubMed Central

Grohmann, L; Brennicke, A; Schuster, W

1992-01-01

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed. Images PMID:1454526

Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function

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

Lassila, JK; Bernstein, SL; Kinney, JN

Bacterial microconnpartnnents (BMCs) sequester enzymes from the cytoplasmic environment by encapsulation inside a selectively permeable protein shell. Bioinformatic analyses indicate that many bacteria encode BMC clusters of unknown function and with diverse combinations of shell proteins. The genome of the halophilic myxobacterium Haliangium ochraceum encodes one of the most atypical sets of shell proteins in terms of composition and primary structure. We found that microconnpartnnent shells could be purified in high yield when all seven H. ochraceum BMC shell genes were expressed from a synthetic operon in Escherichia coll. These shells differ substantially from previously isolated shell systems in thatmore » they are considerably smaller and more homogeneous, with measured diameters of 39 2 nm. The size and nearly uniform geometry allowed the development of a structural model for the shells composed of 260 hexagonal units and 13 hexagons per icosahedral face. We found that new proteins could be recruited to the shells by fusion to a predicted targeting peptide sequence, setting the stage for the use of these remarkably homogeneous shells for applications such as three-dimensional scaffolding and the construction of synthetic BMCs. Our results demonstrate the value of selecting from the diversity of BMC shell building blocks found in genomic sequence data for the construction of novel compartments. (C) 2014 Elsevier Ltd. All rights reserved.« less

Targeted Resequencing and Functional Testing Identifies Low-Frequency Missense Variants in the Gene Encoding GARP as Significant Contributors to Atopic Dermatitis Risk.

PubMed

Manz, Judith; Rodríguez, Elke; ElSharawy, Abdou; Oesau, Eva-Maria; Petersen, Britt-Sabina; Baurecht, Hansjörg; Mayr, Gabriele; Weber, Susanne; Harder, Jürgen; Reischl, Eva; Schwarz, Agatha; Novak, Natalija; Franke, Andre; Weidinger, Stephan

2016-12-01

Gene-mapping studies have consistently identified a susceptibility locus for atopic dermatitis and other inflammatory diseases on chromosome band 11q13.5, with the strongest association observed for a common variant located in an intergenic region between the two annotated genes C11orf30 and LRRC32. Using a targeted resequencing approach we identified low-frequency and rare missense mutations within the LRRC32 gene encoding the protein GARP, a receptor on activated regulatory T cells that binds latent transforming growth factor-β. Subsequent association testing in more than 2,000 atopic dermatitis patients and 2,000 control subjects showed a significant excess of these LRRC32 variants in individuals with atopic dermatitis. Structural protein modeling and bioinformatic analysis predicted a disruption of protein transport upon these variants, and overexpression assays in CD4 + CD25 - T cells showed a significant reduction in surface expression of the mutated protein. Consistently, flow cytometric (FACS) analyses of different T-cell subtypes obtained from atopic dermatitis patients showed a significantly reduced surface expression of GARP and a reduced conversion of CD4 + CD25 - T cells into regulatory T cells, along with lower expression of latency-associated protein upon stimulation in carriers of the LRRC32 A407T variant. These results link inherited disturbances of transforming growth factor-β signaling with atopic dermatitis risk. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

PubMed Central

2015-01-01

Phytopathogenic fungi form intimate associations with host plant species and cause disease. To be successful, fungal pathogens communicate with a susceptible host through the secretion of proteinaceous effectors, hydrolytic enzymes and metabolites. Sclerotinia sclerotiorum and Botrytis cinerea are economically important necrotrophic fungal pathogens that cause disease on numerous crop species. Here, a powerful bioinformatics pipeline was used to predict the refined S. sclerotiorum and B. cinerea secretomes, identifying 432 and 499 proteins respectively. Analyses focusing on S. sclerotiorum revealed that 16% of the secretome encoding genes resided in small, sequence heterogeneous, gene clusters that were distributed over 13 of the 16 predicted chromosomes. Functional analyses highlighted the importance of plant cell hydrolysis, oxidation-reduction processes and the redox state to the S. sclerotiorum and B. cinerea secretomes and potentially host infection. Only 8% of the predicted proteins were distinct between the two secretomes. In contrast to S. sclerotiorum, the B. cinerea secretome lacked CFEM- or LysM-containing proteins. The 115 fungal and oomycete genome comparison identified 30 proteins specific to S. sclerotiorum and B. cinerea, plus 11 proteins specific to S. sclerotiorum and 32 proteins specific to B. cinerea. Expressed sequence tag (EST) and proteomic analyses showed that 246 S. sclerotiorum secretome encoding genes had EST support, including 101 which were only expressed in vitro and 49 which were only expressed in planta, whilst 42 predicted proteins were experimentally proven to be secreted. These detailed in silico analyses of two important necrotrophic pathogens will permit informed choices to be made when candidate effector proteins are selected for function analyses in planta. PMID:26107498

Molecular characterization and heterologous expression of a Xanthophyllomyces dendrorhous α-glucosidase with potential for prebiotics production.

PubMed

Gutiérrez-Alonso, Patricia; Gimeno-Pérez, María; Ramírez-Escudero, Mercedes; Plou, Francisco J; Sanz-Aparicio, Julia; Fernández-Lobato, María

2016-04-01

Basidiomycetous yeast Xanthophyllomyces dendrorhous expresses an α-glucosidase with strong transglycosylation activity producing prebiotic sugars such as panose and an unusual tetrasaccharides mixture including α-(1-6) bonds as major products, which makes it of biotechnological interest. Initial analysis pointed to a homodimeric protein of 60 kDa subunit as responsible for this activity. In this study, the gene Xd-AlphaGlu was characterized. The 4131-bp-long gene is interrupted by 13 short introns and encodes a protein of 990 amino acids (Xd-AlphaGlu). The N-terminal sequence of the previously detected 60 kDa protein resides in this larger protein at residues 583-602. Functionality of the gene was proved in Saccharomyces cerevisiae, which produced a protein of about 130 kDa containing Xd-AlphaGlu sequences. All properties of the heterologously expressed protein, including thermal and pH profiles, activity on different substrates, and ability to produce prebiotic sugars were similar to that of the α-glucosidase produced in X. dendrorhous. No activity was detected in S. cerevisiae containing exclusively the 1256-bp from gene Xd-AlphaGlu that would encode synthesis of the 60 kDa protein previously detected. Data were compatible with an active monomeric α-glucosidase of 990 amino acids and an inactive hydrolysis product of 60 kDa. Protein Xd-AlphaGlu contained most of the elements characteristic of α-glucosidases included in the glycoside hydrolases family GH31 and its structural model based on the homologous human maltase-glucoamylase was obtained. Remarkably, the Xd-AlphaGlu C-terminal domain presents an unusually long 115-residue insertion that could be involved in this enzyme's activity against long-size substrates such as maltoheptaose and soluble starch.

Autophagy is induced through the ROS-TP53-DRAM1 pathway in response to mitochondrial protein synthesis inhibition.

PubMed

Xie, Xiaolei; Le, Li; Fan, Yanxin; Lv, Lin; Zhang, Junjie

2012-07-01

Mitoribosome in mammalian cells is responsible for synthesis of 13 mtDNA-encoded proteins, which are integral parts of four mitochondrial respiratory chain complexes (I, III, IV and V). ERAL1 is a nuclear-encoded GTPase important for the formation of the 28S small mitoribosomal subunit. Here, we demonstrate that knockdown of ERAL1 by RNA interference inhibits mitochondrial protein synthesis and promotes reactive oxygen species (ROS) generation, leading to autophagic vacuolization in HeLa cells. Cells that lack ERAL1 expression showed a significant conversion of LC3-I to LC3-II and an enhanced accumulation of autophagic vacuoles carrying the LC3 marker, all of which were blocked by the autophagy inhibitor 3-MA as well as by the ROS scavenger NAC. Inhibition of mitochondrial protein synthesis either by ERAL1 siRNA or chloramphenicol (CAP), a specific inhibitor of mitoribosomes, induced autophagy in HTC-116 TP53 (+/+) cells, but not in HTC-116 TP53 (-/-) cells, indicating that tumor protein 53 (TP53) is essential for the autophagy induction. The ROS elevation resulting from mitochondrial protein synthesis inhibition induced TP53 expression at transcriptional levels by enhancing TP53 promoter activity, and increased TP53 protein stability by suppressing TP53 ubiquitination through MAPK14/p38 MAPK-mediated TP53 phosphorylation. Upregulation of TP53 and its downstream target gene DRAM1, but not CDKN1A/p21, was required for the autophagy induction in ERAL1 siRNA or CAP-treated cells. Altogether, these data indicate that autophagy is induced through the ROS-TP53-DRAM1 pathway in response to mitochondrial protein synthesis inhibition.

CoSMoS: Conserved Sequence Motif Search in the proteome

PubMed Central

Liu, Xiao I; Korde, Neeraj; Jakob, Ursula; Leichert, Lars I

2006-01-01

Background With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. Nevertheless it is a task performed on a regular basis by researchers in many labs. Results We have now created a database called CoSMoS to find the occurrences and at the same time evaluate the significance of sequence motifs and amino acids encoded in the whole genome of the model organism Escherichia coli K12. We provide a precomputed set of multiple sequence alignments for each individual E. coli protein with all of its homologues in the RefSeq database. The alignments themselves, information about the occurrence of sequence motifs together with information on the conservation of each of the more than 1.3 million amino acids encoded in the E. coli genome can be accessed via the web interface of CoSMoS. Conclusion CoSMoS is a valuable tool to identify highly conserved sequence motifs, to find regions suitable for mutational studies in functional analyses and to predict important structural features in E. coli proteins. PMID:16433915

Novel Insights into the Role of Neurospora crassa NDUFAF2, an Evolutionarily Conserved Mitochondrial Complex I Assembly Factor

PubMed Central

Pereira, Bruno; Videira, Arnaldo

2013-01-01

Complex I deficiency is commonly associated with mitochondrial oxidative phosphorylation diseases. Mutations in nuclear genes encoding structural subunits or assembly factors of complex I have been increasingly identified as the cause of the diseases. One such factor, NDUFAF2, is a paralog of the NDUFA12 structural subunit of the enzyme, but the mechanism by which it exerts its function remains unknown. Herein, we demonstrate that the Neurospora crassa NDUFAF2 homologue, the 13.4L protein, is a late assembly factor that associates with complex I assembly intermediates containing the membrane arm and the connecting part but lacking the N module of the enzyme. Furthermore, we provide evidence that dissociation of the assembly factor is dependent on the incorporation of the putative regulatory module composed of the subunits of 13.4 (NDUFA12), 18.4 (NDUFS6), and 21 (NDUFS4) kDa. Our results demonstrate that the 13.4L protein is a complex I assembly factor functionally conserved from fungi to mammals. PMID:23648483

Solution-processed small molecules as mixed host for highly efficient blue and white phosphorescent organic light-emitting diodes.

PubMed

Fu, Qiang; Chen, Jiangshan; Shi, Changsheng; Ma, Dongge

2012-12-01

The widely used hole-transporting host 4,4',4″-tris(N-carbazolyl)-triphenylamine (TCTA) blended with either a hole-transporting or an electron-transporting small-molecule material as a mixed-host was investigated in the phosphorescent organic light-emitting diodes (OLEDs) fabricated by the low-cost solution-process. The performance of the solution-processed OLEDs was found to be very sensitive to the composition of the mixed-host systems. The incorporation of the hole-transporting 1,1-bis[(di-4-tolylamino)phenyl]cyclohexane (TAPC) into TCTA as the mixed-host was demonstrated to greatly reduce the driving voltage and thus enhance the efficiency due to the improvement of hole injection and transport. On the basis of the mixed-host of TCTA:TAPC, we successfully fabricated low driving voltage and high efficiency blue and white phosphorescent OLEDs. A maximum forward viewing current efficiency of 32.0 cd/A and power efficiency of 25.9 lm/W were obtained in the optimized mixed-host blue OLED, which remained at 29.6 cd/A and 19.1 lm/W at the luminance of 1000 cd/m(2) with a driving voltage as low as 4.9 V. The maximum efficiencies of 37.1 cd/A and 32.1 lm/W were achieved in a single emissive layer white OLED based on the TCTA:TAPC mixed-host. Even at 1000 cd/m(2), the efficiencies still reach 34.2 cd/A and 23.3 lm/W and the driving voltage is only 4.6 V, which is comparable to those reported from the state-of-the-art vacuum-evaporation deposited white OLEDs.

Method for evaluation of laboratory craters using crater detection algorithm for digital topography data

NASA Astrophysics Data System (ADS)

Salamunićcar, Goran; Vinković, Dejan; Lončarić, Sven; Vučina, Damir; Pehnec, Igor; Vojković, Marin; Gomerčić, Mladen; Hercigonja, Tomislav

In our previous work the following has been done: (1) the crater detection algorithm (CDA) based on digital elevation model (DEM) has been developed and the GT-115225 catalog has been assembled [GRS, 48 (5), in press, doi:10.1109/TGRS.2009.2037750]; and (2) the results of comparison between explosion-induced laboratory craters in stone powder surfaces and GT-115225 have been presented using depth/diameter measurements [41stLPSC, Abstract #1428]. The next step achievable using the available technology is to create 3D scans of such labo-ratory craters, in order to compare different properties with simple Martian craters. In this work, we propose a formal method for evaluation of laboratory craters, in order to provide objective, measurable and reproducible estimation of the level of achieved similarity between these laboratory and real impact craters. In the first step, the section of MOLA data for Mars (or SELENE LALT for Moon) is replaced with one or several 3D-scans of laboratory craters. Once embedment was done, the CDA can be used to find out whether this laboratory crater is similar enough to real craters, as to be recognized as a crater by the CDA. The CDA evaluation using ROC' curve represents how true detection rate (TDR=TP/(TP+FN)=TP/GT) depends on the false detection rate (FDR=FP/(TP+FP)). Using this curve, it is now possible to define the measure of similarity between laboratory and real impact craters, as TDR or FDR value, or as a distance from the bottom-right origin of the ROC' curve. With such an approach, the reproducible (formally described) method for evaluation of laboratory craters is provided.

Tryptophan promotes morphological and physiological differentiation in Streptomyces coelicolor.

PubMed

Palazzotto, Emilia; Renzone, Giovanni; Fontana, Pietro; Botta, Luigi; Scaloni, Andrea; Puglia, Anna Maria; Gallo, Giuseppe

2015-12-01

The molecular mechanisms regulating tryptophan biosynthesis in actinomycetes are poorly understood; similarly, the possible roles of tryptophan in the differentiation program of microorganism life-cycle are still underexplored. To unveil the possible regulatory effect of this amino acid on gene expression, an integrated study based on quantitative teverse transcription-PCR (qRT-PCR) and proteomic approaches was performed on the actinomycete model Streptomyces coelicolor. Comparative analyses on the microorganism growth in a minimal medium with or without tryptophan supplementation showed that biosynthetic trp gene expression in S. coelicolor is not subjected to a negative regulation by the presence of the end product. Conversely, tryptophan specifically induces the transcription of trp genes present in the biosynthetic gene cluster of the calcium-dependent antibiotic (CDA), a lipopeptide containing D- and L-tryptophan residues. In addition, tryptophan stimulates the transcription of the CDA gene cluster regulator cdaR and, coherently, CDA production. Surprisingly, tryptophan also promotes the production of actinorhodin, another antibiotic that does not contain this amino acid in its structure. Combined 2D-DIGE and nano liquid chromatography electrospray linear ion trap tandem mass spectrometry (LC-ESI-LIT-MS/MS) analyses revealed that tryptophan exerts a growth-stage-dependent global effect on S. coelicolor proteome, stimulating anabolic pathways and promoting the accumulation of key factors associated with morphological and physiological differentiation at the late growth stages. Phenotypic observations by scanning electron microscopy and spore production assays demonstrated an increased sporulation in the presence of tryptophan. Transcriptional analysis of catabolic genes kynA and kynB suggested that the actinomycete also uses tryptophan as a carbon and nitrogen source. In conclusion, this study originally provides the molecular basis underlying the stimulatory effect of tryptophan on the production of antibiotics and morphological development program of this actinomycete.

Technical Efficiency of Automotive Industry Cluster in Chennai

NASA Astrophysics Data System (ADS)

Bhaskaran, E.

2012-07-01

Chennai is also called as Detroit of India due to its automotive industry presence producing over 40 % of the India's vehicle and components. During 2001-2002, diagnostic study was conducted on the Automotive Component Industries (ACI) in Ambattur Industrial Estate, Chennai and in SWOT analysis it was found that it had faced problems on infrastructure, technology, procurement, production and marketing. In the year 2004-2005 under the cluster development approach (CDA), they formed Chennai auto cluster, under public private partnership concept, received grant from Government of India, Government of Tamil Nadu, Ambattur Municipality, bank loans and stake holders. This results development in infrastructure, technology, procurement, production and marketing interrelationships among ACI. The objective is to determine the correlation coefficient, regression equation, technical efficiency, peer weights, slack variables and return to scale of cluster before and after the CDA. The methodology adopted is collection of primary data from ACI and analyzing using data envelopment analysis (DEA) of input oriented Banker-Charnes-Cooper model. There is significant increase in correlation coefficient and the regression analysis reveals that for one percent increase in employment and net worth, the gross output increases significantly after the CDA. The DEA solver gives the technical efficiency of ACI by taking shift, employment, net worth as input data and quality, gross output and export ratio as output data. From the technical score and ranking of ACI, it is found that there is significant increase in technical efficiency of ACI when compared to CDA. The slack variables obtained clearly reveals the excess employment and net worth and no shortage of gross output. To conclude there is increase in technical efficiency of not only Chennai auto cluster in general but also Chennai auto components industries in particular.

HL7 and DICOM based integration of radiology departments with healthcare enterprise information systems.

PubMed

Blazona, Bojan; Koncar, Miroslav

2007-12-01

Integration based on open standards, in order to achieve communication and information interoperability, is one of the key aspects of modern health care information systems. However, this requirement represents one of the major challenges for the Information and Communication Technology (ICT) solutions, as systems today use diverse technologies, proprietary protocols and communication standards which are often not interoperable. One of the main producers of clinical information in healthcare settings represent Radiology Information Systems (RIS) that communicate using widely adopted DICOM (Digital Imaging and COmmunications in Medicine) standard, but in very few cases can efficiently integrate information of interest with other systems. In this context we identified HL7 standard as the world's leading medical ICT standard that is envisioned to provide the umbrella for medical data semantic interoperability, which amongst other things represents the cornerstone for the Croatia's National Integrated Healthcare Information System (IHCIS). The aim was to explore the ability to integrate and exchange RIS originated data with Hospital Information Systems based on HL7's CDA (Clinical Document Architecture) standard. We explored the ability of HL7 CDA specifications and methodology to address the need of RIS integration HL7 based healthcare information systems. We introduced the use of WADO service interconnection to IHCIS and finally CDA rendering in widely used Internet explorers. The outcome of our pilot work proves our original assumption of HL7 standard being able to adopt radiology data into the integrated healthcare systems. Uniform DICOM to CDA translation scripts and business processes within IHCIS is desired and cost effective regarding to use of supporting IHCIS services aligned to SOA.

Clinical examination of leucite-reinforced glass-ceramic crowns (Empress) in general practice: a retrospective study.

PubMed

Sjögren, G; Lantto, R; Granberg, A; Sundström, B O; Tillberg, A

1999-01-01

The purpose of this study was to retrospectively evaluate leucite reinforced-glass ceramic crowns (Empress) placed in patients who regularly visit general practices. One hundred ten Empress crowns, placed in 29 patients who visited a general practice on a regular basis, were evaluated according to the California Dental Association's (CDA) quality evaluation system. In addition, the occurrence of plaque and certain gingival conditions was evaluated. All crowns were luted with resin composite cement. The mean and median years in function for the crowns were 3.6 and 3.9 years, respectively. Based on the CDA criteria, 92% of the 110 crowns were rated "satisfactory." Eighty-six percent were given the CDA rating "excellent" for margin integrity. Fracture was registered in 6% of the 110 crowns. Of the remaining 103 crowns, the CDA rating excellent was given to 74% for anatomic form, 86% for color, and 90% for surface. No significant differences (P > 0.05) were observed regarding fracture rates between anterior and posterior crowns. With regard to the occurrence of plaque and bleeding on probing, no significant differences (P > 0.05) were observed between the Empress crowns and the controls. Most of the fractured crowns had been placed on molars or premolars. Although the difference between anterior and posterior teeth was not statistically significant with respect to the fracture rates obtained, the number of fractured crowns placed on posterior teeth exceeded that of those placed on anterior teeth. The difference between the fracture rates may have clinical significance, and the risk of fracture has to be taken into consideration when placing crowns on teeth that are likely to be subjected to high stress levels.

More target features in visual working memory leads to poorer search guidance: Evidence from contralateral delay activity

PubMed Central

Schmidt, Joseph; MacNamara, Annmarie; Proudfit, Greg Hajcak; Zelinsky, Gregory J.

2014-01-01

The visual-search literature has assumed that the top-down target representation used to guide search resides in visual working memory (VWM). We directly tested this assumption using contralateral delay activity (CDA) to estimate the VWM load imposed by the target representation. In Experiment 1, observers previewed four photorealistic objects and were cued to remember the two objects appearing to the left or right of central fixation; Experiment 2 was identical except that observers previewed two photorealistic objects and were cued to remember one. CDA was measured during a delay following preview offset but before onset of a four-object search array. One of the targets was always present, and observers were asked to make an eye movement to it and press a button. We found lower magnitude CDA on trials when the initial search saccade was directed to the target (strong guidance) compared to when it was not (weak guidance). This difference also tended to be larger shortly before search-display onset and was largely unaffected by VWM item-capacity limits or number of previews. Moreover, the difference between mean strong- and weak-guidance CDA was proportional to the increase in search time between mean strong-and weak-guidance trials (as measured by time-to-target and reaction-time difference scores). Contrary to most search models, our data suggest that trials resulting in the maintenance of more target features results in poor search guidance to a target. We interpret these counterintuitive findings as evidence for strong search guidance using a small set of highly discriminative target features that remain after pruning from a larger set of features, with the load imposed on VWM varying with this feature-consolidation process. PMID:24599946

More target features in visual working memory leads to poorer search guidance: evidence from contralateral delay activity.

PubMed

Schmidt, Joseph; MacNamara, Annmarie; Proudfit, Greg Hajcak; Zelinsky, Gregory J

2014-03-05

The visual-search literature has assumed that the top-down target representation used to guide search resides in visual working memory (VWM). We directly tested this assumption using contralateral delay activity (CDA) to estimate the VWM load imposed by the target representation. In Experiment 1, observers previewed four photorealistic objects and were cued to remember the two objects appearing to the left or right of central fixation; Experiment 2 was identical except that observers previewed two photorealistic objects and were cued to remember one. CDA was measured during a delay following preview offset but before onset of a four-object search array. One of the targets was always present, and observers were asked to make an eye movement to it and press a button. We found lower magnitude CDA on trials when the initial search saccade was directed to the target (strong guidance) compared to when it was not (weak guidance). This difference also tended to be larger shortly before search-display onset and was largely unaffected by VWM item-capacity limits or number of previews. Moreover, the difference between mean strong- and weak-guidance CDA was proportional to the increase in search time between mean strong-and weak-guidance trials (as measured by time-to-target and reaction-time difference scores). Contrary to most search models, our data suggest that trials resulting in the maintenance of more target features results in poor search guidance to a target. We interpret these counterintuitive findings as evidence for strong search guidance using a small set of highly discriminative target features that remain after pruning from a larger set of features, with the load imposed on VWM varying with this feature-consolidation process.

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins▿

PubMed Central

Plant, Ewan P.; Rakauskaitė, Rasa; Taylor, Deborah R.; Dinman, Jonathan D.

2010-01-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed −1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the −1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a “golden mean” model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins. PMID:20164235

Neurospora crassa 1,3-α-glucan synthase, AGS-1, is required for cell wall biosynthesis during macroconidia development

PubMed Central

Fu, Ci; Tanaka, Asuma

2014-01-01

The Neurospora crassa genome encodes two 1,3-α-glucan synthases. One of these 1,3-α-glucan synthase genes, ags-1, was shown to be required for the synthesis of 1,3-α-glucan in the aerial hyphae and macroconidia cell walls. 1,3-α-Glucan was found in the conidia cell wall, but was absent from the vegetative hyphae cell wall. Deletion of ags-1 affected conidial development. Δags-1 produced only 5 % as many conidia as the WT and most of the conidia produced by Δags-1 were not viable. The ags-1 upstream regulatory elements were shown to direct cell-type-specific expression of red fluorescent protein in conidia and aerial hyphae. A haemagglutinin-tagged AGS-1 was found to be expressed in aerial hyphae and conidia. The research showed that 1,3-α-glucan is an aerial hyphae and conidia cell wall component, and is required for normal conidial differentiation. PMID:24847001

Ectromelia Virus BTB/kelch Proteins, EVM150 and EVM167, Interact with Cullin-3 Based Ubiquitin Ligases

PubMed Central

Wilton, Brianne A.; Campbell, Stephanie; Van Buuren, Nicholas; Garneau, Robyn; Furukawa, Manabu; Xiong, Yue; Barry., Michele

2008-01-01

Cellular proteins containing BTB and kelch domains have been shown to function as adapters for the recruitment of substrates to cullin-3-based ubiquitin ligases. Poxviruses are the only family of viruses known to encode multiple BTB/kelch proteins, suggesting that poxviruses may modulate the ubiquitin pathway through interaction with cullin-3. Ectromelia virus encodes four BTB/kelch proteins and one BTB-only protein. Here we demonstrate that two of the ectromelia virus encoded BTB/kelch proteins, EVM150 and EVM167, interacted with cullin-3. Similar to cellular BTB proteins, the BTB domain of EVM150 and EVM167 was necessary and sufficient for cullin-3 interaction. During infection, EVM150 and EVM167 localized to discrete cytoplasmic regions, which co-localized with cullin-3. Furthermore, EVM150 and EVM167 co-localized and interacted with conjugated ubiquitin, as demonstrated by confocal microscopy and co-immunoprecipitation. Our findings suggest that the ectromelia virus encoded BTB/kelch proteins, EVM150 and EVM167, interact with cullin-3 potentially functioning to recruit unidentified substrates for ubiquitination. PMID:18221766

Characterization of a cDNA encoding a protein involved in formation of the skeleton during development of the sea urchin Lytechinus pictus.

PubMed

Livingston, B T; Shaw, R; Bailey, A; Wilt, F

1991-12-01

In order to investigate the role of proteins in the formation of mineralized tissues during development, we have isolated a cDNA that encodes a protein that is a component of the organic matrix of the skeletal spicule of the sea urchin, Lytechinus pictus. The expression of the RNA encoding this protein is regulated over development and is localized to the descendents of the micromere lineage. Comparison of the sequence of this cDNA to homologous cDNAs from other species of urchin reveal that the protein is basic and contains three conserved structural motifs: a signal peptide, a proline-rich region, and an unusual region composed of a series of direct repeats. Studies on the protein encoded by this cDNA confirm the predicted reading frame deduced from the nucleotide sequence and show that the protein is secreted and not glycosylated. Comparison of the amino acid sequence to databases reveal that the repeat domain is similar to proteins that form a unique beta-spiral supersecondary structure.

A novel highly divergent protein family identified from a viviparous insect by RNA-seq analysis: a potential target for tsetse fly-specific abortifacients.

PubMed

Benoit, Joshua B; Attardo, Geoffrey M; Michalkova, Veronika; Krause, Tyler B; Bohova, Jana; Zhang, Qirui; Baumann, Aaron A; Mireji, Paul O; Takáč, Peter; Denlinger, David L; Ribeiro, Jose M; Aksoy, Serap

2014-04-01

In tsetse flies, nutrients for intrauterine larval development are synthesized by the modified accessory gland (milk gland) and provided in mother's milk during lactation. Interference with at least two milk proteins has been shown to extend larval development and reduce fecundity. The goal of this study was to perform a comprehensive characterization of tsetse milk proteins using lactation-specific transcriptome/milk proteome analyses and to define functional role(s) for the milk proteins during lactation. Differential analysis of RNA-seq data from lactating and dry (non-lactating) females revealed enrichment of transcripts coding for protein synthesis machinery, lipid metabolism and secretory proteins during lactation. Among the genes induced during lactation were those encoding the previously identified milk proteins (milk gland proteins 1-3, transferrin and acid sphingomyelinase 1) and seven new genes (mgp4-10). The genes encoding mgp2-10 are organized on a 40 kb syntenic block in the tsetse genome, have similar exon-intron arrangements, and share regions of amino acid sequence similarity. Expression of mgp2-10 is female-specific and high during milk secretion. While knockdown of a single mgp failed to reduce fecundity, simultaneous knockdown of multiple variants reduced milk protein levels and lowered fecundity. The genomic localization, gene structure similarities, and functional redundancy of MGP2-10 suggest that they constitute a novel highly divergent protein family. Our data indicates that MGP2-10 function both as the primary amino acid resource for the developing larva and in the maintenance of milk homeostasis, similar to the function of the mammalian casein family of milk proteins. This study underscores the dynamic nature of the lactation cycle and identifies a novel family of lactation-specific proteins, unique to Glossina sp., that are essential to larval development. The specificity of MGP2-10 to tsetse and their critical role during lactation suggests that these proteins may be an excellent target for tsetse-specific population control approaches.

Defective transport of the obesity mutant PC1/3 N222D contributes to loss of function.

PubMed

Prabhu, Yogikala; Blanco, Elias H; Liu, Ming; Peinado, Juan R; Wheeler, Matthew C; Gekakis, Nicholas; Arvan, Peter; Lindberg, Iris

2014-07-01

Mutations in the PCSK1 gene encoding prohormone convertase 1/3 (PC1/3) are strongly associated with obesity in humans. The PC1/3(N222D) mutant mouse thus far represents the only mouse model that mimics the PC1/3 obesity phenotype in humans. The present investigation addresses the cell biology of the N222D mutation. Metabolic labeling experiments reveal a clear defect in the kinetics of insulin biosynthesis in islets from PC1/3(N222D) mutant mice, resulting in an increase in both proinsulin and its processing intermediates, predominantly lacking cleavage at the Arg-Arg site. Although the mutant PC1/3 zymogen is correctly processed to the 87-kDa form, pulse-chase immunoprecipitation experiments, labeling, and immunohistochemical experiments using uncleavable variants all demonstrate that the PC1/3-N222D protein is largely mislocalized compared with similar wild-type (WT) constructs, being predominantly retained in the endoplasmic reticulum. The PC1/3-N222D mutant also undergoes more efficient degradation via the ubiquitin-proteasome system than the WT enzyme. Lastly, the mutant PC1/3-N222D protein coimmunoprecipitates with WT PC1/3 and exerts a modest effect on intracellular retention of the WT enzyme. These profound alterations in the cell biology of PC1/3-N222D are likely to contribute to the defective insulin biosynthetic events observed in the mutant mice and may be relevant to the dramatic contributions of polymorphisms in this gene to human obesity.

Defective Transport of the Obesity Mutant PC1/3 N222D Contributes to Loss of Function

PubMed Central

Prabhu, Yogikala; Blanco, Elias H.; Liu, Ming; Peinado, Juan R.; Wheeler, Matthew C.; Gekakis, Nicholas; Arvan, Peter

2014-01-01

Mutations in the PCSK1 gene encoding prohormone convertase 1/3 (PC1/3) are strongly associated with obesity in humans. The PC1/3N222D mutant mouse thus far represents the only mouse model that mimics the PC1/3 obesity phenotype in humans. The present investigation addresses the cell biology of the N222D mutation. Metabolic labeling experiments reveal a clear defect in the kinetics of insulin biosynthesis in islets from PC1/3N222D mutant mice, resulting in an increase in both proinsulin and its processing intermediates, predominantly lacking cleavage at the Arg-Arg site. Although the mutant PC1/3 zymogen is correctly processed to the 87-kDa form, pulse-chase immunoprecipitation experiments, labeling, and immunohistochemical experiments using uncleavable variants all demonstrate that the PC1/3-N222D protein is largely mislocalized compared with similar wild-type (WT) constructs, being predominantly retained in the endoplasmic reticulum. The PC1/3-N222D mutant also undergoes more efficient degradation via the ubiquitin-proteasome system than the WT enzyme. Lastly, the mutant PC1/3-N222D protein coimmunoprecipitates with WT PC1/3 and exerts a modest effect on intracellular retention of the WT enzyme. These profound alterations in the cell biology of PC1/3-N222D are likely to contribute to the defective insulin biosynthetic events observed in the mutant mice and may be relevant to the dramatic contributions of polymorphisms in this gene to human obesity. PMID:24828610

Deficit of heat shock transcription factor 1-heat shock 70 kDa protein 1A axis determines the cell death vulnerability in a model of spinocerebellar ataxia type 6.

PubMed

Li, Li; Saegusa, Hironao; Tanabe, Tsutomu

2009-11-01

Spinocerebellar ataxia type 6 (SCA6) is caused by a small expansion of polyglutamine (polyQ)-encoding CAG repeat in Ca(v)2.1 calcium channel gene. To gain insights into pathogenic mechanism of SCA6, we used HEK293 cells expressing fusion protein of enhanced green fluorescent protein and Ca(v)2.1 carboxyl terminal fragment (EGFP-Ca(v)2.1CT) [L24 and S13 cells containing 24 polyQ (disease range) and 13 polyQ (normal range), respectively] and examined their responses to some stressors. When exposed to CdCl(2), L24 cells showed lower viability than the control S13 cells and caspase-dependent apoptosis was enhanced more in L24 cells. Localization of EGFP-Ca(v)2.1CT was almost confined to the nucleus, where it existed as speckle-like structures. Interestingly, CdCl(2) treatment resulted in disruption of more promyelocytic leukemia nuclear bodies (PML-NBs) in L24 cells than in S13 cells and in cells where PML-NBs were disrupted, aggregates of EGFP-Ca(v)2.1CT became larger. Furthermore, a large number of aggregates were formed in L24 cells than in S13 cells. Results of RNAi experiments indicated that HSPA1A determined the difference against CdCl(2) toxicity. Furthermore, protein expression of heat shock transcription factor 1 (HSF1), which activates HSPA1A expression, was down-regulated in L24 cells. Therefore, HSF1-HSPA1A axis is critical for the vulnerability in L24 cells.

Organization, chromosomal localization and promoter analysis of the gene encoding human acidic fibroblast growth factor intracellular binding protein.

PubMed Central

Kolpakova, E; Frengen, E; Stokke, T; Olsnes, S

2000-01-01

Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that might be involved in the intracellular function of aFGF. Here we present a comparative analysis of the deduced amino acid sequences of human, murine and Drosophila FIBP analogues and demonstrate that FIBP is an evolutionarily conserved protein. The human gene spans more than 5 kb, comprising ten exons and nine introns, and maps to chromosome 11q13.1. Two slightly different splice variants found in different tissues were isolated and characterized. Sequence analysis of the region surrounding the translation start revealed a CpG island, a classical feature of widely expressed genes. Functional studies of the promoter region with a luciferase reporter system suggested a strong transcriptional activity residing within 600 bp of the 5' flanking region. PMID:11104667

Trichoderma genes

DOEpatents

Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

2012-06-19

Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

[Study of neutralization antibodie induced by DNA vaccine of HCV envelope protein 2 in mice].

PubMed

Shao, Shengwen; Zhou, Hongchang; Tong, Yimin; Ren, Yanli; Chen, Zhihui

2011-05-01

To explore the feasibility of induction of neutralization antibodies against hepatitis C virus (HCV) infection by HCV envelope 2 protein (E2) DNA vaccines immunization. Two kinds of expression plasmids of HCV envelope 2 protein, plasmid pCI-1b661 Delta encoding hydrophobic carboxyl terminal truncated E2 and pCI-1b661 Delta encoding E2 with deletion of hypervariable region 1 (HVR1) and carboxyl terminal, were constructed and respectively transfeted 293T cells, and truncated E2 protein in whole cell lysate and supernatant of 293T cells were analyzed by Western blot. After BALB/c mouse were intramuscularly immunized by the plasmids, sera antibodies against HVR1 were detected by ELISA and the neutralization activity of the antibodies were assayed with HCV pseudotype particle (HCVpp). Both plasmids could express secretary truncated E2 protein. All the mice immunized with plasmid pCI-1b661 produced HVR1 antibodies,while no HVR1 antibodies were detected in pCI-1b661 Delta immunized mice. The sera neutralization percentages against HCVpp in pCI1lb661 Delta and pCI-lb661 Delta immunized mice were (78.5 +/- 13.8)% and (38.7 +/- 6.5)%, respectively (P <0.01). Sera neutralization activity against HCVpp was positive correlated with the level of HVR1 antibodies in pCI-1b661 immunized mice (r = 0.967, P<0.01). DNA vaccines expressing truncated E2 protein could induce neutralization antibodies against HCV, and neutralization antibodies mainly was consisted of the antibodies against HVR1.

Efflux pump-mediated benzalkonium chloride resistance in Listeria monocytogenes isolated from retail food.

PubMed

Jiang, Xiaobing; Yu, Tao; Liang, Yu; Ji, Shengdong; Guo, Xiaowei; Ma, Jianmin; Zhou, Lijun

2016-01-18

In this study, efflux pump-mediated benzalkonium chloride (BC) resistance, including plasmid-encoded (Qac protein family and BcrABC) and chromosome-borne efflux pumps, was investigated in Listeria monocytogenes from retail food in China. Among the 59 L. monocytogenes strains, 13 (22.0%) strains were resistant to BC. The PCR results showed that bcrABC was harbored by 2 of 13 BC resistant strains. However, none of the qac genes were detected among the 59 strains. The bcrABC was absent in both of the plasmid cured strains, indicating that this BC resistance determinant was plasmid-encoded in the two bcrABC-positive strains. In the presence of reserpine, most of the bcrABC-negative strains had decreases in the MICs of BC, suggesting the existence of other efflux pumps and their role in BC resistance. After exposed to reserpine, the reduction in BC MICs was observed in the two cured strains, indicating that efflux pumps located on chromosome was also involved in BC resistance. Our findings suggest that food products may act as reservoirs for BC resistant isolates of L. monocytogenes and plasmid- and chromosome-encoded efflux pumps could mediate the BC resistance of L. monocytogenes, which is especially relevant to the adaption of this organism in food-related environments with frequent BC use. Copyright © 2015 Elsevier B.V. All rights reserved.

[Expression and significance of respiratory chain enzyme of cells in urine sediment in MELAS syndrome].

PubMed

Wu, Hai-rong; Ma, Yi-nan; Qi, Yu; Liu, Hong-gang

2013-04-23

To explore the expression and significance of respiratory chain enzyme of cells in urine sediment in mitochondrial encephalopathy myopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome. Through enzyme histochemistry, the authors analyzed the changes of respiratory chain enzyme in urine sediment in 20 MELAS patients due to mitochondrial A3243G mutation (MELAS group) and 20 health peoples (control group). And the impact on the expression of protein encoded by nuclear DNA (A21347) and mitochondrial DNA (A6404) was detected by immunochemistry. Image pro Plus 6.0 software was used for analysis of absorbance (A) of staining images as staining intensity. The data were expressed as M (Q1, Q3) and analyzed through statistical software. The staining intensity of complexes Iin the MELAS group was lower than that in the control group (0.06(0.01, 0.12) vs 0.12(0.01, 0.62), P = 0.010). The intergroup staining intensity of complex II showed no marked difference. Increased density of blue particle and cytoplasmic gathering was found in 13 cased (65%) of the MELAS group under light microscope. The staining intensity of complexes IV was expressed at a low level in the MELAS group (0.14(0.03, 0.32) vs 0.23(0.06, 0.43), P = 0.038). The expression of protein encoded by nuclear DNA (A21347) was lower than that in the control group (0.05(0.02, 0.45) vs 0.17(0.03, 0.70), P = 0.000). The expression of protein encoded by mitochondrial DNA (A6404) was also lower than that in the control group (0.03(0.01, 0.07) vs 0.15 (0.09, 0.23), P = 0.000). Abnormal change of respiratory chain enzyme in urine sediment in MELAS due to mitochondrial A3243G mutation and a low expression of proteins encoded by two kinds of DNA in complexes IV can help to confirm the genetic diagnosis of mitochondrial encephalomyopathies so that different subtypes may be classified and its pathogenesis elucidated.

Screening for ATM Mutations in an African-American Population to Identify a Predictor of Breast Cancer Susceptibility

DTIC Science & Technology

2006-07-01

ATM genetic variant identified affects radiosensitivity and levels of the protein encoded by the ATM gene for each mutation examined. 15. SUBJECT...women without breast cancer. An additional objective is to determine the functional impact upon the protein encoded by the ATM gene for each mutation ...each ATM variant identified affects radiosensitivity and levels of the protein encoded by the ATM gene for mutations identified. Body STATEMENT

Antigenic profiling of Yersinia pestis infection in the Wyoming coyote (Canis latrans)

USGS Publications Warehouse

Vernati, G.; Edwards, W.H.; Rocke, T.E.; Little, S.F.; Andrews, G.P.

2011-01-01

Although Yersinia pestis is classified as a "high-virulence" pathogen, some host species are variably susceptible to disease. Coyotes (Canis latrans) exhibit mild, if any, symptoms during infection, but antibody production occurs postinfection. This immune response has been reported to be against the F1 capsule, although little subsequent characterization has been conducted. To further define the nature of coyote humoral immunity to plague, qualitative serology was conducted to assess the antiplague antibody repertoire. Humoral responses to six plasmid-encoded Y. pestis virulence factors were first examined. Of 20 individual immune coyotes, 90% were reactive to at least one other antigen in the panel other than F1. The frequency of reactivity to low calcium response plasmid (pLcr)-encoded Yersinia protein kinase A (YpkA) and Yersinia outer protein D (YopD) was significantly greater than that previously observed in a murine model for plague. Additionally, both V antigen and plasminogen activator were reactive with over half of the serum samples tested. Reactivity to F1 was markedly less frequent in coyotes (35%). Twenty previously tested antibody-negative samples were also examined. While the majority were negative across the panel, 15% were positive for 1-3 non-F1 antigens. In vivo-induced antigen technology employed to identify novel chromosomal genes of Y. pestis that are up-regulated during infection resulted in the identification of five proteins, including a flagellar component (FliP) that was uniquely reactive with the coyote serum compared with immune serum from two other host species. Collectively, these data suggest that humoral immunity to pLcr-encoded antigens and the pesticin plasmid (pPst)-encoded Pla antigen may be relevant to plague resistance in coyotes. The serologic profile of Y. pestis chromosomal antigens up-regulated in vivo specific to C. latrans may provide insight into the differences in the pathogen-host responses during Y. pestis infection.

In Silico Identification of Epitopes in Mycobacterium avium subsp. paratuberculosis Proteins That Were Upregulated under Stress Conditions

PubMed Central

Gurung, Ratna B.; Purdie, Auriol C.; Begg, Douglas J.

2012-01-01

Johne's disease in ruminants is caused by Mycobacterium avium subsp. paratuberculosis. Diagnosis of M. avium subsp. paratuberculosis infection is difficult, especially in the early stages. To date, ideal antigen candidates are not available for efficient immunization or immunodiagnosis. This study reports the in silico selection and subsequent analysis of epitopes of M. avium subsp. paratuberculosis proteins that were found to be upregulated under stress conditions as a means to identify immunogenic candidate proteins. Previous studies have reported differential regulation of proteins when M. avium subsp. paratuberculosis is exposed to stressors which induce a response similar to dormancy. Dormancy may be involved in evading host defense mechanisms, and the host may also mount an immune response against these proteins. Twenty-five M. avium subsp. paratuberculosis proteins that were previously identified as being upregulated under in vitro stress conditions were analyzed for B and T cell epitopes by use of the prediction tools at the Immune Epitope Database and Analysis Resource. Major histocompatibility complex class I T cell epitopes were predicted using an artificial neural network method, and class II T cell epitopes were predicted using the consensus method. Conformational B cell epitopes were predicted from the relevant three-dimensional structure template for each protein. Based on the greatest number of predicted epitopes, eight proteins (MAP2698c [encoded by desA2], MAP2312c [encoded by fadE19], MAP3651c [encoded by fadE3_2], MAP2872c [encoded by fabG5_2], MAP3523c [encoded by oxcA], MAP0187c [encoded by sodA], and the hypothetical proteins MAP3567 and MAP1168c) were identified as potential candidates for study of antibody- and cell-mediated immune responses within infected hosts. PMID:22496492

Gene amplification of the transcription factor DP1 and CTNND1 in human lung cancer.

PubMed

Castillo, Sandra D; Angulo, Barbara; Suarez-Gauthier, Ana; Melchor, Lorenzo; Medina, Pedro P; Sanchez-Verde, Lydia; Torres-Lanzas, Juan; Pita, Guillermo; Benitez, Javier; Sanchez-Cespedes, Montse

2010-09-01

The search for novel oncogenes is important because they could be the target of future specific anticancer therapies. In the present paper we report the identification of novel amplified genes in lung cancer by means of global gene expression analysis. To screen for amplicons, we aligned the gene expression data according to the position of transcripts in the human genome and searched for clusters of over-expressed genes. We found several clusters with gene over-expression, suggesting an underlying genomic amplification. FISH and microarray analysis for DNA copy number in two clusters, at chromosomes 11q12 and 13q34, confirmed the presence of amplifications spanning about 0.4 and 1 Mb for 11q12 and 13q34, respectively. Amplification at these regions each occurred at a frequency of 3%. Moreover, quantitative RT-PCR of each individual transcript within the amplicons allowed us to verify the increased in gene expression of several genes. The p120ctn and DP1 proteins, encoded by two candidate oncogenes, CTNND1 and TFDP1, at 11q12 and 13q amplicons, respectively, showed very strong immunostaining in lung tumours with gene amplification. We then focused on the 13q34 amplicon and in the TFDP1 candidate oncogene. To further determine the oncogenic properties of DP1, we searched for lung cancer cell lines carrying TFDP1 amplification. Depletion of TFDP1 expression by small interference RNA in a lung cancer cell line (HCC33) with TFDP1 amplification and protein over-expression reduced cell viability by 50%. In conclusion, we report the identification of two novel amplicons, at 13q34 and 11q12, each occurring at a frequency of 3% of non-small cell lung cancers. TFDP1, which encodes the E2F-associated transcription factor DP1 is a candidate oncogene at 13q34. The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series Accession No. GSE21168.

Mitochondrial Hsp60 Chaperonopathy Causes an Autosomal-Recessive Neurodegenerative Disorder Linked to Brain Hypomyelination and Leukodystrophy

PubMed Central

Magen, Daniella; Georgopoulos, Costa; Bross, Peter; Ang, Debbie; Segev, Yardena; Goldsher, Dorit; Nemirovski, Alexandra; Shahar, Eli; Ravid, Sarit; Luder, Anthony; Heno, Bayan; Gershoni-Baruch, Ruth; Skorecki, Karl; Mandel, Hanna

2008-01-01

Hypomyelinating leukodystrophies (HMLs) are disorders involving aberrant myelin formation. The prototype of primary HMLs is the X-linked Pelizaeus-Merzbacher disease (PMD) caused by mutations in PLP1. Recently, homozygous mutations in GJA12 encoding connexin 47 were found in patients with autosomal-recessive Pelizaeus-Merzbacher-like disease (PMLD). However, many patients of both genders with PMLD carry neither PLP1 nor GJA12 mutations. We report a consanguineous Israeli Bedouin kindred with clinical and radiological findings compatible with PMLD, in which linkage to PLP1 and GJA12 was excluded. Using homozygosity mapping and mutation analysis, we have identified a homozygous missense mutation (D29G) not previously described in HSPD1, encoding the mitochondrial heat-shock protein 60 (Hsp60) in all affected individuals. The D29G mutation completely segregates with the disease-associated phenotype. The pathogenic effect of D29G on Hsp60-chaperonin activity was verified by an in vivo E. coli complementation assay, which demonstrated compromised ability of the D29G-Hsp60 mutant protein to support E. coli survival, especially at high temperatures. The disorder, which we have termed MitCHAP-60 disease, can be distinguished from spastic paraplegia 13 (SPG13), another Hsp60-associated autosomal-dominant neurodegenerative disorder, by its autosomal-recessive inheritance pattern, as well as by its early-onset, profound cerebral involvement and lethality. Our findings suggest that Hsp60 defects can cause neurodegenerative pathologies of varying severity, not previously suspected on the basis of the SPG13 phenotype. These findings should help to clarify the important role of Hsp60 in myelinogenesis and neurodegeneration. PMID:18571143

Genetic and Molecular Characterization of the Caenorhabditis Elegans Spermatogenesis-Defective Gene Spe-17

PubMed Central

L'Hernault, S. W.; Benian, G. M.; Emmons, R. B.

1993-01-01

Two self-sterile mutations that define the spermatogenesis-defective gene spe-17 have been analyzed. These mutations affect unc-22 and fail to complement each other for both Unc-22 and spermatogenesis defects. Both of these mutations are deficiencies (hcDf1 and hDf13) that affect more than one transcription unit. Genomic DNA adjacent to and including the region deleted by the smaller deficiency (hcDf1) has been sequenced and four mRNAs (including unc-22) have been localized to this sequenced region. The three non unc-22 mRNAs are shown to be sex-specific: a 1.2-kb mRNA that can be detected in sperm-free hermaphrodites and 1.2- and 0.56-kb mRNAs found in males. hDf13 deletes at least 55 kb of chromosome IV, including all of unc-22, both male-specific mRNAs and at least part of the female-specific mRNA. hcDf1, which is approximately 15.6 kb, deletes only the 5' end of unc-22 and the gene that encodes the 0.56-kb male-specific mRNA. The common defect that apparently accounts for the defective sperm in hcDf1 and hDf13 homozygotes is deletion of the spe-17 gene, which encodes the 0.56-kb mRNA. Strains carrying two copies of either deletion are self-fertile when they are transgenic for any of four extrachromosomal array that include spe-17. We have sequenced two spe-17 cDNAs, and the deduced 142 amino acid protein sequence is highly charged and rich in serine and threonine, but shows no significant homology to any previously determined protein sequence. PMID:8349108

Role of the DLGAP2 Gene Encoding the SAP90/PSD-95-Associated Protein 2 in Schizophrenia

PubMed Central

Li, Jun-Ming; Lu, Chao-Lin; Cheng, Min-Chih; Luu, Sy-Ueng; Hsu, Shih-Hsin; Hu, Tsung-Ming; Tsai, Hsin-Yao; Chen, Chia-Hsiang

2014-01-01

Aberrant synaptic dysfunction is implicated in the pathogenesis of schizophrenia. The DLGAP2 gene encoding the SAP90/PSD-95-associated protein 2 (SAPAP2) located at the post-synaptic density of neuronal cells is involved in the neuronal synaptic function. This study aimed to investigate whether the DLGAP2 gene is associated with schizophrenia. We resequenced the putative promoter region and all the exons of the DLGAP2 gene in 523 patients with schizophrenia and 596 non-psychotic controls from Taiwan and conducted a case-control association analysis. We identified 19 known SNPs in this sample. Association analysis of 9 SNPs with minor allele frequency greater than 5% showed no association with schizophrenia. However, we found a haplotype (CCACCAACT) significantly associated with schizophrenia (odds ratio:2.5, p<0.001). We also detected 16 missense mutations and 1 amino acid-insertion mutation in this sample. Bioinformatic analysis showed some of these mutations were damaging or pathological to the protein function, but we did not find increased burden of these mutations in the patient group. Notably, we identified 5 private rare variants in 5 unrelated patients, respectively, including c.−69+9C>T, c.−69+13C>T, c.−69+47C>T, c.−69+55C>T at intron 1 and c.−32A>G at untranslated exon 2 of the DLGAP2 gene. These rare variants were not detected in 559 control subjects. Further reporter gene assay of these rare variants except c.−69+13C>T showed significantly elevated promoter activity than the wild type, suggesting increased DLGAP2 gene expression may contribute to the pathogenesis of schizophrenia. Our results indicate that DLGAP2 is a susceptible gene of schizophrenia. PMID:24416398

Identification of novel substrates of Shigella T3SA through analysis of its virulence plasmid-encoded secretome

PubMed Central

Pinaud, Laurie; Ferrari, Mariana L.; Friedman, Robin; Jehmlich, Nico; von Bergen, Martin; Phalipon, Armelle; Sansonetti, Philippe J.

2017-01-01

Many human Gram-negative bacterial pathogens express a Type Three Secretion Apparatus (T3SA), including among the most notorious Shigella spp., Salmonella enterica, Yersinia enterocolitica and enteropathogenic Escherichia coli (EPEC). These bacteria express on their surface multiple copies of the T3SA that mediate the delivery into host cells of specific protein substrates critical to pathogenesis. Shigella spp. are Gram-negative bacterial pathogens responsible for human bacillary dysentery. The effector function of several Shigella T3SA substrates has largely been studied but their potential cellular targets are far from having been comprehensively delineated. In addition, it is likely that some T3SA substrates have escaped scrutiny as yet. Indeed, sequencing of the virulence plasmid of Shigella flexneri has revealed numerous open reading frames with unknown functions that could encode additional T3SA substrates. Taking advantage of label-free mass spectrometry detection of proteins secreted by a constitutively secreting strain of S. flexneri, we identified five novel substrates of the T3SA. We further confirmed their secretion through the T3SA and translocation into host cells using β-lactamase assays. The coding sequences of two of these novel T3SA substrates (Orf13 and Orf131a) have a guanine-cytosine content comparable to those of T3SA components and effectors. The three other T3SA substrates identified (Orf48, Orf86 and Orf176) have significant homology with antitoxin moieties of type II Toxin-Antitoxin systems usually implicated in the maintenance of low copy plasmids. While Orf13 and Orf131a might constitute new virulence effectors contributing to S. flexneri pathogenicity, potential roles for the translocation into host cells of antitoxins or antitoxin-like proteins during Shigella infection are discussed. PMID:29073283

Electron cryo-tomographic structure of cystovirus phi 12.

PubMed

Hu, Guo-Bin; Wei, Hui; Rice, William J; Stokes, David L; Gottlieb, Paul

2008-03-01

Bacteriophage phi 12 is a member of the Cystoviridae virus family and contains a genome consisting of three segments of double-stranded RNA (dsRNA). This virus family contains eight identified members, of which four have been classified in regard to their complete genomic sequence and encoded viral proteins. A phospholipid envelope that contains the integral proteins P6, P9, P10, and P13 surrounds the viral particles. In species phi 6, host infection requires binding of a multimeric P3 complex to type IV pili. In species varphi8, phi 12, and phi 13, the attachment apparatus is a heteromeric protein assembly that utilizes the rough lipopolysaccharide (rlps) as a receptor. In phi 8 the protein components are designated P3a and P3b while in species phi 12 proteins P3a and P3c have been identified in the complex. The phospholipid envelope of the cystoviruses surrounds a nucleocapsid (NC) composed of two shells. The outer shell is composed of protein P8 with a T=13 icosahedral lattice while the primary component of the inner shell is a dodecahedral frame composed of dimeric protein P1. For the current study, the 3D architecture of the intact phi 12 virus was obtained by electron cryo-tomography. The nucleocapsid appears to be centered within the membrane envelope and possibly attached to it by bridging structures. Two types of densities were observed protruding from the membrane envelope. The densities of the first type were elongated, running parallel, and closely associated to the envelope outer surface. In contrast, the second density was positioned about 12 nm above the envelope connected to it by a flexible low-density stem. This second structure formed a torroidal structure termed "the donut" and appears to inhibit BHT-induced viral envelope fusion.

AID/APOBEC cytosine deaminase induces genome-wide kataegis

PubMed Central

2012-01-01

Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm), are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC proteins. However, a direct link between APOBECs and kataegis is still lacking. We have sequenced the genomes of yeast mutants induced in diploids by expression of the gene for PmCDA1, a hypermutagenic deaminase from sea lamprey. Analysis of the distribution of 5,138 induced mutations revealed localized clusters very similar to those found in tumors. Our data provide evidence that unleashed cytosine deaminase activity is an evolutionary conserved, prominent source of genome-wide kataegis events. Reviewers This article was reviewed by: Professor Sandor Pongor, Professor Shamil R. Sunyaev, and Dr Vladimir Kuznetsov. PMID:23249472

Application of encoded library technology (ELT) to a protein-protein interaction target: discovery of a potent class of integrin lymphocyte function-associated antigen 1 (LFA-1) antagonists.

PubMed

Kollmann, Christopher S; Bai, Xiaopeng; Tsai, Ching-Hsuan; Yang, Hongfang; Lind, Kenneth E; Skinner, Steven R; Zhu, Zhengrong; Israel, David I; Cuozzo, John W; Morgan, Barry A; Yuki, Koichi; Xie, Can; Springer, Timothy A; Shimaoka, Motomu; Evindar, Ghotas

2014-04-01

The inhibition of protein-protein interactions remains a challenge for traditional small molecule drug discovery. Here we describe the use of DNA-encoded library technology for the discovery of small molecules that are potent inhibitors of the interaction between lymphocyte function-associated antigen 1 and its ligand intercellular adhesion molecule 1. A DNA-encoded library with a potential complexity of 4.1 billion compounds was exposed to the I-domain of the target protein and the bound ligands were affinity selected, yielding an enriched small-molecule hit family. Compounds representing this family were synthesized without their DNA encoding moiety and found to inhibit the lymphocyte function-associated antigen 1/intercellular adhesion molecule-1 interaction with submicromolar potency in both ELISA and cell adhesion assays. Re-synthesized compounds conjugated to DNA or a fluorophore were demonstrated to bind to cells expressing the target protein. Copyright © 2014 Elsevier Ltd. All rights reserved.

Using the social amoeba Dictyostelium to study the functions of proteins linked to neuronal ceroid lipofuscinosis.

PubMed

Huber, Robert J

2016-11-24

Neuronal ceroid lipofuscinosis (NCL), also known as Batten disease, is a debilitating neurological disorder that affects both children and adults. Thirteen genetically distinct genes have been identified that when mutated, result in abnormal lysosomal function and an excessive accumulation of ceroid lipofuscin in neurons, as well as other cell types outside of the central nervous system. The NCL family of proteins is comprised of lysosomal enzymes (PPT1/CLN1, TPP1/CLN2, CTSD/CLN10, CTSF/CLN13), proteins that peripherally associate with membranes (DNAJC5/CLN4, KCTD7/CLN14), a soluble lysosomal protein (CLN5), a protein present in the secretory pathway (PGRN/CLN11), and several proteins that display different subcellular localizations (CLN3, CLN6, MFSD8/CLN7, CLN8, ATP13A2/CLN12). Unfortunately, the precise functions of many of the NCL proteins are still unclear, which has made targeted therapy development challenging. The social amoeba Dictyostelium discoideum has emerged as an excellent model system for studying the normal functions of proteins linked to human neurological disorders. Intriguingly, the genome of this eukaryotic soil microbe encodes homologs of 11 of the 13 known genes linked to NCL. The genetic tractability of the organism, combined with its unique life cycle, makes Dictyostelium an attractive model system for studying the functions of NCL proteins. Moreover, the ability of human NCL proteins to rescue gene-deficiency phenotypes in Dictyostelium suggests that the biological pathways regulating NCL protein function are likely conserved from Dictyostelium to human. In this review, I will discuss each of the NCL homologs in Dictyostelium in turn and describe how future studies can exploit the advantages of the system by testing new hypotheses that may ultimately lead to effective therapy options for this devastating and currently untreatable neurological disorder.

Organic light-emitting diodes with a spacer enhanced exciplex emission

NASA Astrophysics Data System (ADS)

Yan, Fei; Chen, Rui; Sun, Handong; Wei Sun, Xiao

2014-04-01

By introducing a spacer molecule into the blended exciplex emissive layer, the performance of the bulk heterojunction exciplex organic light-emitting diodes (OLEDs) was improved dramatically; the maximum luminous efficiency was enhanced by about 22% from 7.9 cd/A to 9.7 cd/A, and the luminous efficiency drop was reduced by 28% at 400 mA/cm2. Besides the suppressed annihilation of exciton, the time-resolved photoluminescence measurements indicated that the spacer enhanced the delayed fluorescence through increasing the backward intersystem crossing rate from the triplet to singlet exciplex state. This method is useful for developing high performance exciplex OLEDs.

Lie construction affects information storage under high memory load condition.

PubMed

Liu, Yuqiu; Wang, Chunjie; Jiang, Haibo; He, Hongjian; Chen, Feiyan

2017-01-01

Previous studies indicate that lying consumes cognitive resources, especially working memory (WM) resources. Considering the dual functions that WM might play in lying: holding the truth-related information and turning the truth into lies, the present study examined the relationship between the information storage and processing in the lie construction. To achieve that goal, a deception task based on the old/new recognition paradigm was designed, which could manipulate two levels of WM load (low-load task using 4 items and high-load task using 6 items) during the deception process. The analyses based on the amplitude of the contralateral delay activity (CDA), a proved index of the number of representations being held in WM, showed that the CDA amplitude was lower in the deception process than that in the truth telling process under the high-load condition. In contrast, under the low-load condition, no CDA difference was found between the deception and truth telling processes. Therefore, we deduced that the lie construction and information storage compete for WM resources; when the available WM resources cannot meet this cognitive demand, the WM resources occupied by the information storage would be consumed by the lie construction.

Lie construction affects information storage under high memory load condition

PubMed Central

Liu, Yuqiu; Wang, Chunjie; Jiang, Haibo; He, Hongjian; Chen, Feiyan

2017-01-01

Previous studies indicate that lying consumes cognitive resources, especially working memory (WM) resources. Considering the dual functions that WM might play in lying: holding the truth-related information and turning the truth into lies, the present study examined the relationship between the information storage and processing in the lie construction. To achieve that goal, a deception task based on the old/new recognition paradigm was designed, which could manipulate two levels of WM load (low-load task using 4 items and high-load task using 6 items) during the deception process. The analyses based on the amplitude of the contralateral delay activity (CDA), a proved index of the number of representations being held in WM, showed that the CDA amplitude was lower in the deception process than that in the truth telling process under the high-load condition. In contrast, under the low-load condition, no CDA difference was found between the deception and truth telling processes. Therefore, we deduced that the lie construction and information storage compete for WM resources; when the available WM resources cannot meet this cognitive demand, the WM resources occupied by the information storage would be consumed by the lie construction. PMID:28727794

Influence of cytarabine metabolic pathway polymorphisms in acute myeloid leukemia induction treatment.

PubMed

Megías-Vericat, Juan Eduardo; Montesinos, Pau; Herrero, María José; Moscardó, Federico; Bosó, Virginia; Martínez-Cuadrón, David; Rojas, Luis; Rodríguez-Veiga, Rebeca; Boluda, Blanca; Sendra, Luis; Cervera, José; Poveda, José Luis; Sanz, Miguel Ángel; Aliño, Salvador F

2017-12-01

Cytarabine is considered the most effective chemotherapeutic option in acute myeloid leukemia (AML). The impact of 10 polymorphisms in cytarabine metabolic pathway genes were evaluated in 225 adult de novo AML patients. Variant alleles of DCK rs2306744 and CDA rs602950 showed higher complete remission (p = .024, p = .045), with lower survival rates for variant alleles of CDA rs2072671 (p = .015, p = .045, p = .032), rs3215400 (p = .033) and wild-type genotype of rs602950 (p = .039, .014). Induction death (p = .033) and lower survival rates (p = .021, p = .047) were correlated to RRM1 rs9937 variant allele. In addition, variant alleles of CDA rs532545 and rs602950 were related to skin toxicity (p = .031, p = .049) and mucositis to DCK rs2306744 minor allele (p = .046). Other toxicities associated to variant alleles were hepatotoxicity to NT5C2 rs11598702 (p = .032), lung toxicity (p = .031) and thrombocytopenia to DCK rs4694362 (p = .046). This study supports the interest of cytarabine pathway polymorphisms regarding efficacy and toxicity of AML therapy in a coherent integrated manner.

AIDS groups challenge Federal Internet censorship law.

PubMed

1996-05-03

The Communications Decency Act (CDA), a section of the 1996 telecommunications reform law, bans indecent and patently offensive expression from all online systems available to those under the age of 18. AIDS organizations and the American Civil Liberties Union (ACLU) filed suit in U.S. District Court in Philadelphia, PA,to challenge the law. The ACLU contends that the CDA law is unconstitutional because it criminalizes expression that is protected by the First Amendment, and violates constitutional rights to privacy. The CDA also would impede dissemination of HIV prevention information, according to AIDS online services. Operators of these electronic information systems state that providing explicit language about safe sexual practices is essential if teenagers are to understand how to prevent HIV infection. Additionally, content providers argue that it is almost impossible to know what text or images must be censored in order to avoid government prosecution. Expert witnesses testifying for the U.S. Government stated that there are means available to purge Internet sites of materials that might be regarded as indecent. The ACLU recommends utilizing a software package that would enable parents to control their children's Internet access without requiring broad censorship.

Therapeutic and neurotoxic effects of 2-chlorodeoxyadenosine in adults with acute myeloid leukemia.

PubMed

Vahdat, L; Wong, E T; Wile, M J; Rosenblum, M; Foley, K M; Warrell, R P

1994-11-15

Despite expectations that 2-chlorodeoxyadenosine (2-CdA) would prove active primarily in lymphoproliferative diseases, early reports suggested unexpected high activity of this drug in heavily pretreated children with acute myeloblastic leukemia (AML) at a maximally tolerated dose of 8.9 mg/m2/day for 5 days. In view of these findings, we conducted an escalating dose trial of 2-CdA in adult patients with relapsed or resistant AML. Thirty-six patients who had received extensive prior therapy were treated at 9 dose levels of 2-CdA at daily doses ranging from 5 to 21 mg/m2 for 5 days. 2-CdA eliminated leukemic blasts from the peripheral blood in 32 of 36 cases; however, bone marrow hypoplasia was seen only at daily dose levels > or = 15 mg/m2. We observed a total of 3 complete remissions: 1 at the 15 mg/m2/d dose level and 2 at the 21 mg/m2/d dose level; these responses persisted for 3, 2, and 3 months, respectively. Although prolonged myelosuppression would have been dose-limiting at 21 mg/m2/d for 5 days, the most important adverse effect was the development of a sensorimotor peripheral neuropathy. This reaction, whose onset was substantially delayed after completion of drug treatment, was observed in 2 of 5 patients at the 19 mg/m2/d level and in 4 of 4 evaluable patients at the 21 mg/m2/d level. Pathologically, this process was characterized by axonal degeneration and secondary demyelination. Other side effects included reactivation of a posttransplant Epstein-Barr virus-related lymphoma in 1 patient and tumor lysis syndrome. We conclude that the maximally tolerable dose of 2-CdA in adult patients (17 mg/m2/d for 5 days) in approximately twofold in excess of that previously reported in children and that the limiting toxic effect is a degenerative neuropathic disorder. We confirm that this drug has definite activity in AML, but the magnitude of this effect needs to be determined in larger numbers of patients who have received less extensive therapy. This agent deserves further evaluation in patients with both AML and acute lymphoblastic leukemia at these higher doses and perhaps as part of a preparative regimen for patients undergoing bone marrow transplantation.

Mutational analysis of FLASH and PTPN13 genes in colorectal carcinomas.

PubMed

Jeong, Eun Goo; Lee, Sung Hak; Yoo, Nam Jin; Lee, Sug Hyung

2008-01-01

The Fas-Fas ligand system is considered a major pathway for induction of apoptosis in cells and tissues. FLASH was identified as a pro-apoptotic protein that transmits apoptosis signal during Fas-mediated apoptosis. PTPN13 interacts with Fas and functions as both suppressor and inducer of Fas-mediated apoptosis. There are polyadenine tracts in both FLASH (A8 and A9 in exon 8) and PTPN13 (A8 in exon 7) genes that could be frameshift mutation targets in colorectal carcinomas. Because genes encoding proteins in Fas-mediated apoptosis frequently harbor somatic mutations in cancers, we explored the possibility as to whether mutations of FLASH and PTPN13 are a feature of colorectal carcinomas. We analysed human FLASH in exon 8 and PTPN13 in exon 7 for the detection of somatic mutations in 103 colorectal carcinomas by a polymerase chain reaction (PCR)- based single-strand conformation polymorphism (SSCP). We detected two mutations in FLASH gene, but none in PTPN13 gene. However, the two mutations were not frameshift (deletion or insertion) mutations in the polyadenine tracts of FLASH. The two mutations consisted of a deletion mutation (c.3734-3737delAGAA) and a missense mutation (c.3703A>C). These data indicate that frameshift mutation in the polyadenine tracts in both FLASH and PTPN13 genes is rare in colorectal carcinomas. Also, the data suggest that both FLASH and PTPN13 mutations in the polyadenine tracts may not have a crucial role in the pathogenesis of colorectal carcinomas.

L-Ilf3 and L-NF90 Traffic to the Nucleolus Granular Component: Alternatively-Spliced Exon 3 Encodes a Nucleolar Localization Motif

PubMed Central

Viranaicken, Wildriss; Gasmi, Laila; Chaumet, Alexandre; Durieux, Christiane; Georget, Virginie; Denoulet, Philippe; Larcher, Jean-Christophe

2011-01-01

Ilf3 and NF90, two proteins containing double-stranded RNA-binding domains, are generated by alternative splicing and involved in several functions. Their heterogeneity results from posttranscriptional and posttranslational modifications. Alternative splicing of exon 3, coding for a 13 aa N-terminal motif, generates for each protein a long and short isoforms. Subcellular fractionation and localization of recombinant proteins showed that this motif acts as a nucleolar localization signal. Deletion and substitution mutants identified four arginines, essential for nucleolar targeting, and three histidines to stabilize the proteins within the nucleolus. The short isoforms are never found in the nucleoli, whereas the long isoforms are present in the nucleoplasm and the nucleoli. For Ilf3, only the posttranslationally-unmodified long isoform is nucleolar, suggesting that this nucleolar targeting is abrogated by posttranslational modifications. Confocal microscopy and FRAP experiments have shown that the long Ilf3 isoform localizes to the granular component of the nucleolus, and that L-Ilf3 and L-NF90 exchange rapidly between nucleoli. The presence of this 13 aminoacid motif, combined with posttranslational modifications, is responsible for the differences in Ilf3 and NF90 isoforms subcellular localizations. The protein polymorphism of Ilf3/NF90 and the various subcellular localizations of their isoforms may partially explain the various functions previously reported for these proteins. PMID:21811582

Disruption of Fgf13 causes synaptic excitatory-inhibitory imbalance and genetic epilepsy and febrile seizures plus.

PubMed

Puranam, Ram S; He, Xiao Ping; Yao, Lijun; Le, Tri; Jang, Wonjo; Rehder, Catherine W; Lewis, Darrell V; McNamara, James O

2015-06-10

We identified a family in which a translocation between chromosomes X and 14 was associated with cognitive impairment and a complex genetic disorder termed "Genetic Epilepsy and Febrile Seizures Plus" (GEFS(+)). We demonstrate that the breakpoint on the X chromosome disrupted a gene that encodes an auxiliary protein of voltage-gated Na(+) channels, fibroblast growth factor 13 (Fgf13). Female mice in which one Fgf13 allele was deleted exhibited hyperthermia-induced seizures and epilepsy. Anatomic studies revealed expression of Fgf13 mRNA in both excitatory and inhibitory neurons of hippocampus. Electrophysiological recordings revealed decreased inhibitory and increased excitatory synaptic inputs in hippocampal neurons of Fgf13 mutants. We speculate that reduced expression of Fgf13 impairs excitability of inhibitory interneurons, resulting in enhanced excitability within local circuits of hippocampus and the clinical phenotype of epilepsy. These findings reveal a novel cause of this syndrome and underscore the powerful role of FGF13 in control of neuronal excitability. Copyright © 2015 the authors 0270-6474/15/358866-16$15.00/0.

CIP1 polypeptides and their uses

DOEpatents

Foreman, Pamela [Los Altos, CA; Van Solingen, Pieter [Naaldwijk, NL; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA

2011-04-12

Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

Engineering Encodable Lanthanide-Binding Tags (LBTs) into Loop Regions of Proteins

PubMed Central

Barthelmes, Katja; Reynolds, Anne M.; Peisach, Ezra; Jonker, Hendrik R. A.; DeNunzio, Nicholas J.; Allen, Karen N.; Imperiali, Barbara; Schwalbe, Harald

2011-01-01

Lanthanide-binding-tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography and luminescence studies. We have inserted LBTs into three different loop positions (denoted L, R, and S) of the model protein interleukin-1β and varied the length of the spacer between the LBT and the protein (denoted 1-3). Luminescence studies demonstrate that all nine constructs bind Tb3+ tightly in the low nanomolar range. No significant change in the fusion protein occurs from insertion of the LBT, as shown by two X-ray crystallographic structures of the IL1β-S1 and IL1β-L3 constructs and for the remaining constructs by comparing 1H-15N-HSQC NMR spectra with wild-type IL1β. Additionally, binding of LBT-loop IL1β proteins to their native binding partner in vitro remains unaltered. X-ray crystallographic phasing was successful using only the signal from the bound lanthanide. Large residual dipolar couplings (RDCs) could be determined by NMR spectroscopy for all LBT-loop-constructs and revealed that the LBT-2 series were rigidly incorporated into the interleukin-1β structure. The paramagnetic NMR spectra of loop-LBT mutant IL1β-R2 were assigned and the Δχ tensor components were calculated based on RDCs and pseudocontact shifts (PCSs). A structural model of the IL1β-R2 construct was calculated using the paramagnetic restraints. The current data provide support that encodable LBTs serve as versatile biophysical tags when inserted into loop regions of proteins of known structure or predicted via homology modelling. PMID:21182275

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

Hervey, IV, William Judson; Khalsa-Moyers, Gurusahai K; Lankford, Patricia K

Protein enrichments of engineered, affinity-tagged (or bait ) fusion proteins with interaction partners are often laden with background, non-specific proteins, due to interactions that occur in vitro as an artifact of the technique. Furthermore, the in vivo expression of the bait protein may itself affect physiology or metabolism. In this study, intrinsic affinity purification challenges were investigated in a model protein complex, DNA-dependent RNA polymerase (RNAP), encompassing chromosome- and plasmid-encoding strategies for bait proteins in two different microbial species: Escherichia coli and Rhodopseudomonas palustris. Isotope ratio measurements of bait protein expression strains relative to native, wild-type strains were performed bymore » liquid chromatography tandem mass spectrometry (LC-MS-MS) to assess bait protein expression strategies in each species. Authentic interacting proteins of RNAP were successfully discerned from artifactual co-isolating proteins by the isotopic differentiation of interactions as random or targeted (I-DIRT) method (A. J. Tackett et al. J. Proteome Res. 2005, 4 (5), 1752-1756). To investigate broader effects of bait protein production in the bacteria, we compared proteomes from strains harboring a plasmid that encodes an affinity-tagged subunit (RpoA) of the RNAP complex with the corresponding wild-type strains using stable isotope metabolic labeling. The ratio of RpoA abundance in plasmid strains versus wild type was 0.8 for R. palustris and 1.7 for E. coli. While most other proteins showed no appreciable difference, proteins significantly increased in abundance in plasmid-encoded bait-expressing strains of both species included the plasmid encoded antibiotic resistance protein, GenR and proteins involved in amino acid biosynthesis. Together, these local, complex-specific and more global, whole proteome isotopic abundance ratio measurements provided a tool for evaluating both in vivo and in vitro effects of plasmid-encoding strategies for bait protein expression. This approach has the potential for enabling discovery of protein-protein interactions among the growing number of sequenced microbial species without the need for development of chromosomal insertion systems.« less

Targeted next-generation sequencing helps to decipher the genetic and phenotypic heterogeneity of hypertrophic cardiomyopathy

PubMed Central

Cecconi, Massimiliano; Parodi, Maria I.; Formisano, Francesco; Spirito, Paolo; Autore, Camillo; Musumeci, Maria B.; Favale, Stefano; Forleo, Cinzia; Rapezzi, Claudio; Biagini, Elena; Davì, Sabrina; Canepa, Elisabetta; Pennese, Loredana; Castagnetta, Mauro; Degiorgio, Dario; Coviello, Domenico A.

2016-01-01

Hypertrophic cardiomyopathy (HCM) is mainly associated with myosin, heavy chain 7 (MYH7) and myosin binding protein C, cardiac (MYBPC3) mutations. In order to better explain the clinical and genetic heterogeneity in HCM patients, in this study, we implemented a target-next generation sequencing (NGS) assay. An Ion AmpliSeq™ Custom Panel for the enrichment of 19 genes, of which 9 of these did not encode thick/intermediate and thin myofilament (TTm) proteins and, among them, 3 responsible of HCM phenocopy, was created. Ninety-two DNA samples were analyzed by the Ion Personal Genome Machine: 73 DNA samples (training set), previously genotyped in some of the genes by Sanger sequencing, were used to optimize the NGS strategy, whereas 19 DNA samples (discovery set) allowed the evaluation of NGS performance. In the training set, we identified 72 out of 73 expected mutations and 15 additional mutations: the molecular diagnosis was achieved in one patient with a previously wild-type status and the pre-excitation syndrome was explained in another. In the discovery set, we identified 20 mutations, 5 of which were in genes encoding non-TTm proteins, increasing the diagnostic yield by approximately 20%: a single mutation in genes encoding non-TTm proteins was identified in 2 out of 3 borderline HCM patients, whereas co-occuring mutations in genes encoding TTm and galactosidase alpha (GLA) altered proteins were characterized in a male with HCM and multiorgan dysfunction. Our combined targeted NGS-Sanger sequencing-based strategy allowed the molecular diagnosis of HCM with greater efficiency than using the conventional (Sanger) sequencing alone. Mutant alleles encoding non-TTm proteins may aid in the complete understanding of the genetic and phenotypic heterogeneity of HCM: co-occuring mutations of genes encoding TTm and non-TTm proteins could explain the wide variability of the HCM phenotype, whereas mutations in genes encoding only the non-TTm proteins are identifiable in patients with a milder HCM status. PMID:27600940

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

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

Kohler, Annegret; Kuo, Alan; Nagy, Laszlo G.

To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergentmore » evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.« less

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

DOE PAGES

Kohler, Annegret; Kuo, Alan; Nagy, Laszlo G.; ...

2015-02-23

To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergentmore » evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.« less

Chromatic Multifocal Pupillometer for Objective Perimetry and Diagnosis of Patients with Retinitis Pigmentosa.

PubMed

Chibel, Ron; Sher, Ifat; Ben Ner, Daniel; Mhajna, Mohamad O; Achiron, Asaf; Hajyahia, Soad; Skaat, Alon; Berchenko, Yakir; Oberman, Bernice; Kalter-Leibovici, Ofra; Freedman, Laurence; Rotenstreich, Ygal

2016-09-01

To assess visual field (VF) defects and retinal function objectively in healthy participants and patients with retinitis pigmentosa (RP) using a chromatic multifocal pupillometer. Cross-sectional study. The right eyes of 16 healthy participants and 13 RP patients. Pupil responses to red and blue light (peak, 485 and 625 nm, respectively) presented by 76 light-emitting diodes, 1.8-mm spot size at different locations of a 16.2° VF were recorded. Subjective VFs of RP patients were determined using chromatic dark-adapted Goldmann VFs (CDA-GVFs). Six healthy participants underwent 2 pupillometer examinations to determine test-retest reliability. Three parameters of pupil contraction were determined automatically: percentage of change of pupil size (PPC), maximum contraction velocity (MCV; in pixels per second), and latency of MCV (LMCV; in seconds). The fraction of functional VF was determined by CDA-GVF. In healthy participants, higher PPC and MCV were measured in response to blue compared with red light. The LMCV in response to blue light was relatively constant throughout the VF. Healthy participants demonstrated higher PPC and MCV and shorter LMCV in central compared with peripheral test points in response to red light. Test-retest correlation coefficients were 0.7 for PPC and 0.5 for MCV. In RP patients, test point in which the PPC and MCV were lower than 4 standard errors from the mean of healthy participants correlated with areas that were indicated as nonseeing by CDA-GVF. The mean absolute deviation in LMCV parameter in response to the red light between different test point was significantly higher in RP patients (range, 0.16-0.47) than in healthy participants (range, 0.02-0.16; P < 0.0001) and indicated its usefulness as a diagnostic tool with high sensitivity and specificity (area under the receiver operating characteristic curve (AUC), 0.97, Mann-Whitney-Wilcoxon analysis). Randomly reducing the number of test points to a total of 15 points did not significantly reduce the AUC in RP diagnosis based on this parameter. This study demonstrates the feasibility of using a chromatic multifocal pupillometer for objective diagnosis of RP and assessment of VF defects. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Copper-induced activation of TRP channels promotes extracellular calcium entry and activation of CaMK, PKA, PKC, PKG and CBLPK leading to increased expression of antioxidant enzymes in Ectocarpus siliculosus.

PubMed

González, Alberto; Sáez, Claudio A; Morales, Bernardo; Moenne, Alejandra

2018-05-01

The existence of functional Transient Receptor Potential (TRP) channels was analyzed in Ectocarpus siliculosus using agonists of human TRPs and specific antagonists of TRPA1, TRPC5, TRPM8 and TRPV; intracellular calcium was detected for 60 min. Increases in intracellular calcium were observed at 13, 29, 39 and 50-52 min, which appeared to be mediated by the activation of TRPM8/V1 at 13 min, TRPV1 at 29 min, TRPA1/V1 at 39 min and TRPA1/C5 at 50-52 min. In addition, intracellular calcium increases appear to be due to extracellular calcium entry, not requiring protein kinase activation. On the other hand, 2.5 μM copper exposure induced increased intracellular calcium at 13, 29, 39 and 51 min, likely due to the activation of a TRPA1/V1 at 13 min, TRPA1/C5/M8 at 29 min, TRPC5/M8 at 39 min, and a TRPC5/V1 at 51 min. The increases in intracellular calcium induced by copper were due to extracellular calcium entry and required protein kinase activation. Furthermore, from 3 to 24 h, copper exposure induced an increase in the level of transcripts encoding antioxidant enzymes such as superoxide dismutase, ascorbate peroxidase, glutathione reductase and peroxiredoxin. The described upregulation decreased with inhibitors of CaMK, PKA, PKC, PKG and CBLPK, as well as with a mixture of TRP inhibitors. Thus, copper induces the activation of TRP channels allowing extracellular calcium entry as well as the activation of CaMK, PKA, PKC, PKG and CBLPK leading to increased expression of genes encoding antioxidant enzymes in E. siliculosus. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase.

PubMed

Amiour, Nardjis; Imbaud, Sandrine; Clément, Gilles; Agier, Nicolas; Zivy, Michel; Valot, Benoît; Balliau, Thierry; Quilleré, Isabelle; Tercé-Laforgue, Thérèse; Dargel-Graffin, Céline; Hirel, Bertrand

2014-11-20

To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production. The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the "omics" considered at the vegetative stage of plant development, or during the grain filling period. This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three "omics" procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production.

FluG affects secretion in colonies of Aspergillus niger.

PubMed

Wang, Fengfeng; Krijgsheld, Pauline; Hulsman, Marc; de Bekker, Charissa; Müller, Wally H; Reinders, Marcel; de Vries, Ronald P; Wösten, Han A B

2015-01-01

Colonies of Aspergillus niger are characterized by zonal heterogeneity in growth, sporulation, gene expression and secretion. For instance, the glucoamylase gene glaA is more highly expressed at the periphery of colonies when compared to the center. As a consequence, its encoded protein GlaA is mainly secreted at the outer part of the colony. Here, multiple copies of amyR were introduced in A. niger. Most transformants over-expressing this regulatory gene of amylolytic genes still displayed heterogeneous glaA expression and GlaA secretion. However, heterogeneity was abolished in transformant UU-A001.13 by expressing glaA and secreting GlaA throughout the mycelium. Sequencing the genome of UU-A001.13 revealed that transformation had been accompanied by deletion of part of the fluG gene and disrupting its 3' end by integration of a transformation vector. Inactivation of fluG in the wild-type background of A. niger also resulted in breakdown of starch under the whole colony. Asexual development of the ∆fluG strain was not affected, unlike what was previously shown in Aspergillus nidulans. Genes encoding proteins with a signal sequence for secretion, including part of the amylolytic genes, were more often downregulated in the central zone of maltose-grown ∆fluG colonies and upregulated in the intermediate part and periphery when compared to the wild-type. Together, these data indicate that FluG of A. niger is a repressor of secretion.

Protein trans-splicing on an M13 bacteriophage: towards directed evolution of a semisynthetic split intein by phage display.

PubMed

Garbe, Daniel; Thiel, Ilka V; Mootz, Henning D

2010-10-01

Split inteins link their fused peptide or protein sequences with a peptide bond in an autocatalytic reaction called protein trans-splicing. This reaction is becoming increasingly important for a variety of applications in protein semisynthesis, polypeptide circularisation, construction of biosensors, or segmental isotopic labelling of proteins. However, split inteins exhibit greatly varying solubility, efficiency and tolerance towards the nature of the fused sequences as well as reaction conditions. We envisioned that phage display as an in vitro selection technique would provide a powerful tool for the directed evolution of split inteins with improved properties. As a first step towards this goal, we show that presentation of active split inteins on an M13 bacteriophage is feasible. Two different C-terminal intein fragments of the Ssp DnaB intein, artificially split at amino acid positions 104 and 11, were encoded in a phagemid vector in fusion to a truncated gpIII protein. For efficient production of hybrid phages, the presence of a soluble domain tag at their N-termini was necessary. Immunoblot analysis revealed that the hybrid phages supported protein trans-splicing with a protein or a synthetic peptide, respectively, containing the complementary intein fragment. Incorporation of biotin or desthiobiotin by this reaction provides a straightforward strategy for future enrichment of desired mutants from randomised libraries of the C-terminal intein fragments on streptavidin beads. Protein semisynthesis on a phage could also be exploited for the selection of chemically modified proteins with unique properties. © 2010 European Peptide Society and John Wiley & Sons, Ltd.

Recombinant constructs of Borrelia burgdorferi

DOEpatents

Dattwyler, Raymond J.; Gomes-Solecki, Maria J. C.; Luft, Benjamin J.; Dunn, John J.

2007-02-20

Novel chimeric nucleic acids, encoding chimeric Borrelia proteins comprising OspC or an antigenic fragment thereof and OspA or an antigenic fragment thereof, are disclosed. Chimeric proteins encoded by the nucleic acid sequences are also disclosed. The chimeric proteins are useful as vaccine immunogens against Lyme borreliosis, as well as for immunodiagnostic reagents.

An ankyrin-like protein with transmembrane domains is specifically lost after oncogenic transformation of human fibroblasts.

PubMed

Jaquemar, D; Schenker, T; Trueb, B

1999-03-12

We have identified a novel transformation-sensitive mRNA, which is present in cultured fibroblasts but is lacking in SV40 transformed cells as well as in many mesenchymal tumor cell lines. The corresponding gene is located on human chromosome 8 in band 8q13. The open reading frame of the mRNA encodes a protein of 1119 amino acids forming two distinct domains. The N-terminal domain consists of 18 repeats that are related to the cytoskeletal protein ankyrin. The C-terminal domain contains six putative transmembrane segments that resemble many ion channels. This overall structure is reminiscent of TRP-like proteins that function as store-operated calcium channels. The novel protein with an Mr of 130 kDa is expressed at a very low level in human fibroblasts and at a moderate level in liposarcoma cells. Overexpression in eukaryotic cells appears to interfere with normal growth, suggesting that it might play a direct or indirect role in signal transduction and growth control.

Shared and novel molecular responses of mandarin to drought.

PubMed

Gimeno, Jacinta; Gadea, José; Forment, Javier; Pérez-Valle, Jorge; Santiago, Julia; Martínez-Godoy, María A; Yenush, Lynne; Bellés, José M; Brumós, Javier; Colmenero-Flores, José M; Talón, Manuel; Serrano, Ramón

2009-07-01

Drought is the most important stress experienced by citrus crops. A citrus cDNA microarray of about 6.000 genes has been utilized to identify transcriptomic responses of mandarin to water stress. As observed in other plant species challenged with drought stress, key genes for lysine catabolism, proline and raffinose synthesis, hydrogen peroxide reduction, vacuolar malate transport, RCI2 proteolipids and defence proteins such as osmotin, dehydrins and heat-shock proteins are induced in mandarin. Also, some aquaporin genes are repressed. The osmolyte raffinose could be detected in stressed roots while the dehydrin COR15 protein only accumulated in stressed leaves but not in roots. Novel drought responses in mandarin include the induction of genes encoding a new miraculin isoform, chloroplast beta-carotene hydroxylase, oleoyl desaturase, ribosomal protein RPS13A and protein kinase CTR1. These results suggest that drought tolerance in citrus may benefit from inhibition of proteolysis, activation of zeaxanthin and linolenoyl synthesis, reinforcement of ribosomal structure and down-regulation of the ethylene response.

Recombinant HT{sub m4} gene, protein and assays

DOEpatents

Lim, B.; Adra, C.N.; Lelias, J.M.

1996-09-03

The invention relates to a recombinant DNA molecule which encodes a HT{sub m4} protein, a transformed host cell which has been stably transfected with a DNA molecule which encodes a HT{sub m4} protein and a recombinant HT{sub m4} protein. The invention also relates to a method for detecting the presence of a hereditary atopy. 2 figs.

Recombinant HT.sub.m4 gene, protein and assays

DOEpatents

Lim, Bing; Adra, Chaker N.; Lelias, Jean-Michel

1996-01-01

The invention relates to a recombinant DNA molecule which encodes a HT.sub.m4 protein, a transformed host cell which has been stably transfected with a DNA molecule which encodes a HT.sub.m4 protein and a recombinant HT.sub.m4 protein. The invention also relates to a method for detecting the presence of a hereditary atopy.

A member of a new plant gene family encoding a meprin and TRAF homology (MATH) domain-containing protein is involved in restriction of long distance movement of plant viruses

PubMed Central

Cosson, Patrick; Sofer, Luc; Schurdi-Levraud, Valérie

2010-01-01

Restriction of long distance movement of several potyviruses in Arabidopsis thaliana is controlled by at least three dominant restricted TEV movement (RTM) genes, named RTM1, RTM2 and RTM3 and acts as a non-conventional resistance. RTM1 encodes a protein belonging to the jacalin family and RTM2 encodes a protein which has similarities to small heat shock proteins. The recent cloning of RTM3 which encodes a protein belonging to an unknown protein family of 29 members that has a meprin and TRAF homology (MATH) domain in its N-terminal region and a coiled-coil (CC) domain at its C-terminal end is an important breakthrough for a better understanding of this resistance process. Not only the third gene involved in this resistance has been identified and has allowed revealing a new gene family in plant but the discovery that the RTM3 protein interacts directly with RTM1 strongly suggests that the RTM proteins form a multimeric complex. However, these data also highlight striking similarities of the RTM resistance with the well known R-gene mediated resistance. PMID:20930558

Four rice seed cDNA clones belonging to the alpha-amylase/trypsin inhibitor gene family encode potential rice allergens.

PubMed

Alvarez, A M; Fukuhara, E; Nakase, M; Adachi, T; Aoki, N; Nakamura, R; Matsuda, T

1995-07-01

Four rice seed proteins encoded by cDNAs belonging to the alpha-amylase/trypsin inhibitor gene family were overexpressed as TrpE-fusion proteins in E. coli. The expressed rice proteins were detected by SDS-PAGE as major proteins in bacterial cell lysates. Western blot analyses showed that all the recombinant proteins were immunologically reactive to rabbit polyclonal antibodies and to a mouse monoclonal antibody (25B9) specific for a previously isolated rice allergen of 16 kDa. Some truncated proteins from deletion mutants of the cDNAs retained their reactivity to the specific antibodies. These results suggest that the cDNAs encode potential rice allergens and that some epitopes of the recombinant proteins are still immunoreactive when they are expressed as their fragments.

RNA-guided transcriptional regulation

DOEpatents

Church, George M.; Mali, Prashant G.; Esvelt, Kevin M.

2016-02-23

Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

Molecular cloning and nucleotide sequences of the genes for two essential proteins constituting a novel enzyme system for heptaprenyl diphosphate synthesis.

PubMed

Koike-Takeshita, A; Koyama, T; Obata, S; Ogura, K

1995-08-04

The genes encoding two dissociable components essential for Bacillus stearothermophilus heptaprenyl diphosphate synthase (all-trans-hexparenyl-diphosphate:isopentenyl-diphosphate hexaprenyl-trans-transferase, EC 2.5.1.30) were cloned, and their nucleotide sequences were determined. Sequence analyses revealed the presence of three open reading frames within 2,350 base pairs, designated as ORF-1, ORF-2, and ORF-3 in order of nucleotide sequence, which encode proteins of 220, 234, and 323 amino acids, respectively. Deletion experiments have shown that expression of the enzymatic activity requires the presence of ORF-1 and ORF-3, but ORF-2 is not essential. As a result, this enzyme was proved genetically to consist of two different protein compounds with molecular masses of 25 kDa (Component I) and 36 kDa (Component II), encoded by two of the three tandem genes. The protein encoded by ORF-1 has no similarity to any protein so far registered. However, the protein encoded by ORF-3 shows a 32% similarity to the farnesyl diphosphate synthase of the same bacterium and has seven highly conserved regions that have been shown typical in prenyltransferases (Koyama, T., Obata, S., Osabe, M., Takeshita, A., Yokoyama, K., Uchida, M., Nishino, T., and Ogura, K. (1993) J. Biochem. (Tokyo) 113, 355-363).

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

PubMed Central

Glass, Jennifer B.; Kretz, Cecilia B.; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L.; Buck, Kristen N.; Landing, William M.; Morton, Peter L.; Moffett, James W.; Giovannoni, Stephen J.; Vergin, Kevin L.; Stewart, Frank J.

2015-01-01

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3−, NO2−, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu. PMID:26441925

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.

PubMed

Glass, Jennifer B; Kretz, Cecilia B; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L; Buck, Kristen N; Landing, William M; Morton, Peter L; Moffett, James W; Giovannoni, Stephen J; Vergin, Kevin L; Stewart, Frank J

2015-01-01

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

Expression and Characterization of a Novel Antifungal Exo-β-1,3-glucanase from Chaetomium cupreum.

PubMed

Jiang, Cheng; Song, Jinzhu; Cong, Hua; Zhang, Junzheng; Yang, Qian

2017-05-01

A novel β-1,3-glucanase gene, designated Ccglu17A, was cloned from the biological control fungus Chaetomium cupreum Ame. Its 1626-bp open reading frame encoded 541 amino acids. The corresponding amino acid sequence showed highest identity (67 %) with a glycoside hydrolase family 17 β-1,3-glucanase from Chaetomium globosum. The recombinant protein Ccglu17A was successfully expressed in Pichia pastoris, and the enzyme was purified to homogeneity with 10.1-fold purification and 47.8 % recovery yield. The protein's molecular mass was approximately 65 kDa, and its maximum activity appeared at pH 5.0 and temperature 45 °C. Heavy metal ions Fe 2+ , Mn 2+ , Cu 2+ , Co 2+ , Ag + , and Hg 2+ had inhibitory effects on Ccglu17A, but Ba 2+ promoted the enzyme's activity. Ccglu17A exhibited high substrate specificity, almost exclusively catalyzing β-1,3-glycosidic bond cleavage in various polysaccharoses to liberate glucose. The enzyme had a Km of 2.84 mg/mL and Vmax of 10.7 μmol glucose/min/mg protein for laminarin degradation under optimal conditions. Ccglu17A was an exoglucanase with transglycosylation activity based on its hydrolytic properties. It showed potential antifungal activity with a degradative effect on cell walls and inhibitory action against the germination of pathogenic fungus. In conclusion, Ccglu17A is the first functional exo-1,3-β-glucanase to be identified from C. cupreum and has potential applicability in industry and agriculture.

Detection of hepatitis B virus X product using an open reading frame Escherichia coli expression vector.

PubMed Central

Elfassi, E; Haseltine, W A; Dienstag, J L

1986-01-01

The genome of the hepatitis B virus (HBV) contains a sequence, designated X, capable of encoding a protein of 154 amino acids. To determine whether the putative protein synthesized from this region is antigenic, we examined the sera of HBV-infected patients for the ability to react with a hybrid protein that contained 133 amino acids encoded by the X region and portions of the bacterial ompF and beta-galactosidase genes. Some HBV-positive sera tested contained antibodies that specifically recognized the hybrid protein. All sera were from patients diagnosed as suffering from chronic active hepatitis. We conclude that the X region of HBV encodes a protein and that this protein is antigenic in some patients. Images PMID:3515347

Genetic architecture of artemisinin-resistant Plasmodium falciparum

PubMed Central

Miotto, Olivo; Amato, Roberto; Ashley, Elizabeth A; MacInnis, Bronwyn; Almagro-Garcia, Jacob; Amaratunga, Chanaki; Lim, Pharath; Mead, Daniel; Oyola, Samuel O; Dhorda, Mehul; Imwong, Mallika; Woodrow, Charles; Manske, Magnus; Stalker, Jim; Drury, Eleanor; Campino, Susana; Amenga-Etego, Lucas; Thanh, Thuy-Nhien Nguyen; Tran, Hien Tinh; Ringwald, Pascal; Bethell, Delia; Nosten, Francois; Phyo, Aung Pyae; Pukrittayakamee, Sasithon; Chotivanich, Kesinee; Chuor, Char Meng; Nguon, Chea; Suon, Seila; Sreng, Sokunthea; Newton, Paul N; Mayxay, Mayfong; Khanthavong, Maniphone; Hongvanthong, Bouasy; Htut, Ye; Han, Kay Thwe; Kyaw, Myat Phone; Faiz, Md Abul; Fanello, Caterina I; Onyamboko, Marie; Mokuolu, Olugbenga A; Jacob, Christopher G; Takala-Harrison, Shannon; Plowe, Christopher V; Day, Nicholas P; Dondorp, Arjen M; Spencer, Chris C A; McVean, Gilean; Fairhurst, Rick M; White, Nicholas J; Kwiatkowski, Dominic P

2015-01-01

We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin, the frontline antimalarial drug. Across 15 locations in Southeast Asia, we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains, which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin), arps10 (apicoplast ribosomal protein S10), mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd, arps10, mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. PMID:25599401

Stereotypes Associated With Age-related Conditions and Assistive Device Use in Canadian Media.

PubMed

Fraser, Sarah Anne; Kenyon, Virginia; Lagacé, Martine; Wittich, Walter; Southall, Kenneth Edmund

2016-12-01

Newspapers are an important source of information. The discourses within the media can influence public attitudes and support or discourage stereotypical portrayals of older individuals. This study critically examined discourses within a Canadian newspaper in terms of stereotypical depictions of age-related health conditions and assistive technology devices (ATDs). Four years (2009-2013) of Globe and Mail articles were searched for terms relevant to the research question. A total of 65 articles were retained, and a critical discourse analysis (CDA) of the texts was conducted. The articles were coded for stereotypes associated with age-related health conditions and ATDs, consequences of the stereotyping, and context (overall setting or background) of the discourse. The primary code list included 4 contexts, 13 stereotypes, and 9 consequences of stereotyping. CDA revealed discourses relating to (a) maintaining autonomy in a stereotypical world, (b) ATDs as obstacles in employment, (c) barriers to help seeking for age-related conditions, and (d) people in power setting the stage for discrimination. Our findings indicate that discourses in the Canadian media include stereotypes associated with age-related health conditions. Further, depictions of health conditions and ATDs may exacerbate existing stereotypes about older individuals, limit the options available to them, lead to a reduction in help seeking, and lower ATD use. Education about the realities of age-related health changes and ATDs is needed in order to diminish stereotypes and encourage ATD uptake and use. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Ph-Sensor Properties of a Fluorescent Protein from Dendronephthya sp].

PubMed

Pakhomov, A A; Chertkova, R V; Martynov, V I

2015-01-01

Genetically encoded biosensors based on fluorescent proteins are now widely applicable for monitoring pH changes in live cells. Here, we have shown that a fluorescent protein from Dendronephthya sp. (DendFP) exhibits a pronounced pH-sensitivity. Unlike most of known genetically encoded pH-sensors, fluorescence of the protein is not quenched upon medium acidification, but is shifting from the red to green spectral range. Therefore, quantitative measurements of intracellular pH are feasible by ratiometric comparison of emission intensities in the red and green spectral ranges, which makes DendFP advantageous compared with other genetically encoded pH-sensors.

Molecular cloning and characterization of alpha - galactosidase gene from Glaciozyma antarctica

NASA Astrophysics Data System (ADS)

Moheer, Reyad Qaed Al; Bakar, Farah Diba Abu; Murad, Abdul Munir Abdul

2015-09-01

Psychrophilic enzymes are proteins produced by psychrophilic organisms which recently are the limelight for industrial applications. A gene encoding α-galactosidase from a psychrophilic yeast, Glaciozyma antarctica PI12 which belongs to glycoside hydrolase family 27, was isolated and analyzed using several bioinformatic tools. The cDNA of the gene with the size of 1,404-bp encodes a protein with 467 amino acid residues. Predicted molecular weight of protein was 48.59 kDa and hence we name the gene encoding α-galactosidase as GAL48. We found that the predicted protein sequences possessed signal peptide sequence and are highly conserved among other fungal α-galactosidase.

Novel t(5;11)(q32;q13.4) with NUMA1-PDGFRB fusion in a myeloid neoplasm with eosinophilia with response to imatinib mesylate.

PubMed

Zou, Ying S; Hoppman, Nicole L; Singh, Zeba N; Sawhney, Sameer; Kotiah, Sandy D; Baer, Maria R

2017-04-01

We report a NUMA1-PDGFRB fusion in a myeloproliferative neoplasm with eosinophilia in a 61-year old man, with response to imatinib mesylate therapy. A t(5;11) chromosome translocation involving bands 5q32 and 11q13.4 was identified by metaphase chromosome analysis, and rearrangement of the platelet-derived growth factor receptor beta (PDGFRB) gene on 5q32 was demonstrated by FISH using a PDGFRB break-apart probe set. Bacterial artificial chromosome (BAC) FISH mapping of the PDGFRB fusion partner gene narrowed the breakpoint at 11q13.4 to a 150 kb genomic region containing three genes, including NUMA1. Mate pair sequencing analysis demonstrated NUMA1-PDGFRB fusion. The fusion protein includes coiled-coil domains of nuclear mitotic apparatus protein 1 (NuMA1, involved in protein homodimerization and heteroassociation) and tyrosine kinase domains of PDGFRB. Diverse rearrangements involving the PDGFRB gene have been identified in myeloid and lymphoid neoplasms with eosinophilia, but rearrangement of the nuclear mitotic apparatus protein 1 (NUMA1) gene has previously been reported in a human malignancy in only one instance, a NUMA1-RARA fusion caused by a t(11;17) translocation in a patient with acute promyelocytic leukemia. The NUMA1-PDGFRB fusion is the second instance of rearrangement of NUMA1, encoding an element of the mitotic apparatus, in human cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

The genomic structure of the human Charcot-Leyden crystal protein gene is analogous to those of the galectin genes

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

Dyer, K.D.; Handen, J.S.; Rosenberg, H.F.

The Charcot-Leyden crystal (CLC) protein, or eosinophil lysophospholipase, is a characteristic protein of human eosinophils and basophils; recent work has demonstrated that the CLC protein is both structurally and functionally related to the galectin family of {beta}-galactoside binding proteins. The galectins as a group share a number of features in common, including a linear ligand binding site encoded on a single exon. In this work, we demonstrate that the intron-exon structure of the gene encoding CLC is analogous to those encoding the galectins. The coding sequence of the CLC gene is divided into four exons, with the entire {beta}-galactoside bindingmore » site encoded by exon III. We have isolated CLC {beta}-galactoside binding sites from both orangutan (Pongo pygmaeus) and murine (Mus musculus) genomic DNAs, both encoded on single exons, and noted conservation of the amino acids shown to interact directly with the {beta}-galactoside ligand. The most likely interpretation of these results suggests the occurrence of one or more exon duplication and insertion events, resulting in the distribution of this lectin domain to CLC as well as to the multiple galectin genes. 35 refs., 3 figs.« less

Identification of the cleavage sites of the RNA2-encoded polyproteins for two members of the genus Torradovirus by N-terminal sequencing of the virion capsid proteins.

PubMed

Ferriol, I; Silva Junior, D M; Nigg, J C; Zamora-Macorra, E J; Falk, B W

2016-11-01

Torradoviruses, family Secoviridae, are emergent bipartite RNA plant viruses. RNA1 is ca. 7kb and has one open reading frame (ORF) encoding for the protease, helicase and RNA-dependent RNA polymerase (RdRp). RNA2 is ca. 5kb and has two ORFs. RNA2-ORF1 encodes for a putative protein with unknown function(s). RNA2-ORF2 encodes for a putative movement protein and three capsid proteins. Little is known about the replication and polyprotein processing strategies of torradoviruses. Here, the cleavage sites in the RNA2-ORF2-encoded polyproteins of two torradoviruses, Tomato marchitez virus isolate M (ToMarV-M) and tomato chocolate spot virus, were determined by N-terminal sequencing, revealing that the amino acid (aa) at the -1 position of the cleavage sites is a glutamine. Multiple aa sequence comparison confirmed that this glutamine is conserved among other torradoviruses. Finally, site-directed mutagenesis of conserved aas in the ToMarV-M RdRp and protease prevented substantial accumulation of viral coat proteins or RNAs. Copyright © 2016 Elsevier Inc. All rights reserved.

DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences.

PubMed

Kunig, Verena; Potowski, Marco; Gohla, Anne; Brunschweiger, Andreas

2018-06-27

DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.

Dual-Located WHIRLY1 Interacting with LHCA1 Alters Photochemical Activities of Photosystem I and Is Involved in Light Adaptation in Arabidopsis

PubMed Central

Huang, Dongmei; Lin, Wenfang; Deng, Ban

2017-01-01

Plastid-nucleus-located WHIRLY1 protein plays a role in regulating leaf senescence and is believed to associate with the increase of reactive oxygen species delivered from redox state of the photosynthetic electron transport chain. In order to make sure whether WHIRLY1 plays a role in photosynthesis, in this study, the performances of photosynthesis were detected in Arabidopsis whirly1 knockout (kowhy1) and plastid localized WHIRLY1 overexpression (oepWHY1) plants. Loss of WHIRLY1 leads to a higher photochemical quantum yield of photosystem I Y(I) and electron transport rate (ETR) and a lower non-photochemical quenching (NPQ) involved in the thermal dissipation of excitation energy of chlorophyll fluorescence than the wild type. Further analyses showed that WHIRLY1 interacts with Light-harvesting protein complex I (LHCA1) and affects the expression of genes encoding photosystem I (PSI) and light harvest complexes (LHCI). Moreover, loss of WHIRLY1 decreases chloroplast NAD(P)H dehydrogenase-like complex (NDH) activity and the accumulation of NDH supercomplex. Several genes encoding the PSI-NDH complexes are also up-regulated in kowhy1 and the whirly1whirly3 double mutant (ko1/3) but steady in oepWHY1 plants. However, under high light conditions (800 μmol m−2 s−1), both kowhy1 and ko1/3 plants show lower ETR than wild-type which are contrary to that under normal light condition. Moreover, the expression of several PSI-NDH encoding genes and ERF109 which is related to jasmonate (JA) response varied in kowhy1 under different light conditions. These results indicate that WHIRLY1 is involved in the alteration of ETR by affecting the activities of PSI and supercomplex formation of PSI with LHCI or NDH and may acting as a communicator between the plastids and the nucleus. PMID:29112140

CYP714B1 and CYP714B2 encode gibberellin 13-oxidases that reduce gibberellin activity in rice.

PubMed

Magome, Hiroshi; Nomura, Takahito; Hanada, Atsushi; Takeda-Kamiya, Noriko; Ohnishi, Toshiyuki; Shinma, Yuko; Katsumata, Takumi; Kawaide, Hiroshi; Kamiya, Yuji; Yamaguchi, Shinjiro

2013-01-29

Bioactive gibberellins (GAs) control many aspects of growth and development in plants. GA(1) has been the most frequently found bioactive GA in various tissues of flowering plants, but the enzymes responsible for GA(1) biosynthesis have not been fully elucidated due to the enzymes catalyzing the 13-hydroxylation step not being identified. Because of the lack of mutants defective in this enzyme, biological significance of GA 13-hydroxylation has been unknown. Here, we report that two cytochrome P450 genes, CYP714B1 and CYP714B2, encode GA 13-oxidase in rice. Transgenic Arabidopsis plants that overexpress CYP714B1 or CYP714B2 show semidwarfism. There was a trend that the levels of 13-OH GAs including GA(1) were increased in these transgenic plants. Functional analysis using yeast or insect cells shows that recombinant CYP714B1 and CYP714B2 proteins can convert GA(12) into GA(53) (13-OH GA(12)) in vitro. Moreover, the levels of 13-OH GAs including GA(1) were decreased, whereas those of 13-H GAs including GA(4) (which is more active than GA(1)) were increased, in the rice cyp714b1 cyp714b2 double mutant. These results indicate that CYP714B1 and CYP714B2 play a predominant role in GA 13-hydroxylation in rice. The double mutant plants appear phenotypically normal until heading, but show elongated uppermost internode at the heading stage. Moreover, CYP714B1 and CYP714B2 expression was up-regulated by exogenous application of bioactive GAs. Our results suggest that GA 13-oxidases play a role in fine-tuning plant growth by decreasing GA bioactivity in rice and that they also participate in GA homeostasis.

Genome Sequence of Microbulbifer mangrovi DD-13T Reveals Its Versatility to Degrade Multiple Polysaccharides.

PubMed

Imran, Md; Pant, Poonam; Shanbhag, Yogini P; Sawant, Samir V; Ghadi, Sanjeev C

2017-02-01

Microbulbifer mangrovi strain DD-13 T is a novel-type species isolated from the mangroves of Goa, India. The draft genome sequence of strain DD-13 comprised 4,528,106 bp with G+C content of 57.15%. Out of 3479 open reading frames, functions for 3488 protein coding sequences were predicted on the basis of similarity with the cluster of orthologous groups. In addition to protein coding sequences, 34 tRNA genes and 3 rRNA genes were detected. Analysis of nucleotide sequence of predicted gene using a Carbohydrate-Active Enzymes (CAZymes) Analysis Toolkit indicates that strain DD-13 encodes a large set of CAZymes including 255 glycoside hydrolases, 76 carbohydrate esterases, 17 polysaccharide lyases, and 113 carbohydrate-binding modules (CBMs). Many genes from strain DD-13 were annotated as carbohydrases specific for degradation of agar, alginate, carrageenan, chitin, xylan, pullulan, cellulose, starch, β-glucan, pectin, etc. Some of polysaccharide-degrading genes were highly modular and were appended at least with one CBM indicating the versatility of strain DD-13 to degrade complex polysaccharides. The cell growth of strain DD-13 was validated using pure polysaccharides such as agarose or alginate as carbon source as well as by using red and brown seaweed powder as substrate. The homologous carbohydrase produced by strain DD-13 during growth degraded the polysaccharide, ensuring the production of metabolizable reducing sugars. Additionally, several other polysaccharides such as carrageenan, xylan, pullulan, pectin, starch, and carboxymethyl cellulose were also corroborated as growth substrate for strain DD-13 and were associated with concomitant production of homologous carbohydrase.