Nuclear pre-mRNA processing in plants

International Nuclear Information System (INIS)

Reddy, A.S.N.; Golovkin, M.

2008-01-01

This volume of CTMI, entitled Nuclear premRNA Processing in Plants, with 16 chapters from leading scientists in this area, summarizes recent advances in nuclear pre-mRNA processing and its role in plant growth and development. It provides researchers in the field, as well as those in related areas, with an up-to-date and comprehensive, yet concise, overview of the current status and future potential of this research in understanding plant biology. The first four chapters focus on spliceosome composition, genome-wide alternative splicing, and splice site requirements for U1 and U12 introns using computational and empirical approaches. Analysis of sequenced plant genomes has revealed that 80% of all protein-coding nuclear genes contain one or more introns. The lack of an in vitro plant splicing system has made it difficult to identify general and plant-specific components of splicing machinery in plants. The next three chapters focus on serine/arginine-rich (SR) proteins, a family of highly conserved proteins, which are known to play key roles in constitutive and regulated splicing of pre-mRNA and other aspects of RNA metabolism in metazoans. These proteins engage both in RNA binding and protein.protein interactions and function as splicing regulators at multiple stages of spliceosome assembly. This family of proteins has expanded considerably in plants with several plant-specific SR proteins. Several serendipitous discoveries made using forward genetics are indicating that RNA metabolism (alternative splicing, alternative polyadenylation, mRNA transport) plays an important role in many aspects of plant growth and development and in plant responses to biotic and abiotic stresses. The next seven chapters focus on these aspects of RNA metabolism. The plant hormone abscisic acid (ABA) regulates a number of physiological processes during plant growth and development. The next chapter or A.B. Rose discusses the ways introns affect gene expression both positively and

AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana.

Science.gov (United States)

Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

2016-10-18

N 6 -Methyladenosine (m 6 A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m 6 A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m 6 A functions in plants. Therefore, computational prediction of mRNA m 6 A sites becomes emergently important. Here, we present a method to predict the m 6 A sites for A. thaliana mRNA sequence(s). To predict the m 6 A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m 6 A sites. The server also provides a comprehensive database of predicted transcriptome-wide m 6 A sites and curated m 6 A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites, which is freely accessible for public use at .

Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants

DEFF Research Database (Denmark)

Rougemaille, Mathieu; Gudipati, Rajani K; Olesen, Jens Raabjerg

2007-01-01

The nuclear exosome is involved in numerous RNA metabolic processes. Exosome degradation of rRNA, snoRNA, snRNA and tRNA in Saccharomyces cerevisiae is activated by TRAMP complexes, containing either the Trf4p or Trf5p poly(A) polymerase. These enzymes are presumed to facilitate exosome access...... is required for both retention and degradation of nuclear restricted mRNAs. We show here that Trf4p, in the context of TRAMP, is an mRNA surveillance factor. However, unlike Rrp6p, Trf4p only partakes in RNA degradation and not in transcript retention. Surprisingly, a polyadenylation-defective Trf4p protein...

Influence of Pre-Training Predator Stress on the Expression of c-fos mRNA in the Hippocampus, Amygdala, and Striatum Following Long-Term Spatial Memory Retrieval.

Science.gov (United States)

Vanelzakker, Michael B; Zoladz, Phillip R; Thompson, Vanessa M; Park, Collin R; Halonen, Joshua D; Spencer, Robert L; Diamond, David M

2011-01-01

We have studied the influence of pre-training psychological stress on the expression of c-fos mRNA following long-term spatial memory retrieval. Rats were trained to learn the location of a hidden escape platform in the radial-arm water maze, and then their memory for the platform location was assessed 24 h later. Rat brains were extracted 30 min after the 24-h memory test trial for analysis of c-fos mRNA. Four groups were tested: (1) Rats given standard training (Standard); (2) Rats given cat exposure (Predator Stress) 30 min prior to training (Pre-Training Stress); (3) Rats given water exposure only (Water Yoked); and (4) Rats given no water exposure (Home Cage). The Standard trained group exhibited excellent 24 h memory which was accompanied by increased c-fos mRNA in the dorsal hippocampus and basolateral amygdala (BLA). The Water Yoked group exhibited no increase in c-fos mRNA in any brain region. Rats in the Pre-Training Stress group were classified into two subgroups: good and bad memory performers. Neither of the two Pre-Training Stress subgroups exhibited a significant change in c-fos mRNA expression in the dorsal hippocampus or BLA. Instead, stressed rats with good memory exhibited significantly greater c-fos mRNA expression in the dorsolateral striatum (DLS) compared to stressed rats with bad memory. This finding suggests that stressed rats with good memory used their DLS to generate a non-spatial (cue-based) strategy to learn and subsequently retrieve the memory of the platform location. Collectively, these findings provide evidence at a molecular level for the involvement of the hippocampus and BLA in the retrieval of spatial memory and contribute novel observations on the influence of pre-training stress in activating the DLS in response to long-term memory retrieval.

Influence of Pre-Training Predator Stress on the Expression of c-fos mRNA in the Hippocampus, Amygdala and Striatum Following Long-Term Spatial Memory Retrieval

Directory of Open Access Journals (Sweden)

Michael B VanElzakker

2011-06-01

Full Text Available We have studied the influence of pre-training psychological stress on the expression of c-fos mRNA following long-term spatial memory retrieval. Rats were trained to learn the location of a hidden escape platform in the radial-arm water maze, and then their memory for the platform location was assessed 24 hr later. Rat brains were extracted 30 min after the 24 hr memory test trial for analysis of c-fos mRNA. Four groups were tested: 1 Rats given standard training (Standard; 2 Rats given cat exposure (Predator Stress 30 min prior to training (Pre-Training Stress; 3 Rats given water exposure only (Water Yoked; and 4 Rats given no water exposure (Home Cage. The Standard trained group exhibited excellent 24 hr memory which was accompanied by increased c-fos mRNA in the dorsal hippocampus and basolateral amygdala (BLA. The Water Yoked group exhibited no increase in c-fos mRNA in any brain region. Rats in the Pre-Training Stress group were classified into two subgroups: good and bad memory performers. Neither of the two Pre-Training Stress subgroups exhibited a significant change in c-fos mRNA expression in the dorsal hippocampus or BLA. Instead, stressed rats with good memory exhibited significantly greater c-fos mRNA expression in the dorsolateral striatum (DLS compared to stressed rats with bad memory. This finding suggests that stressed rats with good memory used their DLS to generate a non-spatial (cue-based strategy to learn and subsequently retrieve the memory of the platform location. Collectively, these findings provide evidence at a molecular level for the involvement of the hippocampus and BLA in the retrieval of spatial memory and contribute novel observations on the influence of pre-training stress in activating the DLS in response to long-term memory retrieval.

Influence of Pre-Training Predator Stress on the Expression of c-fos mRNA in the Hippocampus, Amygdala, and Striatum Following Long-Term Spatial Memory Retrieval

Science.gov (United States)

VanElzakker, Michael B.; Zoladz, Phillip R.; Thompson, Vanessa M.; Park, Collin R.; Halonen, Joshua D.; Spencer, Robert L.; Diamond, David M.

2011-01-01

We have studied the influence of pre-training psychological stress on the expression of c-fos mRNA following long-term spatial memory retrieval. Rats were trained to learn the location of a hidden escape platform in the radial-arm water maze, and then their memory for the platform location was assessed 24 h later. Rat brains were extracted 30 min after the 24-h memory test trial for analysis of c-fos mRNA. Four groups were tested: (1) Rats given standard training (Standard); (2) Rats given cat exposure (Predator Stress) 30 min prior to training (Pre-Training Stress); (3) Rats given water exposure only (Water Yoked); and (4) Rats given no water exposure (Home Cage). The Standard trained group exhibited excellent 24 h memory which was accompanied by increased c-fos mRNA in the dorsal hippocampus and basolateral amygdala (BLA). The Water Yoked group exhibited no increase in c-fos mRNA in any brain region. Rats in the Pre-Training Stress group were classified into two subgroups: good and bad memory performers. Neither of the two Pre-Training Stress subgroups exhibited a significant change in c-fos mRNA expression in the dorsal hippocampus or BLA. Instead, stressed rats with good memory exhibited significantly greater c-fos mRNA expression in the dorsolateral striatum (DLS) compared to stressed rats with bad memory. This finding suggests that stressed rats with good memory used their DLS to generate a non-spatial (cue-based) strategy to learn and subsequently retrieve the memory of the platform location. Collectively, these findings provide evidence at a molecular level for the involvement of the hippocampus and BLA in the retrieval of spatial memory and contribute novel observations on the influence of pre-training stress in activating the DLS in response to long-term memory retrieval. PMID:21738501

Research on pre-processing of QR Code

Science.gov (United States)

Sun, Haixing; Xia, Haojie; Dong, Ning

2013-10-01

QR code encodes many kinds of information because of its advantages: large storage capacity, high reliability, full arrange of utter-high-speed reading, small printing size and high-efficient representation of Chinese characters, etc. In order to obtain the clearer binarization image from complex background, and improve the recognition rate of QR code, this paper researches on pre-processing methods of QR code (Quick Response Code), and shows algorithms and results of image pre-processing for QR code recognition. Improve the conventional method by changing the Souvola's adaptive text recognition method. Additionally, introduce the QR code Extraction which adapts to different image size, flexible image correction approach, and improve the efficiency and accuracy of QR code image processing.

Conversion of pre-RISC to holo-RISC by Ago2 during assembly of RNAi complexes

Science.gov (United States)

Kim, Kevin; Lee, Young Sik; Carthew, Richard W.

2007-01-01

In the Drosophila RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) direct Argonaute2 (Ago2), an endonuclease, within the RNA-induced silencing complex (RISC) to cleave complementary mRNA targets. In vitro studies have shown that, for each siRNA duplex, RISC retains only one strand, the guide, and releases the other, the passenger, to form a holo-RISC complex. Here, we have isolated a new Ago2 mutant allele and provide, for the first time, in vivo evidence that endogenous Ago2 slicer activity is important to mount an RNAi response in Drosophila. We demonstrate in vivo that efficient removal of the passenger strand from RISC requires the cleavage activity of Ago2. We have also identified a new intermediate complex in the RISC assembly pathway, pre-RISC, in which Ago2 is stably bound to double-stranded siRNA. PMID:17123955

Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries

Directory of Open Access Journals (Sweden)

Daniela Toro-Ascuy

2016-11-01

Full Text Available The human immunodeficiency virus type-1 (HIV-1 unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1, Staufen double-stranded RNA binding protein 1/2 (STAU1/2, or components of miRNA-induced silencing complex (miRISC and processing bodies (PBs. More recently, the HIV-1 unspliced mRNA was shown to contain N6-methyladenosine (m6A, allowing the recruitment of YTH N6-methyladenosine RNA binding protein 2 (YTHDF2, an m6A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.

Principles of mRNA transport in yeast.

Science.gov (United States)

Heym, Roland Gerhard; Niessing, Dierk

2012-06-01

mRNA localization and localized translation is a common mechanism by which cellular asymmetry is achieved. In higher eukaryotes the mRNA transport machinery is required for such diverse processes as stem cell division and neuronal plasticity. Because mRNA localization in metazoans is highly complex, studies at the molecular level have proven to be cumbersome. However, active mRNA transport has also been reported in fungi including Saccharomyces cerevisiae, Ustilago maydis and Candida albicans, in which these events are less difficult to study. Amongst them, budding yeast S. cerevisiae has yielded mechanistic insights that exceed our understanding of other mRNA localization events to date. In contrast to most reviews, we refrain here from summarizing mRNA localization events from different organisms. Instead we give an in-depth account of ASH1 mRNA localization in budding yeast. This approach is particularly suited to providing a more holistic view of the interconnection between the individual steps of mRNA localization, from transcriptional events to cytoplasmic mRNA transport and localized translation. Because of our advanced mechanistic understanding of mRNA localization in yeast, the present review may also be informative for scientists working, for example, on mRNA localization in embryogenesis or in neurons.

MRN1 implicates chromatin remodeling complexes and architectural factors in mRNA maturation

DEFF Research Database (Denmark)

Düring, Louis; Thorsen, Michael; Petersen, Darima

2012-01-01

A functional relationship between chromatin structure and mRNA processing events has been suggested, however, so far only a few involved factors have been characterized. Here we show that rsc nhp6¿¿ mutants, deficient for the function of the chromatin remodeling factor RSC and the chromatin....... Genetic interactions are observed between 2 µm-MRN1 and the splicing deficient mutants snt309¿, prp3, prp4, and prp22, and additional genetic analyses link MRN1, SNT309, NHP6A/B, SWI/SNF, and RSC supporting the notion of a role of chromatin structure in mRNA processing....

Intergenic mRNA molecules resulting from trans-splicing.

Science.gov (United States)

Finta, Csaba; Zaphiropoulos, Peter G

2002-02-22

Accumulated recent evidence is indicating that alternative splicing represents a generalized process that increases the complexity of human gene expression. Here we show that mRNA production may not necessarily be limited to single genes, as human liver also has the potential to produce a variety of hybrid cytochrome P450 3A mRNA molecules. The four known cytochrome P450 3A genes in humans, CYP3A4, CYP3A5, CYP3A7, and CYP3A43, share a high degree of similarity, consist of 13 exons with conserved exon-intron boundaries, and form a cluster on chromosome 7. The chimeric CYP3A mRNA molecules described herein are characterized by CYP3A43 exon 1 joined at canonical splice sites to distinct sets of CYP3A4 or CYP3A5 exons. Because the CYP3A43 gene is in a head-to-head orientation with the CYP3A4 and CYP3A5 genes, bypassing transcriptional termination can not account for the formation of hybrid CYP3A mRNAs. Thus, the mechanism generating these molecules has to be an RNA processing event that joins exons of independent pre-mRNA molecules, i.e. trans-splicing. Using quantitative real-time polymerase chain reaction, the ratio of one CYP3A43/3A4 intergenic combination was estimated to be approximately 0.15% that of the CYP3A43 mRNAs. Moreover, trans-splicing has been found not to interfere with polyadenylation. Heterologous expression of the chimeric species composed of CYP3A43 exon 1 joined to exons 2-13 of CYP3A4 revealed catalytic activity toward testosterone.

High-Resolution Imaging Reveals New Features of Nuclear Export of mRNA through the Nuclear Pore Complexes

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Joseph M. Kelich

2014-08-01

Full Text Available The nuclear envelope (NE of eukaryotic cells provides a physical barrier for messenger RNA (mRNA and the associated proteins (mRNPs traveling from sites of transcription in the nucleus to locations of translation processing in the cytoplasm. Nuclear pore complexes (NPCs embedded in the NE serve as a dominant gateway for nuclear export of mRNA. However, the fundamental characterization of export dynamics of mRNPs through the NPC has been hindered by several technical limits. First, the size of NPC that is barely below the diffraction limit of conventional light microscopy requires a super-resolution microscopy imaging approach. Next, the fast transit of mRNPs through the NPC further demands a high temporal resolution by the imaging approach. Finally, the inherent three-dimensional (3D movements of mRNPs through the NPC demand the method to provide a 3D mapping of both transport kinetics and transport pathways of mRNPs. This review will highlight the recently developed super-resolution imaging techniques advanced from 1D to 3D for nuclear export of mRNPs and summarize the new features in the dynamic nuclear export process of mRNPs revealed from these technical advances.

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

Energy Technology Data Exchange (ETDEWEB)

Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

2011-09-10

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

International Nuclear Information System (INIS)

Bloch, Donald B.; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

2011-01-01

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: → A two-hybrid assay was developed to study interactions in macromolecular complexes. → The assay was applied to interactions between components of mRNA P-bodies. → The assay effectively and efficiently identified protein interaction domains. → P-body assembly in mammalian cells differs from that in other species.

Trace spaces in a pre-cubical complex

DEFF Research Database (Denmark)

Raussen, Martin

2009-01-01

In directed algebraic topology, directed irreversible (d)-paths and spaces consisting of d-paths are studied from a topological and from a categorical point of view. Motivated by models for concurrent computation, we study in this paper spaces of d-paths in a pre-cubical complex. Such paths...... are equipped with a natural arc length which moreover is shown to be invariant under directed homotopies. D-paths up to reparametrization (called traces) can thus be represented by arc length parametrized d-paths. Under weak additional conditions, it is shown that trace spaces in a pre-cubical complex...... are separable metric spaces which are locally contractible and locally compact. Moreover, they have the homotopy type of a CW-complex....

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion.

Science.gov (United States)

Singh, Guramrit; Pratt, Gabriel; Yeo, Gene W; Moore, Melissa J

2015-01-01

Throughout their lifetimes, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Since the discovery of the first mRNP component more than 40 years ago, what is known as the mRNA interactome now comprises >1,000 proteins. These proteins bind mRNAs in myriad ways with varying affinities and stoichiometries, with many assembling onto nascent RNAs in a highly ordered process during transcription and precursor mRNA (pre-mRNA) processing. The nonrandom distribution of major mRNP proteins observed in transcriptome-wide studies leads us to propose that mRNPs are organized into three major domains loosely corresponding to 5' untranslated regions (UTRs), open reading frames, and 3' UTRs. Moving from the nucleus to the cytoplasm, mRNPs undergo extensive remodeling as they are first acted upon by the nuclear pore complex and then by the ribosome. When not being actively translated, cytoplasmic mRNPs can assemble into large multi-mRNP assemblies or be permanently disassembled and degraded. In this review, we aim to give the reader a thorough understanding of past and current eukaryotic mRNP research.

Comparative performance evaluation of transform coding in image pre-processing

Science.gov (United States)

Menon, Vignesh V.; NB, Harikrishnan; Narayanan, Gayathri; CK, Niveditha

2017-07-01

We are in the midst of a communication transmute which drives the development as largely as dissemination of pioneering communication systems with ever-increasing fidelity and resolution. Distinguishable researches have been appreciative in image processing techniques crazed by a growing thirst for faster and easier encoding, storage and transmission of visual information. In this paper, the researchers intend to throw light on many techniques which could be worn at the transmitter-end in order to ease the transmission and reconstruction of the images. The researchers investigate the performance of different image transform coding schemes used in pre-processing, their comparison, and effectiveness, the necessary and sufficient conditions, properties and complexity in implementation. Whimsical by prior advancements in image processing techniques, the researchers compare various contemporary image pre-processing frameworks- Compressed Sensing, Singular Value Decomposition, Integer Wavelet Transform on performance. The paper exposes the potential of Integer Wavelet transform to be an efficient pre-processing scheme.

Characterization of the ptr5+ gene involved in nuclear mRNA export in fission yeast

International Nuclear Information System (INIS)

Watanabe, Nobuyoshi; Ikeda, Terumasa; Mizuki, Fumitaka; Tani, Tokio

2012-01-01

Highlights: ► We cloned the ptr5 + gene involved in nuclear mRNA export in fission yeast. ► The ptr5 + gene was found to encode nucleoporin 85 (Nup85). ► Seh1p and Mlo3p are multi-copy suppressors for the ptr5 mutation. ► Ptr5p/Nup85p functions in nuclear mRNA export through the mRNA export factor Rae1p. ► Ptr5p/Nup85p interacts genetically with pre-mRNA splicing factors. -- Abstract: To analyze the mechanisms of mRNA export from the nucleus to the cytoplasm, we have isolated eleven mutants, ptr [poly(A) + RNA transport] 1 to 11, which accumulate poly(A) + RNA in the nucleus at a nonpermissive temperature in Schizosaccharomyces pombe. Of those, the ptr5–1 mutant shows dots- or a ring-like accumulation of poly(A) + RNA at the nuclear periphery after shifting to the nonpermissive temperature. We cloned the ptr5 + gene and found that it encodes a component of the nuclear pore complex (NPC), nucleoporin 85 (Nup85). The ptr5–1 mutant shows no defects in protein transport, suggesting the specific involvement of Ptr5p/Nup85p in nuclear mRNA export in S. pombe. We identified Seh1p, a nucleoporin interacting with Nup85p, an mRNA-binding protein Mlo3p, and Sac3p, a component of the TREX-2 complex involved in coupling of nuclear mRNA export with transcription, as multi-copy suppressors for the ptr5–1 mutation. In addition, we found that the ptr5–1 mutation is synthetically lethal with a mutation of the mRNA export factor Rae1p, and that the double mutant exaggerates defective nuclear mRNA export, suggesting that Ptr5p/Nup85p is involved in nuclear mRNA export through Rae1p. Interestingly, the ptr5–1 mutation also showed synthetic effects with several prp pre-mRNA splicing mutations, suggesting a functional linkage between the NPCs and the splicing apparatus in the yeast nucleus.

A study of complex particle emission in the pre-equilibrium statistical model

International Nuclear Information System (INIS)

Miao Rongzhi; Wu Guohua

1986-01-01

A concept of the quasi-composite system in the process of the pre-equilibrium emission is presented in this paper. On the basis of the principle of detailed balance, the existence of the factor, [γ β ω(π β , 0, ν β , 0, E-U)g π,ν ], has been proved with an account of the distinguishabllity between protons and neutrons. A formula for the rate of the complex particle emission in the pre-equilibrium process can be obtained. The theoretical calculation results fit the experimental data quite well, especially in the high energy part of the energy spectrum the agreement are much better than ever before

Clinical values of AFP, GPC3 mRNA in peripheral blood for prediction of hepatocellular carcinoma recurrence following OLT: AFP, GPC3 mRNA for prediction of HCC.

Science.gov (United States)

Wang, Yuliang; Shen, Zhongyang; Zhu, Zhijun; Han, Ruifa; Huai, Mingsheng

2011-03-01

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Annually, about 200,000 patients died of HCC in China. Liver transplantation (LT) holds great theoretical appeal in treating HCC. However, the high recurrence rate after transplantation is the most important limiting factor for long-term survival. To assess the value of alpha-fetoprotein (AFP) messenger RNA (mRNA), Glypican-3 (GPC3) mRNA-expressing cells in the peripheral blood (PB) for prediction of HCC recurrence following orthotopic liver transplantation (OLT). 29 patients with HCC who underwent OLT with a minimum clinical follow-up of 12 months were included in this retrospective study. We detected AFP mRNA, GPC3 mRNA-expressing cells in the PB by TaqMan real-time reverse transcriptase-polymerase chain reaction (RT-PCR), pre-, intra- and post-operatively. The early recurrence of patients was evaluated. 8 (28%), 15 (52%), and 9 (31%) patients had AFP mRNA detected pre-, intra-, and post-operatively, respectively. With 12 months of follow-up, HCC recurred in 7 (24%) patients. Univariate analysis revealed that positive pre- and post-operative AFP mRNA, TNM stage as well as vascular invasion were significant predictors for the HCC recurrence. Multivariate analysis revealed that being positive for AFP mRNA pre-operatively remained a significant risk factor for HCC recurrence after OLT. GPC3 mRNA was expressed in all PB samples. There was no significant difference in the expression levels of GPC3 mRNA between the HCC and control groups. There were no significant differences in GPC3 mRNA expression values between those patients with and without tumor recurrence. The pre-operative detection of circulating AFP mRNA-expressing cells could be a useful predictor for HCC recurrence following OLT. GPC3 mRNA-expressing cells in PB seem to have no diagnostic value.

Characterization of the ptr5{sup +} gene involved in nuclear mRNA export in fission yeast

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Nobuyoshi; Ikeda, Terumasa; Mizuki, Fumitaka [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto 860-8555 (Japan); Tani, Tokio, E-mail: ttani@sci.kumamoto-u.ac.jp [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto 860-8555 (Japan)

2012-02-03

Highlights: Black-Right-Pointing-Pointer We cloned the ptr5{sup +} gene involved in nuclear mRNA export in fission yeast. Black-Right-Pointing-Pointer The ptr5{sup +} gene was found to encode nucleoporin 85 (Nup85). Black-Right-Pointing-Pointer Seh1p and Mlo3p are multi-copy suppressors for the ptr5 mutation. Black-Right-Pointing-Pointer Ptr5p/Nup85p functions in nuclear mRNA export through the mRNA export factor Rae1p. Black-Right-Pointing-Pointer Ptr5p/Nup85p interacts genetically with pre-mRNA splicing factors. -- Abstract: To analyze the mechanisms of mRNA export from the nucleus to the cytoplasm, we have isolated eleven mutants, ptr [poly(A){sup +} RNA transport] 1 to 11, which accumulate poly(A){sup +} RNA in the nucleus at a nonpermissive temperature in Schizosaccharomyces pombe. Of those, the ptr5-1 mutant shows dots- or a ring-like accumulation of poly(A){sup +} RNA at the nuclear periphery after shifting to the nonpermissive temperature. We cloned the ptr5{sup +} gene and found that it encodes a component of the nuclear pore complex (NPC), nucleoporin 85 (Nup85). The ptr5-1 mutant shows no defects in protein transport, suggesting the specific involvement of Ptr5p/Nup85p in nuclear mRNA export in S. pombe. We identified Seh1p, a nucleoporin interacting with Nup85p, an mRNA-binding protein Mlo3p, and Sac3p, a component of the TREX-2 complex involved in coupling of nuclear mRNA export with transcription, as multi-copy suppressors for the ptr5-1 mutation. In addition, we found that the ptr5-1 mutation is synthetically lethal with a mutation of the mRNA export factor Rae1p, and that the double mutant exaggerates defective nuclear mRNA export, suggesting that Ptr5p/Nup85p is involved in nuclear mRNA export through Rae1p. Interestingly, the ptr5-1 mutation also showed synthetic effects with several prp pre-mRNA splicing mutations, suggesting a functional linkage between the NPCs and the splicing apparatus in the yeast nucleus.

Conceptual modeling in systems biology fosters empirical findings: the mRNA lifecycle.

Directory of Open Access Journals (Sweden)

Dov Dori

Full Text Available One of the main obstacles to understanding complex biological systems is the extent and rapid evolution of information, way beyond the capacity individuals to manage and comprehend. Current modeling approaches and tools lack adequate capacity to model concurrently structure and behavior of biological systems. Here we propose Object-Process Methodology (OPM, a holistic conceptual modeling paradigm, as a means to model both diagrammatically and textually biological systems formally and intuitively at any desired number of levels of detail. OPM combines objects, e.g., proteins, and processes, e.g., transcription, in a way that is simple and easily comprehensible to researchers and scholars. As a case in point, we modeled the yeast mRNA lifecycle. The mRNA lifecycle involves mRNA synthesis in the nucleus, mRNA transport to the cytoplasm, and its subsequent translation and degradation therein. Recent studies have identified specific cytoplasmic foci, termed processing bodies that contain large complexes of mRNAs and decay factors. Our OPM model of this cellular subsystem, presented here, led to the discovery of a new constituent of these complexes, the translation termination factor eRF3. Association of eRF3 with processing bodies is observed after a long-term starvation period. We suggest that OPM can eventually serve as a comprehensive evolvable model of the entire living cell system. The model would serve as a research and communication platform, highlighting unknown and uncertain aspects that can be addressed empirically and updated consequently while maintaining consistency.

RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

KAUST Repository

Köster, Tino

2017-04-13

RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

KAUST Repository

Kö ster, Tino; Marondedze, Claudius; Meyer, Katja; Staiger, Dorothee

2017-01-01

RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

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Woo, Ho-Hyung; Baker, Terri; Laszlo, Csaba; Chambers, Setsuko K.

2013-01-01

CSF-1 mRNA 3′UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3′UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3′UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of

LAMMER kinase Kic1 is involved in pre-mRNA processing

International Nuclear Information System (INIS)

Tang, Zhaohua; Luca, Maria; Portillio, Jessica; Ngo, Benson; Chang, Cathey; Wen, Teresa; Murray, Johanne; Carr, Antony

2011-01-01

The LAMMER kinases are conserved through evolution. They play vital roles in cell growth/differentiation, development, and metabolism. One of the best known functions of the kinases in animal cells is the regulation of pre-mRNA splicing. Kic1 is the LAMMER kinase in fission yeast Schizosaccharomyces pombe. Despite the reported pleiotropic effects of kic1 + deletion/overexpression on various cellular processes the involvement of Kic1 in splicing remains elusive. In this study, we demonstrate for the first time that Kic1 not only is required for efficient splicing but also affects mRNA export, providing evidence for the conserved roles of LAMMER kinases in the unicellular context of fission yeast. Consistent with the hypothesis of its direct participation in multiple steps of pre-mRNA processing, Kic1 is predominantly present in the nucleus during interphase. In addition, the kinase activity of Kic1 plays a role in modulating its own cellular partitioning. Interestingly, Kic1 expression oscillates in a cell cycle-dependent manner and the peak level coincides with mitosis and cytokinesis, revealing a potential mechanism for controlling the kinase activity during the cell cycle. The novel information about the in vivo functions and regulation of Kic1 offers insights into the conserved biological roles fundamental to LAMMER kinases in eukaryotes.

A non-inflammatory form of immune competence prevails in acute pre-pubescent malnutrition: new evidence based on critical mRNA transcripts in the mouse.

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Monk, Jennifer M; Richard, Cynthia L; Woodward, Bill

2012-05-01

The declining inflammatory immune competence of acute (i.e. wasting) pre-pubescent protein-energy malnutrition has been regarded as reflecting an unregulated immunological disintegration. Recent evidence, however, suggests that malnutrition stimulates a regulated immunological reconfiguration to achieve a non-inflammatory form of competence, perhaps offering protection against autoimmune reactions - the 'Tolerance Model'. Our objective was to determine the influence of acute pre-pubescent malnutrition on the expression of genes critical to tolerogenic regulation. Male and female C57BL/6J mice, initially 19 d old, consumed a complete purified diet either ad libitum (age-matched controls) or in restricted daily quantities (mimicking marasmus), or consumed an isoenergetic low-protein diet ad libitum (mimicking incipient kwashiorkor) for 14 d (six animals per dietary group). Gene expression in the spleen, typically an inflammatory organ, and in the small intestine, a site designed for non-inflammatory defence, was assessed by real-time quantitative RT-PCR, and normalised to β-actin. In the spleen of the malnourished groups, both IL-10 and transforming growth factor-β1 mRNA expression increased compared with controls (P 0.05). Moreover, forkhead box P3 mRNA expression, indicative of cell-based tolerogenic potential, was sustained in both the spleen and intestine of the malnourished groups (P>0.05). Thus, despite limited supplies of energy and substrates, the spleen shifted towards a non-inflammatory character and the intestine was sustained in this mode in advanced pre-pubescent weight loss. These findings provide the first support for the Tolerance Model at the level of mRNA transcript expression.

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

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Nam, Ki Hyun; Haitjema, Charles; Liu, Xueqi; Ding, Fran; Wang, Hongwei; DeLisa, Matthew P.; Ke, Ailong (Yale); (Cornell); (Tsinghua)

2012-10-10

Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3 single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing, Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.

Complex mutual regulation of facilitates chromatin transcription (FACT) subunits on both mRNA and protein levels in human cells.

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Safina, Alfiya; Garcia, Henry; Commane, Mairead; Guryanova, Olga; Degan, Seamus; Kolesnikova, Kateryna; Gurova, Katerina V

2013-08-01

Facilitates chromatin transcription (FACT) is a chromatin remodeling complex with two subunits: SSRP1 and SPT16. Mechanisms controlling FACT levels are of interest, since the complex is not expressed in most differentiated cells, but is frequently upregulated in cancer, particularly in poorly differentiated, aggressive tumors. Moreover, inhibition of FACT expression or function in tumor cells interferes with their survival. Here we demonstrate that SSRP1 and SPT16 protein levels decline upon induction of cellular differentiation or senescence in vitro and that similar declines in protein levels for both SSRP1 and SPT16 occur upon RNAi-mediated knockdown of either SSRP1 or SPT16. The interdependence of SSRP1 and SPT16 protein levels was found to be due to their association with SSRP1 and SPT16 mRNAs, which stabilizes the proteins. In particular, presence of SSRP1 mRNA is critical for SPT16 protein stability. In addition, binding of SSRP1 and SPT16 mRNAs to the FACT complex increases the stability and efficiency of translation of the mRNAs. These data support a model in which the FACT complex is stable when SSRP1 mRNA is present, but quickly degrades when SSRP1 mRNA levels drop. In the absence of FACT complex, SSRP1 and SPT16 mRNAs are unstable and inefficiently translated, making reactivation of FACT function unlikely in normal cells. Thus, we have described a complex and unusual mode of regulation controlling cellular FACT levels that results in amplified and stringent control of FACT activity. The FACT dependence of tumor cells suggests that mechanisms controlling FACT levels could be targeted for anticancer therapy.

Characterization of 16S rRNA Processing with Pre-30S Subunit Assembly Intermediates from E. coli.

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Smith, Brian A; Gupta, Neha; Denny, Kevin; Culver, Gloria M

2018-06-08

Ribosomal RNA (rRNA) is a major component of ribosomes and is fundamental to the process of translation. In bacteria, 16S rRNA is a component of the small ribosomal subunit and plays a critical role in mRNA decoding. rRNA maturation entails the removal of intervening spacer sequences contained within the pre-rRNA transcript by nucleolytic enzymes. Enzymatic activities involved in maturation of the 5'-end of 16S rRNA have been identified, but those involved in 3'-end maturation of 16S rRNA are more enigmatic. Here, we investigate molecular details of 16S rRNA maturation using purified in vivo-formed small subunit (SSU) assembly intermediates (pre-SSUs) from wild-type Escherichia coli that contain precursor 16S rRNA (17S rRNA). Upon incubation of pre-SSUs with E. coli S100 cell extracts or purified enzymes implicated in 16S rRNA processing, the 17S rRNA is processed into additional intermediates and mature 16S rRNA. These results illustrate that exonucleases RNase R, RNase II, PNPase, and RNase PH can process the 3'-end of pre-SSUs in vitro. However, the endonuclease YbeY did not exhibit nucleolytic activity with pre-SSUs under these conditions. Furthermore, these data demonstrate that multiple pathways facilitate 16S rRNA maturation with pre-SSUs in vitro, with the dominant pathways entailing complete processing of the 5'-end of 17S rRNA prior to 3'-end maturation or partial processing of the 5'-end with concomitant processing of the 3'-end. These results reveal the multifaceted nature of SSU biogenesis and suggest that E. coli may be able to escape inactivation of any one enzyme by using an existing complementary pathway. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Conversation on Data Mining Strategies in LC-MS Untargeted Metabolomics: Pre-Processing and Pre-Treatment Steps

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Fidele Tugizimana

2016-11-01

Full Text Available Untargeted metabolomic studies generate information-rich, high-dimensional, and complex datasets that remain challenging to handle and fully exploit. Despite the remarkable progress in the development of tools and algorithms, the “exhaustive” extraction of information from these metabolomic datasets is still a non-trivial undertaking. A conversation on data mining strategies for a maximal information extraction from metabolomic data is needed. Using a liquid chromatography-mass spectrometry (LC-MS-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter. Data obtained in positive mode generated from a LC-MS-based untargeted metabolomic study (sorghum plants responding dynamically to infection by a fungal pathogen were used. Raw data were pre-processed with MarkerLynxTM software (Waters Corporation, Manchester, UK. Here, two parameters were varied: the intensity threshold (50–100 counts and the mass tolerance (0.005–0.01 Da. After the pre-processing, the datasets were imported into SIMCA (Umetrics, Umea, Sweden for more data cleaning and statistical modeling. In addition, different scaling (unit variance, Pareto, etc. and data transformation (log and power methods were explored. The results showed that the pre-processing parameters (or algorithms influence the output dataset with regard to the number of defined features. Furthermore, the study demonstrates that the pre-treatment of data prior to statistical modeling affects the subspace approximation outcome: e.g., the amount of variation in X-data that the model can explain and predict. The pre-processing and pre-treatment steps subsequently influence the number of statistically significant extracted/selected features (variables. Thus, as informed by the results, to maximize the value of untargeted metabolomic data

Complexity on Acute Myeloid Leukemia mRNA Transcript Variant

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Carlo Cattani

2011-01-01

Full Text Available This paper deals with the sequence analysis of acute myeloid leukemia mRNA. Six transcript variants of mlf1 mRNA, with more than 2000 bps, are analyzed by focusing on the autocorrelation of each distribution. Through the correlation matrix, some patches and similarities are singled out and commented, with respect to similar distributions. The comparison of Kolmogorov fractal dimension will be also given in order to classify the six variants. The existence of a fractal shape, patterns, and symmetries are discussed as well.

GABAergic Neurons in the Rat Medial Septal Complex Express Relaxin-3 Receptor (RXFP3 mRNA

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Hector Albert-Gascó

2018-01-01

Full Text Available The medial septum (MS complex modulates hippocampal function and related behaviors. Septohippocampal projections promote and control different forms of hippocampal synchronization. Specifically, GABAergic and cholinergic projections targeting the hippocampal formation from the MS provide bursting discharges to promote theta rhythm, or tonic activity to promote gamma oscillations. In turn, the MS is targeted by ascending projections from the hypothalamus and brainstem. One of these projections arises from the nucleus incertus in the pontine tegmentum, which contains GABA neurons that co-express the neuropeptide relaxin-3 (Rln3. Both stimulation of the nucleus incertus and septal infusion of Rln3 receptor agonist peptides promotes hippocampal theta rhythm. The Gi/o-protein-coupled receptor, relaxin-family peptide receptor 3 (RXFP3, is the cognate receptor for Rln3 and identification of the transmitter phenotype of neurons expressing RXFP3 in the septohippocampal system can provide further insights into the role of Rln3 transmission in the promotion of septohippocampal theta rhythm. Therefore, we used RNAscope multiplex in situ hybridization to characterize the septal neurons expressing Rxfp3 mRNA in the rat. Our results demonstrate that Rxfp3 mRNA is abundantly expressed in vesicular GABA transporter (vGAT mRNA- and parvalbumin (PV mRNA-positive GABA neurons in MS, whereas ChAT mRNA-positive acetylcholine neurons lack Rxfp3 mRNA. Approximately 75% of Rxfp3 mRNA-positive neurons expressed vGAT mRNA (and 22% were PV mRNA-positive, while the remaining 25% expressed Rxfp3 mRNA only, consistent with a potential glutamatergic phenotype. Similar proportions were observed in the posterior septum. The occurrence of RXFP3 in PV-positive GABAergic neurons gives support to a role for the Rln3-RXFP3 system in septohippocampal theta rhythm.

Antisense targeting of 3' end elements involved in DUX4 mRNA processing is an efficient therapeutic strategy for facioscapulohumeral dystrophy: a new gene-silencing approach.

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Marsollier, Anne-Charlotte; Ciszewski, Lukasz; Mariot, Virginie; Popplewell, Linda; Voit, Thomas; Dickson, George; Dumonceaux, Julie

2016-04-15

Defects in mRNA 3'end formation have been described to alter transcription termination, transport of the mRNA from the nucleus to the cytoplasm, stability of the mRNA and translation efficiency. Therefore, inhibition of polyadenylation may lead to gene silencing. Here, we choose facioscapulohumeral dystrophy (FSHD) as a model to determine whether or not targeting key 3' end elements involved in mRNA processing using antisense oligonucleotide drugs can be used as a strategy for gene silencing within a potentially therapeutic context. FSHD is a gain-of-function disease characterized by the aberrant expression of the Double homeobox 4 (DUX4) transcription factor leading to altered pathogenic deregulation of multiple genes in muscles. Here, we demonstrate that targeting either the mRNA polyadenylation signal and/or cleavage site is an efficient strategy to down-regulate DUX4 expression and to decrease the abnormally high-pathological expression of genes downstream of DUX4. We conclude that targeting key functional 3' end elements involved in pre-mRNA to mRNA maturation with antisense drugs can lead to efficient gene silencing and is thus a potentially effective therapeutic strategy for at least FSHD. Moreover, polyadenylation is a crucial step in the maturation of almost all eukaryotic mRNAs, and thus all mRNAs are virtually eligible for this antisense-mediated knockdown strategy. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

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Xie, Fang-Fei; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Hong; Wu, Jian; Guo, Yu-Fan; Zeng, Ke-Qin; Wang, Ming-Jun; Zhu, Xiao-Wei; Xia, Wei; Wang, Lan; He, Pei; Bing, Peng-Fei; Lu, Xin; Zhang, Yong-Hong; Lei, Shu-Feng

2018-01-01

DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1 ) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P correlation (R T4  > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

Expression of calmodulin mRNA in rat olfactory neuroepithelium.

Science.gov (United States)

Biffo, S; Goren, T; Khew-Goodall, Y S; Miara, J; Margolis, F L

1991-04-01

A calmodulin (CaM) cDNA was isolated by differential hybridization screening of a lambda gt10 library prepared from rat olfactory mucosa. This cDNA fragment, containing most of the open reading frame of the rat CaMI gene, was subcloned and used to characterize steady-state expression of CaM mRNA in rat olfactory neuroepithelium and bulb. Within the bulb mitral cells are the primary neuronal population expressing CaM mRNA. The major CaM mRNA expressed in the olfactory mucosa is 1.7 kb with smaller contributions from mRNAs of 4.0 and 1.4 kb. CaM mRNA was primarily associated with the olfactory neurons and, despite the cellular complexity of the tissue and the known involvement of CaM in diverse cellular processes, was only minimally evident in sustentacular cells, gland cells or respiratory epithelium. Following bulbectomy CaM mRNA declines in the olfactory neuroepithelium as does olfactory marker protein (OMP) mRNA. In contrast to the latter, CaM mRNA makes a partial recovery by one month after surgery. These results, coupled with those from in situ hybridization, indicate that CaM mRNA is expressed in both mature and immature olfactory neurons. The program regulating CaM gene expression in olfactory neurons is distinct from those controlling expression of B50/GAP43 in immature, or OMP in mature, neurons respectively.

Inactivation of a single copy of Crebbp selectively alters pre-mRNA processing in mouse hematopoietic stem cells.

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Madeleine E Lemieux

Full Text Available Global expression analysis of fetal liver hematopoietic stem cells (FL HSCs revealed the presence of unspliced pre-mRNA for a number of genes in normal FL HSCs. In a subset of these genes, Crebbp+/- FL HSCs had less unprocessed pre-mRNA without a corresponding reduction in total mRNA levels. Among the genes thus identified were the key regulators of HSC function Itga4, Msi2 and Tcf4. A similar but much weaker effect was apparent in Ep300+/- FL HSCs, indicating that, in this context as in others, the two paralogs are not interchangeable. As a group, the down-regulated intronic probe sets could discriminate adult HSCs from more mature cell types, suggesting that the underlying mechanism is regulated with differentiation stage and is active in both fetal and adult hematopoiesis. Consistent with increased myelopoiesis in Crebbp hemizygous mice, targeted reduction of CREBBP abundance by shRNA in the multipotent EML cell line triggered spontaneous myeloid differentiation in the absence of the normally required inductive signals. In addition, differences in protein levels between phenotypically distinct EML subpopulations were better predicted by taking into account not only the total mRNA signal but also the amount of unspliced message present. CREBBP thus appears to selectively influence the timing and degree of pre-mRNA processing of genes essential for HSC regulation and thereby has the potential to alter subsequent cell fate decisions in HSCs.

A review of blood sample handling and pre-processing for metabolomics studies.

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Hernandes, Vinicius Veri; Barbas, Coral; Dudzik, Danuta

2017-09-01

Metabolomics has been found to be applicable to a wide range of clinical studies, bringing a new era for improving clinical diagnostics, early disease detection, therapy prediction and treatment efficiency monitoring. A major challenge in metabolomics, particularly untargeted studies, is the extremely diverse and complex nature of biological specimens. Despite great advances in the field there still exist fundamental needs for considering pre-analytical variability that can introduce bias to the subsequent analytical process and decrease the reliability of the results and moreover confound final research outcomes. Many researchers are mainly focused on the instrumental aspects of the biomarker discovery process, and sample related variables sometimes seem to be overlooked. To bridge the gap, critical information and standardized protocols regarding experimental design and sample handling and pre-processing are highly desired. Characterization of a range variation among sample collection methods is necessary to prevent results misinterpretation and to ensure that observed differences are not due to an experimental bias caused by inconsistencies in sample processing. Herein, a systematic discussion of pre-analytical variables affecting metabolomics studies based on blood derived samples is performed. Furthermore, we provide a set of recommendations concerning experimental design, collection, pre-processing procedures and storage conditions as a practical review that can guide and serve for the standardization of protocols and reduction of undesirable variation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

mRNA Cancer Vaccines-Messages that Prevail.

Science.gov (United States)

Grunwitz, Christian; Kranz, Lena M

2017-01-01

During the last decade, mRNA became increasingly recognized as a versatile tool for the development of new innovative therapeutics. Especially for vaccine development, mRNA is of outstanding interest and numerous clinical trials have been initiated. Strikingly, all of these studies have proven that large-scale GMP production of mRNA is feasible and concordantly report a favorable safety profile of mRNA vaccines. Induction of T-cell immunity is a multi-faceted process comprising antigen acquisition, antigen processing and presentation, as well as immune stimulation. The effectiveness of mRNA vaccines is critically dependent on making the antigen(s) of interest available to professional antigen-presenting cells, especially DCs. Efficient delivery of mRNA into DCs in vivo remains a major challenge in the mRNA vaccine field. This review summarizes the principles of mRNA vaccines and highlights the importance of in vivo mRNA delivery and recent advances in harnessing their therapeutic potential.

LMKB/MARF1 localizes to mRNA processing bodies, interacts with Ge-1, and regulates IFI44L gene expression.

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Donald B Bloch

Full Text Available The mRNA processing body (P-body is a cellular structure that regulates the stability of cytoplasmic mRNA. MARF1 is a murine oocyte RNA-binding protein that is associated with maintenance of mRNA homeostasis and genomic stability. In this study, autoantibodies were used to identify Limkain B (LMKB, the human orthologue of MARF1, as a P-body component. Indirect immunofluorescence demonstrated that Ge-1 (a central component of the mammalian core-decapping complex co-localized with LMKB in P-bodies. Two-hybrid and co-immunoprecipitation assays were used to demonstrate interaction between Ge-1 and LMKB. The C-terminal 120 amino acids of LMKB mediated interaction with Ge-1 and the N-terminal 1094 amino acids of Ge-1 were required for interaction with LMKB. LMKB is the first protein identified to date that interacts with this portion of Ge-1. LMKB was expressed in human B and T lymphocyte cell lines; depletion of LMKB increased expression of IFI44L, a gene that has been implicated in the cellular response to Type I interferons. The interaction between LMKB/MARF1, a protein that contains RNA-binding domains, and Ge-1, which interacts with core-decapping proteins, suggests that LMKB has a role in the regulation of mRNA stability. LMKB appears to have different functions in different cell types: maintenance of genomic stability in developing oocytes and possible dampening of the inflammatory response in B and T cells.

Decreases in Casz1 mRNA by an siRNA Complex Do not Alter Blood Pressure in Mice.

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Ji, Su-Min; Shin, Young-Bin; Park, So-Yon; Lee, Hyeon-Ju; Oh, Bermseok

2012-03-01

Recent genomewide association studies of large samples have identified genes that are associated with blood pressure. The Global Blood Pressure Genetics (Global BPgen) and Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) consortiums identified 14 loci that govern blood pressure on a genomewide significance level, one of which is CASZ1 confirmed in both Europeans and Asians. CASZ1 is a zinc finger transcription factor that controls apoptosis and cell fate and suppresses neuroblastoma tumor growth by reprogramming gene expression, like a tumor suppressor. To validate the function of CASZ1 in blood pressure, we decreased Casz1 mRNA levels in mice by siRNA. Casz1 siRNA reduced mRNA levels by 59% in a mouse cell line. A polyethylenimine-mixed siRNA complex was injected into mouse tail veins, reducing Casz1 mRNA expression to 45% in the kidney. However, blood pressure in the treated mice was unaffected, despite a 55% reduction in Casz1 mRNA levels in the kidney on multiple siRNA injections daily. Even though Casz1 siRNA-treated mice did not experience any significant change in blood pressure, our study demonstrates the value of in vivo siRNA injection in analyzing the function of candidate genes identified by genomewide association studies.

Depletion of key protein components of the RISC pathway impairs pre-ribosomal RNA processing.

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Liang, Xue-Hai; Crooke, Stanley T

2011-06-01

Little is known about whether components of the RNA-induced silencing complex (RISC) mediate the biogenesis of RNAs other than miRNA. Here, we show that depletion of key proteins of the RISC pathway by antisense oligonucleotides significantly impairs pre-rRNA processing in human cells. In cells depleted of Drosha or Dicer, different precursors to 5.8S rRNA strongly accumulated, without affecting normal endonucleolytic cleavages. Moderate yet distinct processing defects were also observed in Ago2-depleted cells. Physical links between pre-rRNA and these proteins were identified by co-immunoprecipitation analyses. Interestingly, simultaneous depletion of Dicer and Drosha led to a different processing defect, causing slower production of 28S rRNA and its precursor. Both Dicer and Ago2 were detected in the nuclear fraction, and reduction of Dicer altered the structure of the nucleolus, where pre-rRNA processing occurs. Together, these results suggest that Drosha and Dicer are implicated in rRNA biogenesis.

The function of the inner nuclear envelope protein SUN1 in mRNA export is regulated by phosphorylation.

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Li, Ping; Stumpf, Maria; Müller, Rolf; Eichinger, Ludwig; Glöckner, Gernot; Noegel, Angelika A

2017-08-22

SUN1, a component of the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex, functions in mammalian mRNA export through the NXF1-dependent pathway. It associates with mRNP complexes by direct interaction with NXF1. It also binds to the NPC through association with the nuclear pore component Nup153, which is involved in mRNA export. The SUN1-NXF1 association is at least partly regulated by a protein kinase C (PKC) which phosphorylates serine 113 (S113) in the N-terminal domain leading to reduced interaction. The phosphorylation appears to be important for the SUN1 function in nuclear mRNA export since GFP-SUN1 carrying a S113A mutation was less efficient in restoring mRNA export after SUN1 knockdown as compared to the wild type protein. By contrast, GFP-SUN1-S113D resembling the phosphorylated state allowed very efficient export of poly(A)+RNA. Furthermore, probing a possible role of the LINC complex component Nesprin-2 in this process we observed impaired mRNA export in Nesprin-2 knockdown cells. This effect might be independent of SUN1 as expression of a GFP tagged SUN-domain deficient SUN1, which no longer can interact with Nesprin-2, did not affect mRNA export.

Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling

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Mo Min

2008-05-01

Full Text Available Abstract Background The polyadenylation of mRNA is one of the critical processing steps during expression of almost all eukaryotic genes. It is tightly integrated with transcription, particularly its termination, as well as other RNA processing events, i.e. capping and splicing. The poly(A tail protects the mRNA from unregulated degradation, and it is required for nuclear export and translation initiation. In recent years, it has been demonstrated that the polyadenylation process is also involved in the regulation of gene expression. The polyadenylation process requires two components, the cis-elements on the mRNA and a group of protein factors that recognize the cis-elements and produce the poly(A tail. Here we report a comprehensive pairwise protein-protein interaction mapping and gene expression profiling of the mRNA polyadenylation protein machinery in Arabidopsis. Results By protein sequence homology search using human and yeast polyadenylation factors, we identified 28 proteins that may be components of Arabidopsis polyadenylation machinery. To elucidate the protein network and their functions, we first tested their protein-protein interaction profiles. Out of 320 pair-wise protein-protein interaction assays done using the yeast two-hybrid system, 56 (~17% showed positive interactions. 15 of these interactions were further tested, and all were confirmed by co-immunoprecipitation and/or in vitro co-purification. These interactions organize into three distinct hubs involving the Arabidopsis polyadenylation factors. These hubs are centered around AtCPSF100, AtCLPS, and AtFIPS. The first two are similar to complexes seen in mammals, while the third one stands out as unique to plants. When comparing the gene expression profiles extracted from publicly available microarray datasets, some of the polyadenylation related genes showed tissue-specific expression, suggestive of potential different polyadenylation complex configurations. Conclusion An

High-Risk Human Papillomavirus (hrHPV) E6/E7 mRNA Testing by PreTect HPV-Proofer for Detection of Cervical High-Grade Intraepithelial Neoplasia and Cancer among hrHPV DNA-Positive Women with Normal Cytology

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Rijkaart, D. C.; Heideman, D. A. M.; Coupe, V. M. H.; Brink, A. A. T. P.; Verheijen, R. H. M.; Skomedal, H.; Karlsen, F.; Morland, E.; Snijders, P. J. F.

2012-01-01

Our aim was to investigate whether high-risk HPV (hrHPV) mRNA detection by PreTect HPV-Proofer can be used to stratify hrHPV DNA-positive women of different cytology classes for risk of high-grade cervical intraepithelial neoplasia or worse (cervical precancer or cancer, i.e., cervical intraepithelial neoplasia grade 2 or higher [≥CIN2]). A total of 375 women participating in population-based screening, with a GP5+/6+-PCR hrHPV DNA-positive cervical scrape with normal cytology (n = 202), borderline or mild dyskaryosis (BMD) (n = 88), or moderate dyskaryosis or worse (>BMD) (n = 85), were enrolled. Cervical scrapes were additionally subjected to HPV16/18/31/33/45 E6/E7 mRNA analysis by PreTect HPV-Proofer (mRNA test). Referral and follow-up policies were based on cytology, hrHPV DNA, and mRNA testing. The primary study endpoint was the number of ≥CIN2 detected within 3 years of follow-up. The mRNA positivity increased with the severity of cytological abnormality, ranging from 32% (64/202) in hrHPV DNA-positive women with normal cytology to 47% (41/88) in BMD and 68% (58/85) in >BMD groups (P cytology, i.e., 0.55 (95% confidence interval [95% CI], 0.34 to 0.76) in mRNA-positive versus 0.20 (95% CI, 0.07 to 0.33) in mRNA-negative women. In hrHPV DNA-positive women with BMD or >BMD, the result of the mRNA test did not influence the ≥CIN2 risk. In conclusion, mRNA testing by PreTect HPV-Proofer might be of value to select hrHPV DNA-positive women with normal cytology in need of immediate referral for colposcopy. PMID:22553244

Interactions between mRNA export commitment, 3'-end quality control, and nuclear degradation

DEFF Research Database (Denmark)

Libri, Domenico; Dower, Ken; Boulay, Jocelyne

2002-01-01

Several aspects of eukaryotic mRNA processing are linked to transcription. In Saccharomyces cerevisiae, overexpression of the mRNA export factor Sub2p suppresses the growth defect of hpr1 null cells, yet the protein Hpr1p and the associated THO protein complex are implicated in transcriptional el...... results show that several classes of defective RNPs are subject to a quality control step that impedes release from transcription site foci and suggest that suboptimal messenger ribonucleoprotein assembly leads to RNA degradation by Rrp6p....

Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis.

Science.gov (United States)

Qi, Lei; Yue, Lei; Feng, Deqin; Qi, Fengxia; Li, Jie; Dong, Xiuzhu

2017-07-07

Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively. A predominant uridine downstream PSSs served as a processing signature. Remarkably, 5΄P-seq detected overrepresented uPSS and iPSS in the polycistronic operons encoding ribosomal proteins, and the majority upstream and proximal ribosome binding sites, suggesting a regulatory role of processing on translation initiation. The processed transcripts showed increased stability and translation efficiency. Particularly, processing within the tricistronic transcript of rplA-rplJ-rplL enhanced the translation of rplL, which can provide a driving force for the 1:4 stoichiometry of L10 to L12 in the ribosome. Growth-associated mRNA processing intensities were also correlated with the cellular ribosomal protein levels, thereby suggesting that mRNA processing is involved in tuning growth-dependent ribosome synthesis. In conclusion, our findings suggest that mRNA processing-mediated post-transcriptional regulation is a potential mechanism of ribosomal protein synthesis and stoichiometry. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

KAUST Repository

Ding, Feng; Cui, Peng; Wang, Zhenyu; Zhang, ShouDong; Ali, Shahjahan; Xiong, Liming

2014-01-01

Background: Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress

Applying the breaks on gene expression - mRNA deadenylation by Pop2p

DEFF Research Database (Denmark)

Andersen, Kasper Røjkjær; Jonstrup, Anette Thyssen; Van, Lan Bich

When driving a car, control of the brakes is just as important as control of the accelerator pedal. Likewise, in gene expression, regulation of mRNA degradation is as important as regulation of its synthesis (Mühlemann, 2005). The rate-determining step of mRNA decay in eukaryotes seems to be the ......When driving a car, control of the brakes is just as important as control of the accelerator pedal. Likewise, in gene expression, regulation of mRNA degradation is as important as regulation of its synthesis (Mühlemann, 2005). The rate-determining step of mRNA decay in eukaryotes seems...... to be the shortening of the poly(A) tail (deadenylation), as this step is slower than the subsequent decapping and degradation of the mRNA body. The Mega-Dalton Ccr4-Not complex contains two exonucleases, Ccr4p and Pop2p, responsible for this process. It is not known at present why two conserved nucleases are needed...

Attenuation in the rph-pyrE operon of Escherichia coli and processing of the dicistronic mRNA

DEFF Research Database (Denmark)

Poulsen, Peter; Jensen, Kaj Frank

1992-01-01

We have substituted on a plasmid the native promoter of the Escherichia coli rph-pyrE operon with an inducible transcription-initiation signal. The plasmid was used to study the mRNA chains derived from the operon at different intracellular concentrations of UTP and as a function of time following...... induction of transcription. The results showed that dicistronic rph-pyrE mRNA was formed when the UTP pool was low, and that a monocistronic rph mRNA was the major transcription product in high-UTP pools, thus supporting an UTP-controlled attenuation mechanism for regulation of pyrE gene expression. However......, the dicistronic rph-pyrE transcript was rapidly processed into two monocistronic mRNA units, and a cleavage site was mapped near the attenuator in the intercistronic region, close to the site where transcription was terminated in high-UTP pools. Furthermore, the major 3' end of the pyrE mRNA was mapped near...

Regulation of mRNA translation influences hypoxia tolerance

International Nuclear Information System (INIS)

Koritzinsky, M.; Wouters, B.G.; Koumenis, C.

2003-01-01

Hypoxia is a heterogenous but common characteristic of human tumours and poor oxygenation is associated with poor prognosis. We believe that the presence of viable hypoxic tumor cells reflects in part an adaptation and tolerance of these cells to oxygen deficiency. Since oxidative phosphorylation is compromized during hypoxia, adaptation may involve both the upregulation of glycolysis as well as downregulation of energy consumption. mRNA translation is one of the most energy costly cellular processes, and we and others have shown that global mRNA translation is rapidly inhibited during hypoxia. However, some mRNAs, including those coding for HIF-1 α and VEGF, remain efficiently translated during hypoxia. Clearly, the mechanisms responsible for the overall inhibition of translation during hypoxia does not compromize the translation of certain hypoxia-induced mRNA species. We therefore hypothesize that the inhibition of mRNA translation serves to promote hypoxia tolerance in two ways: i) through conservation of energy and ii) through differential gene expression involved in hypoxia adaptation. We have recently identified two pathways that are responsible for the global inhibition of translation during hypoxia. The phosphorylation of the eukaryotic initiation factor eIF2 α by the ER resident kinase PERK results in down-regulation of protein synthesis shortly after the onset of hypoxia. In addition, the initiation complex eIF4F is disrupted during long lasting hypoxic conditions. The identification of the molecular pathways responsible for the inhibition of overall translation during hypoxia has rendered it possible to investigate their importance for hypoxia tolerance. We have found that mouse embryo fibroblasts that are knockout for PERK and therefore not able to inhibit protein synthesis efficiently during oxygen deficiency are significantly less tolerant to hypoxia than their wildtype counterparts. We are currently also investigating the functional significance

The 1996 ENDF pre-processing codes

International Nuclear Information System (INIS)

Cullen, D.E.

1996-01-01

The codes are named 'the Pre-processing' codes, because they are designed to pre-process ENDF/B data, for later, further processing for use in applications. This is a modular set of computer codes, each of which reads and writes evaluated nuclear data in the ENDF/B format. Each code performs one or more independent operations on the data, as described below. These codes are designed to be computer independent, and are presently operational on every type of computer from large mainframe computer to small personal computers, such as IBM-PC and Power MAC. The codes are available from the IAEA Nuclear Data Section, free of charge upon request. (author)

Nuclear trafficking of the HIV-1 pre-integration complex depends on the ADAM10 intracellular domain

International Nuclear Information System (INIS)

Endsley, Mark A.; Somasunderam, Anoma D.; Li, Guangyu; Oezguen, Numan; Thiviyanathan, Varatharasa; Murray, James L.; Rubin, Donald H.; Hodge, Thomas W.

2014-01-01

Previously, we showed that ADAM10 is necessary for HIV-1 replication in primary human macrophages and immortalized cell lines. Silencing ADAM10 expression interrupted the HIV-1 life cycle prior to nuclear translocation of viral cDNA. Furthermore, our data indicated that HIV-1 replication depends on the expression of ADAM15 and γ-secretase, which proteolytically processes ADAM10. Silencing ADAM15 or γ-secretase expression inhibits HIV-1 replication between reverse transcription and nuclear entry. Here, we show that ADAM10 expression also supports replication in CD4 + T lymphocytes. The intracellular domain (ICD) of ADAM10 associates with the HIV-1 pre-integration complex (PIC) in the cytoplasm and immunoprecipitates and co-localizes with HIV-1 integrase, a key component of PIC. Taken together, our data support a model whereby ADAM15/γ-secretase processing of ADAM10 releases the ICD, which then incorporates into HIV-1 PIC to facilitate nuclear trafficking. Thus, these studies suggest ADAM10 as a novel therapeutic target for inhibiting HIV-1 prior to nuclear entry. - Highlights: • Nuclear trafficking of the HIV-1 pre-integration complex depends on ADAM10. • ADAM10 associates with HIV-1 integrase in the pre-integration complex. • HIV-1 replication depends on the expression of ADAM15 and γ-secretase. • Silencing ADAM15 or γ-secretase expression inhibits nuclear import of viral cDNA. • ADAM10 is important for HIV-1 replication in human macrophages and CD4 + T lymphocytes

Nuclear trafficking of the HIV-1 pre-integration complex depends on the ADAM10 intracellular domain

Energy Technology Data Exchange (ETDEWEB)

Endsley, Mark A., E-mail: maendsle@utmb.edu [Department Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555 (United States); Somasunderam, Anoma D., E-mail: asomasun@utmb.edu [Department Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555 (United States); Li, Guangyu, E-mail: LIG001@mail.etsu.edu [Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 (United States); Oezguen, Numan, E-mail: numan.oezguen@bcm.edu [Department of Pathology and Immunology, Microbiome Center, Texas Children' s Hospital, Houston, TX 77030 (United States); Thiviyanathan, Varatharasa, E-mail: Varatharasa.Thiviyanathan@uth.tmc.edu [Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030 (United States); Murray, James L., E-mail: jmurray100@yahoo.com [GeneTAG Technology, Inc., 3155 Northwoods Place, Norcross, GA 30071 (United States); Rubin, Donald H., E-mail: don.h.rubin@vanderbilt.edu [Research Medicine, VA Tennessee Valley Healthcare System, 1310 24th Ave. South, Nashville, TN 37212 (United States); Departments of Medicine, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, 1161 21st Ave South, Nashville, TN 37232 (United States); Hodge, Thomas W., E-mail: twhodge3@gmail.com [Pre-clinical and Antiviral Research, Tamir Biotechnology, Inc., 12625 High Bluff Dr., Suite 113, San Diego, CA 92130 (United States); and others

2014-04-15

Previously, we showed that ADAM10 is necessary for HIV-1 replication in primary human macrophages and immortalized cell lines. Silencing ADAM10 expression interrupted the HIV-1 life cycle prior to nuclear translocation of viral cDNA. Furthermore, our data indicated that HIV-1 replication depends on the expression of ADAM15 and γ-secretase, which proteolytically processes ADAM10. Silencing ADAM15 or γ-secretase expression inhibits HIV-1 replication between reverse transcription and nuclear entry. Here, we show that ADAM10 expression also supports replication in CD4{sup +} T lymphocytes. The intracellular domain (ICD) of ADAM10 associates with the HIV-1 pre-integration complex (PIC) in the cytoplasm and immunoprecipitates and co-localizes with HIV-1 integrase, a key component of PIC. Taken together, our data support a model whereby ADAM15/γ-secretase processing of ADAM10 releases the ICD, which then incorporates into HIV-1 PIC to facilitate nuclear trafficking. Thus, these studies suggest ADAM10 as a novel therapeutic target for inhibiting HIV-1 prior to nuclear entry. - Highlights: • Nuclear trafficking of the HIV-1 pre-integration complex depends on ADAM10. • ADAM10 associates with HIV-1 integrase in the pre-integration complex. • HIV-1 replication depends on the expression of ADAM15 and γ-secretase. • Silencing ADAM15 or γ-secretase expression inhibits nuclear import of viral cDNA. • ADAM10 is important for HIV-1 replication in human macrophages and CD4{sup +} T lymphocytes.

The bio-complex "reaction pattern in vertebrate cells" reduces cytokine-induced cellular adhesion molecule mRNA expression in human endothelial cells by attenuation of NF-kappaB translocation.

Science.gov (United States)

Rönnau, Cindy; Liebermann, Herbert E H; Helbig, Franz; Staudt, Alexander; Felix, Stephan B; Ewert, Ralf; Landsberger, Martin

2009-02-28

The bio-complex "reaction pattern in vertebrate cells" (RiV) is mainly represented by characteristic exosome-like particles--probably as reaction products of cells to specific stress. The transcription factor NF-kappaB plays a central role in inflammation. We tested the hypothesis that RiV particle preparations (RiV-PP) reduce cellular adhesion molecule (CAM) expression (ICAM-1, VCAM-1, E-selectin) by the attenuation of NF-kappaB translocation in human umbilical vein endothelial cells (HUVEC). After 4 hours, pre-incubation of HUVEC with RiV-PP before stimulation with TNF-alpha significantly reduced ICAM-1 (65.5+/-10.3%) and VCAM-1 (71.1+/-12.3%) mRNA expression compared to TNF-alpha-treated cells (100%, n=7). ICAM-1 surface expression was significantly albeit marginally reduced in RiV/TNF-alpha- treated cells (92.0+/-5.6%, n=4). No significant effect was observed on VCAM-1 surface expression. In RiV/TNF-alpha-treated cells (n=4), NF-kappaB subunits p50 (85.7+/-4.1%) and p65 (85.0+/-1.8%) nuclear translocation was significantly reduced. RiV-PP may exert an anti-inflammatory effect in HUVEC by reducing CAM mRNA expression via attenuation of p50 and p65 translocation.

Pre-maxillary complex morphology in bilateral cleft and hypothesis on laterality of deviated pre-maxilla

Directory of Open Access Journals (Sweden)

Jyotsna Murthy

2016-01-01

Full Text Available Introduction: Pre-maxillary complex (pre-maxilla [PMX] + vomer morphology in bilateral complete cleft of primary and secondary palate (BCLCP is very complex and less reviewed in literature. Materials and Methods: In this retrospective cross-sectional study, 200 consecutive BCLCP patients were selected. Their pre-operative clinical photographs and dental casts were evaluated by a single investigator at two different points of time, to study the morphology of PMX and vomer with special emphasis on deviation of vomer and rotation of PMX. Results: It is found that in above 70% of patients, PMX and vomer both displaced or deviated towards left side in horizontal plane and PMX rotated anticlockwise at PMX vomerine suture (PVS. In 10% of cases, both PMX and vomer are displaced towards the right side, PMX rotated clockwise at PVS. In 11% of cases, vomer is displaced towards the left side, but PMX rotated clockwise at PVS. In 5% of cases, vomer is displaced towards the right side, but PMX rotated anticlockwise at PVS. Both PMX and vomer are in midline in 4% of cases. Conclusion: Specific morphological deviation of vomer and PMX has been studied. We put forward the probable hypothesis to explain the deviation and rotation of PMX.

Studies on the role of NonA in mRNA biogenesis

International Nuclear Information System (INIS)

Kozlova, Natalia; Braga, Jose; Lundgren, Josefin; Rino, Jose; Young, Patrick; Carmo-Fonseca, Maria; Visa, Neus

2006-01-01

The NonA protein of Drosophila melanogaster is an abundant nuclear protein that belongs to the DBHS (Drosophila behavior, human splicing) protein family. The DBHS proteins bind both DNA and RNA in vitro and have been involved in different aspects of gene expression, including pre-mRNA splicing, transcription regulation and nuclear retention of mRNA. We have used double-stranded RNA interference in Drosophila S2 cells to silence the expression of NonA and to investigate its role in mRNA biogenesis. We show that knockdown of NonA does not affect transcription nor splicing. We demonstrate that NonA forms a complex with the essential nuclear export factor NXF1 in an RNA-dependent manner. We have constructed stable S2 cell lines that express full-length and truncated NXF1 fused to GFP in order to perform fluorescence recovery after photobleaching experiments. We show that knockdown of NonA reduces the intranuclear mobility of NXF1-GFP associated with poly(A) + RNA in vivo, while the mobility of the truncated NXF1-GFP that does not bind RNA is not affected. Our data suggest that NonA facilitates the intranuclear mobility of mRNP particles

A Point Mutation in the Exon Junction Complex Factor Y14 Disrupts Its Function in mRNA Cap Binding and Translation Enhancement*

Science.gov (United States)

Chuang, Tzu-Wei; Lee, Kuo-Ming; Lou, Yuan-Chao; Lu, Chia-Chen; Tarn, Woan-Yuh

2016-01-01

Eukaryotic mRNA biogenesis involves a series of interconnected steps mediated by RNA-binding proteins. The exon junction complex core protein Y14 is required for nonsense-mediated mRNA decay (NMD) and promotes translation. Moreover, Y14 binds the cap structure of mRNAs and inhibits the activity of the decapping enzyme Dcp2. In this report, we show that an evolutionarily conserved tryptophan residue (Trp-73) of Y14 is critical for its binding to the mRNA cap structure. A Trp-73 mutant (W73V) bound weakly to mRNAs and failed to protect them from degradation. However, this mutant could still interact with the NMD and mRNA degradation factors and retained partial NMD activity. In addition, we found that the W73V mutant could not interact with translation initiation factors. Overexpression of W73V suppressed reporter mRNA translation in vitro and in vivo and reduced the level of a set of nascent proteins. These results reveal a residue of Y14 that confers cap-binding activity and is essential for Y14-mediated enhancement of translation. Finally, we demonstrated that Y14 may selectively and differentially modulate protein biosynthesis. PMID:26887951

A Point Mutation in the Exon Junction Complex Factor Y14 Disrupts Its Function in mRNA Cap Binding and Translation Enhancement.

Science.gov (United States)

Chuang, Tzu-Wei; Lee, Kuo-Ming; Lou, Yuan-Chao; Lu, Chia-Chen; Tarn, Woan-Yuh

2016-04-15

Eukaryotic mRNA biogenesis involves a series of interconnected steps mediated by RNA-binding proteins. The exon junction complex core protein Y14 is required for nonsense-mediated mRNA decay (NMD) and promotes translation. Moreover, Y14 binds the cap structure of mRNAs and inhibits the activity of the decapping enzyme Dcp2. In this report, we show that an evolutionarily conserved tryptophan residue (Trp-73) of Y14 is critical for its binding to the mRNA cap structure. A Trp-73 mutant (W73V) bound weakly to mRNAs and failed to protect them from degradation. However, this mutant could still interact with the NMD and mRNA degradation factors and retained partial NMD activity. In addition, we found that the W73V mutant could not interact with translation initiation factors. Overexpression of W73V suppressed reporter mRNA translation in vitro and in vivo and reduced the level of a set of nascent proteins. These results reveal a residue of Y14 that confers cap-binding activity and is essential for Y14-mediated enhancement of translation. Finally, we demonstrated that Y14 may selectively and differentially modulate protein biosynthesis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Universal Poisson Statistics of mRNAs with Complex Decay Pathways.

Science.gov (United States)

Thattai, Mukund

2016-01-19

Messenger RNA (mRNA) dynamics in single cells are often modeled as a memoryless birth-death process with a constant probability per unit time that an mRNA molecule is synthesized or degraded. This predicts a Poisson steady-state distribution of mRNA number, in close agreement with experiments. This is surprising, since mRNA decay is known to be a complex process. The paradox is resolved by realizing that the Poisson steady state generalizes to arbitrary mRNA lifetime distributions. A mapping between mRNA dynamics and queueing theory highlights an identifiability problem: a measured Poisson steady state is consistent with a large variety of microscopic models. Here, I provide a rigorous and intuitive explanation for the universality of the Poisson steady state. I show that the mRNA birth-death process and its complex decay variants all take the form of the familiar Poisson law of rare events, under a nonlinear rescaling of time. As a corollary, not only steady-states but also transients are Poisson distributed. Deviations from the Poisson form occur only under two conditions, promoter fluctuations leading to transcriptional bursts or nonindependent degradation of mRNA molecules. These results place severe limits on the power of single-cell experiments to probe microscopic mechanisms, and they highlight the need for single-molecule measurements. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

HLA-G allelic variants are associated with differences in the HLA-G mRNA isoform profile and HLA-G mRNA levels

DEFF Research Database (Denmark)

Hviid, Thomas Vauvert F; Hylenius, Sine; Rørbye, Christina

2003-01-01

between mother and fetus in several ways. Finally, the expression of membrane-bound HLA-G and soluble HLA-G has been proposed to influence the outcome of pregnancy, and an aberrant HLA-G expression in pre-eclamptic placentas and spontaneous abortions has been reported. Here, an association between certain...... HLA-G polymorphisms and the mRNA levels of the different alternatively spliced HLA-G isoforms in first trimester trophoblast cell populations is reported. Several alternatively spliced HLA-G mRNA isoforms, including a 14-bp polymorphism in the 3'UTR end (exon 8) of the HLA-G gene, are expressed...

Sulphur cement pre-composition and process for preparing such sulphur cement pre-composition

NARCIS (Netherlands)

2013-01-01

The invention provides a process for the preparation of a sulphur cement pre-composition comprising reacting sulphur modifier with polysulphide-containing organosilane to obtain in the presence of sulphur the sulphur cement pre-composition, wherein the organosilane has the general molecular formula:

NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing

Energy Technology Data Exchange (ETDEWEB)

Yoshikatsu, Yuki [Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, Tokushima 770-8506 (Japan); Ishida, Yo-ichi; Sudo, Haruka [Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Yuasa, Keizo; Tsuji, Akihiko [Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, Tokushima 770-8506 (Japan); Nagahama, Masami, E-mail: nagahama@my-pharm.ac.jp [Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan)

2015-08-28

Nuclear VCP-like 2 (NVL2) is a member of the chaperone-like AAA-ATPase family and is involved in the biosynthesis of 60S ribosomal subunits in mammalian cells. We previously showed the interaction of NVL2 with a DExD/H-box RNA helicase MTR4/DOB1, which is a known cofactor for an exoribonuclease complex, the exosome. This finding implicated NVL2 in RNA metabolic processes during ribosome biogenesis. In the present study, we found that a series of mutations within the ATPase domain of NVL2 causes a defect in pre-rRNA processing into mature 28S and 5.8S rRNAs. Co-immunoprecipitation analysis showed that NVL2 was associated with the nuclear exosome complex, which includes RRP6 as a nucleus-specific catalytic subunit. This interaction was prevented by depleting either MTR4 or RRP6, indicating their essential role in mediating this interaction with NVL2. Additionally, knockdown of MPP6, another cofactor for the nuclear exosome, also prevented the interaction by causing MTR4 to dissociate from the nuclear exosome. These results suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex. - Highlights: • ATPase-deficient mutants of NVL2 have decreased pre-rRNA processing. • NVL2 associates with the nuclear exosome through interactions with MTR4 and RRP6. • MPP6 stabilizes MTR4-RRP6 interaction and allows NVL2 to interact with the complex.

Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation.

Directory of Open Access Journals (Sweden)

Clément Chevalier

2010-03-01

Full Text Available Staphylococcus aureus RNAIII is the intracellular effector of the quorum sensing system that temporally controls a large number of virulence factors including exoproteins and cell-wall-associated proteins. Staphylocoagulase is one major virulence factor, which promotes clotting of human plasma. Like the major cell surface protein A, the expression of staphylocoagulase is strongly repressed by the quorum sensing system at the post-exponential growth phase. Here we used a combination of approaches in vivo and in vitro to analyze the mechanism used by RNAIII to regulate the expression of staphylocoagulase. Our data show that RNAIII represses the synthesis of the protein through a direct binding with the mRNA. Structure mapping shows that two distant regions of RNAIII interact with coa mRNA and that the mRNA harbors a conserved signature as found in other RNAIII-target mRNAs. The resulting complex is composed of an imperfect duplex masking the Shine-Dalgarno sequence of coa mRNA and of a loop-loop interaction occurring downstream in the coding region. The imperfect duplex is sufficient to prevent the formation of the ribosomal initiation complex and to repress the expression of a reporter gene in vivo. In addition, the double-strand-specific endoribonuclease III cleaves the two regions of the mRNA bound to RNAIII that may contribute to the degradation of the repressed mRNA. This study validates another direct target of RNAIII that plays a role in virulence. It also illustrates the diversity of RNAIII-mRNA topologies and how these multiple RNAIII-mRNA interactions would mediate virulence regulation.

Collagen mRNA levels changes during colorectal cancer carcinogenesis

DEFF Research Database (Denmark)

Skovbjerg, Hanne; Anthonsen, Dorit; Lothe, Inger M B

2009-01-01

BACKGROUND: Invasive growth of epithelial cancers is a complex multi-step process which involves dissolution of the basement membrane. Type IV collagen is a major component in most basement membranes. Type VII collagen is related to anchoring fibrils and is found primarily in the basement membrane...... zone of stratified epithelia. Immunohistochemical studies have previously reported changes in steady-state levels of different alpha(IV) chains in several epithelial cancer types. In the present study we aimed to quantitatively determine the mRNA levels of type IV collagen (alpha1/alpha 4/alpha 6......) and type VII collagen (alpha1) during colorectal cancer carcinogenesis. METHODS: Using quantitative RT-PCR, we have determined the mRNA levels for alpha1(IV), alpha 4(IV), alpha 6(IV), and alpha1(VII) in colorectal cancer tissue (n = 33), adenomas (n = 29) and in normal tissue from the same individuals...

RNA-induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators.

Science.gov (United States)

Redfern, Andrew D; Colley, Shane M; Beveridge, Dianne J; Ikeda, Naoya; Epis, Michael R; Li, Xia; Foulds, Charles E; Stuart, Lisa M; Barker, Andrew; Russell, Victoria J; Ramsay, Kerry; Kobelke, Simon J; Li, Xiaotao; Hatchell, Esme C; Payne, Christine; Giles, Keith M; Messineo, Adriana; Gatignol, Anne; Lanz, Rainer B; O'Malley, Bert W; Leedman, Peter J

2013-04-16

The cytoplasmic RNA-induced silencing complex (RISC) contains dsRNA binding proteins, including protein kinase RNA activator (PACT), transactivation response RNA binding protein (TRBP), and Dicer, that process pre-microRNAs into mature microRNAs (miRNAs) that target specific mRNA species for regulation. There is increasing evidence for important functional interactions between the miRNA and nuclear receptor (NR) signaling networks, with recent data showing that estrogen, acting through the estrogen receptor, can modulate initial aspects of nuclear miRNA processing. Here, we show that the cytoplasmic RISC proteins PACT, TRBP, and Dicer are steroid receptor RNA activator (SRA) binding NR coregulators that target steroid-responsive promoters and regulate NR activity and downstream gene expression. Furthermore, each of the RISC proteins, together with Argonaute 2, associates with SRA and specific pre-microRNAs in both the nucleus and cytoplasm, providing evidence for links between NR-mediated transcription and some of the factors involved in miRNA processing.

An essential nuclear protein in trypanosomes is a component of mRNA transcription/export pathway.

Directory of Open Access Journals (Sweden)

Mariana Serpeloni

Full Text Available In eukaryotic cells, different RNA species are exported from the nucleus via specialized pathways. The mRNA export machinery is highly integrated with mRNA processing, and includes a different set of nuclear transport adaptors as well as other mRNA binding proteins, RNA helicases, and NPC-associated proteins. The protozoan parasite Trypanosoma cruzi is the causative agent of Chagas disease, a widespread and neglected human disease which is endemic to Latin America. Gene expression in Trypanosoma has unique characteristics, such as constitutive polycistronic transcription of protein-encoding genes and mRNA processing by trans-splicing. In general, post-transcriptional events are the major points for regulation of gene expression in these parasites. However, the export pathway of mRNA from the nucleus is poorly understood. The present study investigated the function of TcSub2, which is a highly conserved protein ortholog to Sub2/ UAP56, a component of the Transcription/Export (TREX multiprotein complex connecting transcription with mRNA export in yeast/human. Similar to its orthologs, TcSub2 is a nuclear protein, localized in dispersed foci all over the nuclei -except the fibrillar center of nucleolus- and at the interface between dense and non-dense chromatin areas, proposing the association of TcSub2 with transcription/processing sites. These findings were analyzed further by BrUTP incorporation assays and confirmed that TcSub2 is physically associated with active RNA polymerase II (RNA pol II, but not RNA polymerase I (RNA pol I or Spliced Leader (SL transcription, demonstrating participation particularly in nuclear mRNA metabolism in T. cruzi. The double knockout of the TcSub2 gene is lethal in T. cruzi, suggesting it has an essential function. Alternatively, RNA interference assays were performed in Trypanosoma brucei. It allowed demonstrating that besides being an essential protein, its knockdown causes mRNA accumulation in the nucleus and

Superior pre-attentive auditory processing in musicians.

Science.gov (United States)

Koelsch, S; Schröger, E; Tervaniemi, M

1999-04-26

The present study focuses on influences of long-term experience on auditory processing, providing the first evidence for pre-attentively superior auditory processing in musicians. This was revealed by the brain's automatic change-detection response, which is reflected electrically as the mismatch negativity (MMN) and generated by the operation of sensoric (echoic) memory, the earliest cognitive memory system. Major chords and single tones were presented to both professional violinists and non-musicians under ignore and attend conditions. Slightly impure chords, presented among perfect major chords elicited a distinct MMN in professional musicians, but not in non-musicians. This demonstrates that compared to non-musicians, musicians are superior in pre-attentively extracting more information out of musically relevant stimuli. Since effects of long-term experience on pre-attentive auditory processing have so far been reported for language-specific phonemes only, results indicate that sensory memory mechanisms can be modulated by training on a more general level.

The 1989 ENDF pre-processing codes

International Nuclear Information System (INIS)

Cullen, D.E.; McLaughlin, P.K.

1989-12-01

This document summarizes the 1989 version of the ENDF pre-processing codes which are required for processing evaluated nuclear data coded in the format ENDF-4, ENDF-5, or ENDF-6. The codes are available from the IAEA Nuclear Data Section, free of charge upon request. (author)

Self-amplifying mRNA vaccines.

Science.gov (United States)

Brito, Luis A; Kommareddy, Sushma; Maione, Domenico; Uematsu, Yasushi; Giovani, Cinzia; Berlanda Scorza, Francesco; Otten, Gillis R; Yu, Dong; Mandl, Christian W; Mason, Peter W; Dormitzer, Philip R; Ulmer, Jeffrey B; Geall, Andrew J

2015-01-01

This chapter provides a brief introduction to nucleic acid-based vaccines and recent research in developing self-amplifying mRNA vaccines. These vaccines promise the flexibility of plasmid DNA vaccines with enhanced immunogenicity and safety. The key to realizing the full potential of these vaccines is efficient delivery of nucleic acid to the cytoplasm of a cell, where it can amplify and express the encoded antigenic protein. The hydrophilicity and strong net negative charge of RNA impedes cellular uptake. To overcome this limitation, electrostatic complexation with cationic lipids or polymers and physical delivery using electroporation or ballistic particles to improve cellular uptake has been evaluated. This chapter highlights the rapid progress made in using nonviral delivery systems for RNA-based vaccines. Initial preclinical testing of self-amplifying mRNA vaccines has shown nonviral delivery to be capable of producing potent and robust innate and adaptive immune responses in small animals and nonhuman primates. Historically, the prospect of developing mRNA vaccines was uncertain due to concerns of mRNA instability and the feasibility of large-scale manufacturing. Today, these issues are no longer perceived as barriers in the widespread implementation of the technology. Currently, nonamplifying mRNA vaccines are under investigation in human clinical trials and can be produced at a sufficient quantity and quality to meet regulatory requirements. If the encouraging preclinical data with self-amplifying mRNA vaccines are matched by equivalently positive immunogenicity, potency, and tolerability in human trials, this platform could establish nucleic acid vaccines as a versatile new tool for human immunization. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparison of pre-processing methods for multiplex bead-based immunoassays.

Science.gov (United States)

Rausch, Tanja K; Schillert, Arne; Ziegler, Andreas; Lüking, Angelika; Zucht, Hans-Dieter; Schulz-Knappe, Peter

2016-08-11

High throughput protein expression studies can be performed using bead-based protein immunoassays, such as the Luminex® xMAP® technology. Technical variability is inherent to these experiments and may lead to systematic bias and reduced power. To reduce technical variability, data pre-processing is performed. However, no recommendations exist for the pre-processing of Luminex® xMAP® data. We compared 37 different data pre-processing combinations of transformation and normalization methods in 42 samples on 384 analytes obtained from a multiplex immunoassay based on the Luminex® xMAP® technology. We evaluated the performance of each pre-processing approach with 6 different performance criteria. Three performance criteria were plots. All plots were evaluated by 15 independent and blinded readers. Four different combinations of transformation and normalization methods performed well as pre-processing procedure for this bead-based protein immunoassay. The following combinations of transformation and normalization were suitable for pre-processing Luminex® xMAP® data in this study: weighted Box-Cox followed by quantile or robust spline normalization (rsn), asinh transformation followed by loess normalization and Box-Cox followed by rsn.

A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAAn Repeats Associated with Friedreich’s Ataxia

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Ryan J. McGinty

2017-09-01

Full Text Available Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich’s ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1 of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAAn repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach.

Determinants of functional coupling between astrocytes and respiratory neurons in the pre-Bötzinger complex.

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Christian Schnell

Full Text Available Respiratory neuronal network activity is thought to require efficient functioning of astrocytes. Here, we analyzed neuron-astrocyte communication in the pre-Bötzinger Complex (preBötC of rhythmic slice preparations from neonatal mice. In astrocytes that exhibited rhythmic potassium fluxes and glutamate transporter currents, we did not find a translation of respiratory neuronal activity into phase-locked astroglial calcium signals. In up to 20% of astrocytes, 2-photon calcium imaging revealed spontaneous calcium fluctuations, although with no correlation to neuronal activity. Calcium signals could be elicited in preBötC astrocytes by metabotropic glutamate receptor activation or after inhibition of glial glutamate uptake. In the latter case, astrocyte calcium elevation preceded a surge of respiratory neuron discharge activity followed by network failure. We conclude that astrocytes do not exhibit respiratory-rhythmic calcium fluctuations when they are able to prevent synaptic glutamate accumulation. Calcium signaling is, however, observed when glutamate transport processes in astrocytes are suppressed or neuronal discharge activity is excessive.

Human intronless genes: Functional groups, associated diseases, evolution, and mRNA processing in absence of splicing

International Nuclear Information System (INIS)

Grzybowska, Ewa A.

2012-01-01

Highlights: ► Functional characteristics of intronless genes (IGs). ► Diseases associated with IGs. ► Origin and evolution of IGs. ► mRNA processing without splicing. -- Abstract: Intronless genes (IGs) constitute approximately 3% of the human genome. Human IGs are essentially different in evolution and functionality from the IGs of unicellular eukaryotes, which represent the majority in their genomes. Functional analysis of IGs has revealed a massive over-representation of signal transduction genes and genes encoding regulatory proteins important for growth, proliferation, and development. IGs also often display tissue-specific expression, usually in the nervous system and testis. These characteristics translate into IG-associated diseases, mainly neuropathies, developmental disorders, and cancer. IGs represent recent additions to the genome, created mostly by retroposition of processed mRNAs with retained functionality. Processing, nuclear export, and translation of these mRNAs should be hampered dramatically by the lack of splice factors, which normally tightly cover mature transcripts and govern their fate. However, natural IGs manage to maintain satisfactory expression levels. Different mechanisms by which IGs solve the problem of mRNA processing and nuclear export are discussed here, along with their possible impact on reporter studies.

Matrin 3 binds and stabilizes mRNA.

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Maayan Salton

Full Text Available Matrin 3 (MATR3 is a highly conserved, inner nuclear matrix protein with two zinc finger domains and two RNA recognition motifs (RRM, whose function is largely unknown. Recently we found MATR3 to be phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Here, we show that MATR3 interacts in an RNA-dependent manner with several proteins with established roles in RNA processing, and maintains its interaction with RNA via its RRM2 domain. Deep sequencing of the bound RNA (RIP-seq identified several small noncoding RNA species. Using microarray analysis to explore MATR3's role in transcription, we identified 77 transcripts whose amounts depended on the presence of MATR3. We validated this finding with nine transcripts which were also bound to the MATR3 complex. Finally, we demonstrated the importance of MATR3 for maintaining the stability of several of these mRNA species and conclude that it has a role in mRNA stabilization. The data suggest that the cellular level of MATR3, known to be highly regulated, modulates the stability of a group of gene transcripts.

Clinical significance of LUNX mRNA, CK19 mRNA, CEA mRNA expression in detecting micrometastasis from lung cancer

International Nuclear Information System (INIS)

Zhu Guangying; Liu Delin; Chen Jie

2003-01-01

Objective: To evaluate the sensitivity, specificity and clinical significance of CK19 mRNA, CEA mRNA and LUNX mRNA for detecting micrometastasis by sampling the peripheral blood and regional lymph nodes of lung cancer patients. Methods: Reverse transcriptase chain reaction (RT-PCR) was used to detect LUNX mRNA, CK19 mRNA, CEA mRNA for micrometastasis by sampling the peripheral blood of 48 lung cancer patients and 44 regional lymph nodes of such patients treated by curative resection. Peripheral blood of 30 patients with pulmonary benign lesions and 10 normal healthy volunteers and lymph nodes of 6 patients with benign pulmonary diseases served as control. Results: 1) LUNX mRNA, CK19 mRNA, CEA mRNA were expressed in all (35/35) lung cancer tissues. 2) In the peripheral blood from 48 lung cancer patients, 30 (62.5%) were positive for LUNX mRNA, 24 (50.0%) positive for CK19 mRNA and 32(66.7%) positive for CEA mRNA. The positive detection rates of micrometastasis in 44 lymph nodes from lung cancer patients were 36.4% (16 out of 44) for LUNX mRNA, 27.3% (12 out of 44) for CK19 mRNA and 40.9% (18 out of 44) for CEA mRNA. 3) In the 30 blood samples from patients with pulmonary benign diseases, 2 (6.7%) expressed CK19 mRNA, but none expressed LUNX mRNA or CEA mRNA. All the 3 molecular markers were negative in the 10 blood samples from healthy volunteers. In 11 lymph nodes from patients with pulmonary benign lesions, none was positive for any of the three markers. 4) In 44 regional lymph nodes from lung cancer patients, 6 (13.6%) were positive for metastasis by histopathological examination, with a positive rate significantly lower than that of the RT-PCR (P<0.05). 5) The micrometastatic positive rate in the peripheral blood of 40 non-small cell lung cancer (NSCLC) patients was significantly related to TNM stage (P=0.01). Conclusions: LUNX mRNA, CK19 MRNA, CEA mRNA are all appropriate target genes for the detection of micrometastasis from lung cancer. LUNX mRNA and CEA mRNA

Performance of Pre-processing Schemes with Imperfect Channel State Information

DEFF Research Database (Denmark)

Christensen, Søren Skovgaard; Kyritsi, Persa; De Carvalho, Elisabeth

2006-01-01

Pre-processing techniques have several benefits when the CSI is perfect. In this work we investigate three linear pre-processing filters, assuming imperfect CSI caused by noise degradation and channel temporal variation. Results indicate, that the LMMSE filter achieves the lowest BER and the high......Pre-processing techniques have several benefits when the CSI is perfect. In this work we investigate three linear pre-processing filters, assuming imperfect CSI caused by noise degradation and channel temporal variation. Results indicate, that the LMMSE filter achieves the lowest BER...... and the highest SINR when the CSI is perfect, whereas the simple matched filter may be a good choice when the CSI is imperfect. Additionally the results give insight into the inherent trade-off between robustness against CSI imperfections and spatial focusing ability....

Evidence for functional pre-coupled complexes of receptor heteromers and adenylyl cyclase.

Science.gov (United States)

Navarro, Gemma; Cordomí, Arnau; Casadó-Anguera, Verónica; Moreno, Estefanía; Cai, Ning-Sheng; Cortés, Antoni; Canela, Enric I; Dessauer, Carmen W; Casadó, Vicent; Pardo, Leonardo; Lluís, Carme; Ferré, Sergi

2018-03-28

G protein-coupled receptors (GPCRs), G proteins and adenylyl cyclase (AC) comprise one of the most studied transmembrane cell signaling pathways. However, it is unknown whether the ligand-dependent interactions between these signaling molecules are based on random collisions or the rearrangement of pre-coupled elements in a macromolecular complex. Furthermore, it remains controversial whether a GPCR homodimer coupled to a single heterotrimeric G protein constitutes a common functional unit. Using a peptide-based approach, we here report evidence for the existence of functional pre-coupled complexes of heteromers of adenosine A 2A receptor and dopamine D 2 receptor homodimers coupled to their cognate Gs and Gi proteins and to subtype 5 AC. We also demonstrate that this macromolecular complex provides the necessary frame for the canonical Gs-Gi interactions at the AC level, sustaining the ability of a Gi-coupled GPCR to counteract AC activation mediated by a Gs-coupled GPCR.

Exogenous mRNA encoding tetanus or botulinum neurotoxins expressed in Aplysia neurons

NARCIS (Netherlands)

Mochida, Sumiko; Poulain, Bernard; Eisel, Ulrich; Binz, Thomas; Kurazono, Hisao; Niemann, Heiner; Tauc, Ladislav; Bullock, Theodore H.

1990-01-01

Injection of exogenous mRNA purified from various tissue preparations into cellular translation systems such as Xenopus oocytes has allowed expression of complex proteins (e.g., receptors for neurotransmitters). No evidence for expression of injected exogenous mRNA, however, has been reported in

Process for calcium xylonate production as a concrete admixture derived from in-situ fermentation of wheat straw pre-hydrolysate.

Science.gov (United States)

Zhou, Xin; Zhou, Xuelian; Tang, Xiusheng; Xu, Yong

2018-08-01

One of the major obstacles in process of lignocellulosic biorefinery is the utilization of pre-hydrolysate from pre-treatment. Although lignocellulosic pre-hydrolysate can serve as an economic starting material for xylonic acid production, the advancement of xylonic acid or xylonate is still limited by further commercial value or applications. In the present study, xylose in the high concentration wheat straw pre-hydrolysate was first in-situ biooxidized to xylonate by Gluconobacter oxydans. To meet the needs of commercialization, crude powdered calcium xylonate was prepared by drying process and calcium xylonate content in the prepared crude product was more than 70%. Then, the calcium xylonate product was evaluated as concrete admixture without any complex purification steps and the results demonstrated that xylonate could improve the performance of concrete. Overall, the crude xylonate product directly produced from low-cost wheat straw pre-hydrolysate can potentially be developed as retarding reducer, which could subsequently benefit lignocellulosic biorefinery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Enhancing Elementary Pre-service Teachers' Plant Processes Conceptions

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Thompson, Stephen L.; Lotter, Christine; Fann, Xumei; Taylor, Laurie

2016-06-01

Researchers examined how an inquiry-based instructional treatment emphasizing interrelated plant processes influenced 210 elementary pre-service teachers' (PTs) conceptions of three plant processes, photosynthesis, cellular respiration, and transpiration, and the interrelated nature of these processes. The instructional treatment required PTs to predict the fate of a healthy plant in a sealed terrarium (Plant-in-a-Jar), justify their predictions, observe the plant over a 5-week period, and complete guided inquiry activities centered on one of the targeted plant processes each week. Data sources included PTs' pre- and post-predictions with accompanying justifications, course artifacts such as weekly terrarium observations and science journal entries, and group models of the interrelated plant processes occurring within the sealed terraria. A subset of 33 volunteer PTs also completed interviews the week the Plant-in-a-Jar scenario was introduced and approximately 4 months after the instructional intervention ended. Pre- and post-predictions from all PTs as well as interview responses from the subgroup of PTs, were coded into categories based on key plant processes emphasized in the Next Generation Science Standards. Study findings revealed that PTs developed more accurate conceptions of plant processes and their interrelated nature as a result of the instructional intervention. Primary patterns of change in PTs' plant process conceptions included development of more accurate conceptions of how water is used by plants, more accurate conceptions of photosynthesis features, and more accurate conceptions of photosynthesis and cellular respiration as transformative processes.

Developmentally regulated expression and complex processing of barley pri-microRNAs

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Kruszka Katarzyna

2013-01-01

Full Text Available Abstract Background MicroRNAs (miRNAs regulate gene expression via mRNA cleavage or translation inhibition. In spite of barley being a cereal of great economic importance, very little data is available concerning its miRNA biogenesis. There are 69 barley miRNA and 67 pre-miRNA sequences available in the miRBase (release 19. However, no barley pri-miRNA and MIR gene structures have been shown experimentally. In the present paper, we examine the biogenesis of selected barley miRNAs and the developmental regulation of their pri-miRNA processing to learn more about miRNA maturation in barely. Results To investigate the organization of barley microRNA genes, nine microRNAs - 156g, 159b, 166n, 168a-5p/168a-3p, 171e, 397b-3p, 1120, and 1126 - were selected. Two of the studied miRNAs originate from one MIR168a-5p/168a-3p gene. The presence of all miRNAs was confirmed using a Northern blot approach. The miRNAs are encoded by genes with diverse organizations, representing mostly independent transcription units with or without introns. The intron-containing miRNA transcripts undergo complex splicing events to generate various spliced isoforms. We identified miRNAs that were encoded within introns of the noncoding genes MIR156g and MIR1126. Interestingly, the intron that encodes miR156g is spliced less efficiently than the intron encoding miR1126 from their specific precursors. miR397b-3p was detected in barley as a most probable functional miRNA, in contrast to rice where it has been identified as a complementary partner miRNA*. In the case of miR168a-5p/168a-3p, we found the generation of stable, mature molecules from both pre-miRNA arms, confirming evolutionary conservation of the stability of both species, as shown in rice and maize. We suggest that miR1120, located within the 3′ UTR of a protein-coding gene and described as a functional miRNA in wheat, may represent a siRNA generated from a mariner-like transposable element. Conclusions Seven of the

NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing.

Science.gov (United States)

Yoshikatsu, Yuki; Ishida, Yo-ichi; Sudo, Haruka; Yuasa, Keizo; Tsuji, Akihiko; Nagahama, Masami

2015-08-28

Nuclear VCP-like 2 (NVL2) is a member of the chaperone-like AAA-ATPase family and is involved in the biosynthesis of 60S ribosomal subunits in mammalian cells. We previously showed the interaction of NVL2 with a DExD/H-box RNA helicase MTR4/DOB1, which is a known cofactor for an exoribonuclease complex, the exosome. This finding implicated NVL2 in RNA metabolic processes during ribosome biogenesis. In the present study, we found that a series of mutations within the ATPase domain of NVL2 causes a defect in pre-rRNA processing into mature 28S and 5.8S rRNAs. Co-immunoprecipitation analysis showed that NVL2 was associated with the nuclear exosome complex, which includes RRP6 as a nucleus-specific catalytic subunit. This interaction was prevented by depleting either MTR4 or RRP6, indicating their essential role in mediating this interaction with NVL2. Additionally, knockdown of MPP6, another cofactor for the nuclear exosome, also prevented the interaction by causing MTR4 to dissociate from the nuclear exosome. These results suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex. Copyright © 2015 Elsevier Inc. All rights reserved.

Industrial complex for solid radwaste management (ICSRM) at Chernobyl nuclear power plant pre-commissioning of the facilities

Energy Technology Data Exchange (ETDEWEB)

Pietsch, Thomas [NUKEM Technologies GmbH, Alzenau (Germany); NUKEM Technologies GmbH, Slavutich (Ukraine)

2009-07-01

NUKEM was awarded to build the industrial complex for solid radwaste management (ICSRM) at the NPP Chernobyl. ICSRM consists of four facilities: SLWS (solid low waste storage), solid waste retrieval facility, solid waste processing plant, repository for the disposal of short-lived waste. The contribution describes the approach for testing and pre-commissioning the following systems: sorting, compaction, incineration, transport systems, monitoring, tracking and retrieval. Start-up of the facilities is planned for 2009.

Industrial complex for solid radwaste management (ICSRM) at Chernobyl nuclear power plant pre-commissioning of the facilities

International Nuclear Information System (INIS)

Pietsch, Thomas

2009-01-01

NUKEM was awarded to build the industrial complex for solid radwaste management (ICSRM) at the NPP Chernobyl. ICSRM consists of four facilities: SLWS (solid low waste storage), solid waste retrieval facility, solid waste processing plant, repository for the disposal of short-lived waste. The contribution describes the approach for testing and pre-commissioning the following systems: sorting, compaction, incineration, transport systems, monitoring, tracking and retrieval. Start-up of the facilities is planned for 2009.

Logics of pre-merger decision-making processes: the case of Karolinska University Hospital.

Science.gov (United States)

Choi, Soki; Brommels, Mats

2009-01-01

The purpose of this paper is to examine how and why a decision to merge two university hospitals in a public context might occur by using an in-depth case study of the pre-merger process of Karolinska University Hospital. Based on extensive document analysis and 35 key informant interviews the paper reconstructed the pre-merger process, searched for empirical patterns, and interpreted those by applying neo-institutional theory. Spanning nearly a decade, the pre-merger process goes from idea generation through transition to decision, and took place on two arenas, political, and scientific. Both research excellence and economic efficiency are stated merger motives. By applying a neo-institutional perspective, the paper finds that the two initial phases are driven by decision rationality, which is typical for political organizations and that the final phase demonstrated action rationality, which is typical for private firms. Critical factors behind this radical change of decision logic are means convergence, uniting key stakeholder groups, and an economic and political crisis, triggering critical incidents, which ultimately legitimized the formal decision. It is evident from the paper that merger decisions in the public sector might not necessarily result from stated and/or economic drivers only. This paper suggests that a change of decision logic from decision to action rationality might promote effective decision making on large and complex issues in a public context. This is the first systematic in-depth study of a university hospital merger employing a decision-making perspective.

Enhancing Elementary Pre-Service Teachers' Plant Processes Conceptions

Science.gov (United States)

Thompson, Stephen L.; Lotter, Christine; Fann, Xumei; Taylor, Laurie

2016-01-01

Researchers examined how an inquiry-based instructional treatment emphasizing interrelated plant processes influenced 210 elementary pre-service teachers' (PTs) conceptions of three plant processes, photosynthesis, cellular respiration, and transpiration, and the interrelated nature of these processes. The instructional treatment required PTs to…

An investigation of nutrient-dependent mRNA translation in Drosophila larvae

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Sabarish Nagarajan

2014-10-01

Full Text Available The larval period of the Drosophila life cycle is characterized by immense growth. In nutrient rich conditions, larvae increase in mass approximately two hundred-fold in five days. However, upon nutrient deprivation, growth is arrested. The prevailing view is that dietary amino acids drive this larval growth by activating the conserved insulin/PI3 kinase and Target of rapamycin (TOR pathways and promoting anabolic metabolism. One key anabolic process is protein synthesis. However, few studies have attempted to measure mRNA translation during larval development or examine the signaling requirements for nutrient-dependent regulation. Our work addresses this issue. Using polysome analyses, we observed that starvation rapidly (within thirty minutes decreased larval mRNA translation, with a maximal decrease at 6–18 hours. By analyzing individual genes, we observed that nutrient-deprivation led to a general reduction in mRNA translation, regardless of any starvation-mediated changes (increase or decrease in total transcript levels. Although sugars and amino acids are key regulators of translation in animal cells and are the major macronutrients in the larval diet, we found that they alone were not sufficient to maintain mRNA translation in larvae. The insulin/PI3 kinase and TOR pathways are widely proposed as the main link between nutrients and mRNA translation in animal cells. However, we found that genetic activation of PI3K and TOR signaling, or regulation of two effectors – 4EBP and S6K – could not prevent the starvation-mediated translation inhibition. Similarly, we showed that the nutrient stress-activated eIF2α kinases, GCN2 and PERK, were not required for starvation-induced inhibition of translation in larvae. These findings indicate that nutrient control of mRNA translation in larvae is more complex than simply amino acid activation of insulin and TOR signaling.

Examination of Speed Contribution of Parallelization for Several Fingerprint Pre-Processing Algorithms

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GORGUNOGLU, S.

2014-05-01

Full Text Available In analysis of minutiae based fingerprint systems, fingerprints needs to be pre-processed. The pre-processing is carried out to enhance the quality of the fingerprint and to obtain more accurate minutiae points. Reducing the pre-processing time is important for identification and verification in real time systems and especially for databases holding large fingerprints information. Parallel processing and parallel CPU computing can be considered as distribution of processes over multi core processor. This is done by using parallel programming techniques. Reducing the execution time is the main objective in parallel processing. In this study, pre-processing of minutiae based fingerprint system is implemented by parallel processing on multi core computers using OpenMP and on graphics processor using CUDA to improve execution time. The execution times and speedup ratios are compared with the one that of single core processor. The results show that by using parallel processing, execution time is substantially improved. The improvement ratios obtained for different pre-processing algorithms allowed us to make suggestions on the more suitable approaches for parallelization.

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

Science.gov (United States)

Zur, Hadas; Tuller, Tamir

2016-01-01

mRNA translation is the fundamental process of decoding the information encoded in mRNA molecules by the ribosome for the synthesis of proteins. The centrality of this process in various biomedical disciplines such as cell biology, evolution and biotechnology, encouraged the development of dozens of mathematical and computational models of translation in recent years. These models aimed at capturing various biophysical aspects of the process. The objective of this review is to survey these models, focusing on those based and/or validated on real large-scale genomic data. We consider aspects such as the complexity of the models, the biophysical aspects they regard and the predictions they may provide. Furthermore, we survey the central systems biology discoveries reported on their basis. This review demonstrates the fundamental advantages of employing computational biophysical translation models in general, and discusses the relative advantages of the different approaches and the challenges in the field. PMID:27591251

Cup regulates oskar mRNA stability during oogenesis.

Science.gov (United States)

Broyer, Risa M; Monfort, Elena; Wilhelm, James E

2017-01-01

The proper regulation of the localization, translation, and stability of maternally deposited transcripts is essential for embryonic development in many organisms. These different forms of regulation are mediated by the various protein subunits of the ribonucleoprotein (RNP) complexes that assemble on maternal mRNAs. However, while many of the subunits that regulate the localization and translation of maternal transcripts have been identified, relatively little is known about how maternal mRNAs are stockpiled and stored in a stable form to support early development. One of the best characterized regulators of maternal transcripts is Cup - a broadly conserved component of the maternal RNP complex that in Drosophila acts as a translational repressor of the localized message oskar. In this study, we have found that loss of cup disrupts the localization of both the oskar mRNA and its associated proteins to the posterior pole of the developing oocyte. This defect is not due to a failure to specify the oocyte or to disruption of RNP transport. Rather, the localization defects are due to a drop in oskar mRNA levels in cup mutant egg chambers. Thus, in addition to its role in regulating oskar mRNA translation, Cup also plays a critical role in controlling the stability of the oskar transcript. This suggests that Cup is ideally positioned to coordinate the translational control function of the maternal RNP complex with its role in storing maternal transcripts in a stable form. Published by Elsevier Inc.

Digital soil mapping: strategy for data pre-processing

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Alexandre ten Caten

2012-08-01

Full Text Available The region of greatest variability on soil maps is along the edge of their polygons, causing disagreement among pedologists about the appropriate description of soil classes at these locations. The objective of this work was to propose a strategy for data pre-processing applied to digital soil mapping (DSM. Soil polygons on a training map were shrunk by 100 and 160 m. This strategy prevented the use of covariates located near the edge of the soil classes for the Decision Tree (DT models. Three DT models derived from eight predictive covariates, related to relief and organism factors sampled on the original polygons of a soil map and on polygons shrunk by 100 and 160 m were used to predict soil classes. The DT model derived from observations 160 m away from the edge of the polygons on the original map is less complex and has a better predictive performance.

CCS mRNA transcripts and serum CCS protein as copper marker in adults suffering inflammatory processes.

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Araya, Magdalena; Gutiérrez, Ricardo; Arredondo, Miguel

2014-08-01

The chaperone to Zn-Cu superoxide dismutase (CCS) has been postulated as a candidate copper indicator, changing in a consistent manner in induced and recovered copper deficiency, in experimental cell and animal models. In real life people have various conditions that may modify molecules acting as acute phase proteins, such as serum ceruloplasmin and copper concentration and could alter CCS responses. With the hypothesis that CCS mRNA transcripts and protein would be different in individuals suffering inflammatory processes in comparison to healthy individuals, we assessed adult individuals who, although not ill had conditions known to induce variable degrees of inflammation. Screening of 600 adults resulted in two study groups, formed on the basis of their clinical history and levels of serum C reactive protein (CRP): Group 1 (n = 61, mean (range) CRP = 0.9 (0.3-2.0 mg/dL) and Group 2 (n = 150, mean (range) CRP = 6.1 (4.3-8.7 mg/dL). Results showed that mRNA transcripts relative abundance was not different for CCS, MTIIA, TNF-alpha and Cu-Zn-SOD by group (p > 0.05, one way Anova), nor between sexes (p > 0.05, one way Anova). Distribution of CCS mRNA transcripts and CCS protein in serum did not show any differences or trends. Results disproved our hypothesis that CCS abundance of transcripts and CCS protein would be different in individuals suffering inflammatory processes, adding further support to the idea that CCS may be a copper marker.

Myb-binding protein 1a (Mybbp1a) regulates levels and processing of pre-ribosomal RNA.

Science.gov (United States)

Hochstatter, Julia; Hölzel, Michael; Rohrmoser, Michaela; Schermelleh, Lothar; Leonhardt, Heinrich; Keough, Rebecca; Gonda, Thomas J; Imhof, Axel; Eick, Dirk; Längst, Gernot; Németh, Attila

2012-07-13

Ribosomal RNA gene transcription, co-transcriptional processing, and ribosome biogenesis are highly coordinated processes that are tightly regulated during cell growth. In this study we discovered that Mybbp1a is associated with both the RNA polymerase I complex and the ribosome biogenesis machinery. Using a reporter assay that uncouples transcription and RNA processing, we show that Mybbp1a represses rRNA gene transcription. In addition, overexpression of the protein reduces RNA polymerase I loading on endogenous rRNA genes as revealed by chromatin immunoprecipitation experiments. Accordingly, depletion of Mybbp1a results in an accumulation of the rRNA precursor in vivo but surprisingly also causes growth arrest of the cells. This effect can be explained by the observation that the modulation of Mybbp1a protein levels results in defects in pre-rRNA processing within the cell. Therefore, the protein may play a dual role in the rRNA metabolism, potentially linking and coordinating ribosomal DNA transcription and pre-rRNA processing to allow for the efficient synthesis of ribosomes.

Pre-Service Teachers' Perceptions with Regard to Teaching-Learning Processes

Science.gov (United States)

Özdas, Faysal

2018-01-01

Teaching-learning process has a great important medium where pre-service teachers develop experiences and competences. Pre-service teachers are introduced to this process in a professional sense through the school experience course in teacher training. In this process, it is crucial to identify the encountered difficulties and matters. For this…

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Science.gov (United States)

Robinson, Philip J; Trnka, Michael J; Bushnell, David A; Davis, Ralph E; Mattei, Pierre-Jean; Burlingame, Alma L; Kornberg, Roger D

2016-09-08

A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

American Elementary Education Pre-Service Teachers' Attitudes towards Biotechnology Processes

Science.gov (United States)

Chabalengula, Vivien Mweene; Mumba, Frackson; Chitiyo, Jonathan

2011-01-01

This study examined elementary education pre-service teachers' attitudes towards biotechnology processes. A sample comprised 88 elementary education pre-service teachers at a mid-sized university in the Midwest of the USA. Sixty and 28 of these pre-service teachers were enrolled in Introductory Science Methods course and Advance Science Methods…

mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway.

Science.gov (United States)

Ávila, Andréa Rodrigues; Cabezas-Cruz, Alexjandro; Gissot, Mathieu

2018-01-25

Control of gene expression is crucial for parasite survival and is the result of a series of processes that are regulated to permit fine-tuning of gene expression in response to biological changes during the life-cycle of apicomplexan parasites. Control of mRNA nuclear export is a key process in eukaryotic cells but is poorly understood in apicomplexan parasites. Here, we review recent knowledge regarding this process with an emphasis on T. gondii. We describe the presence of divergent orthologs and discuss structural and functional differences in export factors between apicomplexans and other eukaryotic lineages. Undoubtedly, the use of the CRISPR/Cas9 system in high throughput screenings associated with the discovery of mRNA nuclear export complexes by proteomic analysis will contribute to identify these divergent factors. Ligand-based or structure-based strategies may be applied to investigate the potential use of these proteins as targets for new antiprotozoal agents.

Dissociation of SERPINE1 mRNA from the translational repressor proteins Ago2 and TIA-1 upon platelet activation.

Science.gov (United States)

Corduan, Aurélie; Plé, Hélène; Laffont, Benoit; Wallon, Thérèse; Plante, Isabelle; Landry, Patricia; Provost, Patrick

2015-05-01

Platelets play an important role in haemostasis, as well as in thrombosis and coagulation processes. They harbour a wide variety of messenger RNAs (mRNAs), that can template de novo protein synthesis, and an abundant array of microRNAs, which are known to mediate mRNA translational repression through proteins of the Argonaute (Ago) family. The relationship between platelet microRNAs and proteins capable of mediating translational repression, however, remains unclear. Here, we report that half of platelet microRNAs is associated to mRNA-regulatory Ago2 protein complexes, in various proportions. Associated to these Ago2 complexes are platelet mRNAs known to support de novo protein synthesis. Reporter gene activity assays confirmed the capacity of the platelet microRNAs, found to be associated to Ago2 complexes, to regulate translation of these platelet mRNAs through their 3'UTR. Neither the microRNA repertoire nor the microRNA composition of Ago2 complexes of human platelets changed upon activation with thrombin. However, under conditions favoring de novo synthesis of Plasminogen Activator Inhibitor-1 (PAI-1) protein, we documented a rapid dissociation of the encoding platelet SERPINE1 mRNA from Ago2 protein complexes as well as from the translational repressor protein T-cell-restricted intracellular antigen-1 (TIA-1). These findings are consistent with a scenario by which lifting of the repressive effects of Ago2 and TIA-1 protein complexes, involving a rearrangement of proteinmRNA complexes rather than disassembly of Ago2microRNA complexes, would allow translation of SERPINE1 mRNA into PAI-1 in response to platelet activation.

A combined acidification/PEO flocculation process to improve the lignin removal from the pre-hydrolysis liquor of kraft-based dissolving pulp production process.

Science.gov (United States)

Shi, Haiqiang; Fatehi, Pedram; Xiao, Huining; Ni, Yonghao

2011-04-01

The presence of lignin impairs the utilization of the hemicelluloses dissolved in the pre-hydrolysis liquor (PHL) of the kraft-based dissolving pulp production process. In this paper, a novel process was developed by combining the acidification and poly ethylene oxide (PEO) flocculation concepts to improve the lignin removal. The results showed that the lignin removal was improved by the addition of PEO to the acidified PHL, particularly at a low pH of 1.5. The main mechanisms involved are the lignin/PEO complex formation and the bridging of the formed complexes. This hypothesis was supported by the turbidity, FTIR and particle size measurements. Interestingly, the hemicelluloses removal from the acidification/PEO flocculation was marginal, which would be beneficial for the down-stream ethanol production from the PHL. Additionally, a process flow diagram was proposed that incorporates this new concept into the existing configuration of kraft-based dissolving pulp production process. Copyright © 2011 Elsevier Ltd. All rights reserved.

Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae.

Science.gov (United States)

Uthe, Henriette; Vanselow, Jens T; Schlosser, Andreas

2017-02-27

Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15 N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis.

Pre-processing of input files for the AZTRAN code

International Nuclear Information System (INIS)

Vargas E, S.; Ibarra, G.

2017-09-01

The AZTRAN code began to be developed in the Nuclear Engineering Department of the Escuela Superior de Fisica y Matematicas (ESFM) of the Instituto Politecnico Nacional (IPN) with the purpose of numerically solving various models arising from the physics and engineering of nuclear reactors. The code is still under development and is part of the AZTLAN platform: Development of a Mexican platform for the analysis and design of nuclear reactors. Due to the complexity to generate an input file for the code, a script based on D language is developed, with the purpose of making its elaboration easier, based on a new input file format which includes specific cards, which have been divided into two blocks, mandatory cards and optional cards, including a pre-processing of the input file to identify possible errors within it, as well as an image generator for the specific problem based on the python interpreter. (Author)

The recursive combination filter approach of pre-processing for the estimation of standard deviation of RR series.

Science.gov (United States)

Mishra, Alok; Swati, D

2015-09-01

Variation in the interval between the R-R peaks of the electrocardiogram represents the modulation of the cardiac oscillations by the autonomic nervous system. This variation is contaminated by anomalous signals called ectopic beats, artefacts or noise which mask the true behaviour of heart rate variability. In this paper, we have proposed a combination filter of recursive impulse rejection filter and recursive 20% filter, with recursive application and preference of replacement over removal of abnormal beats to improve the pre-processing of the inter-beat intervals. We have tested this novel recursive combinational method with median method replacement to estimate the standard deviation of normal to normal (SDNN) beat intervals of congestive heart failure (CHF) and normal sinus rhythm subjects. This work discusses the improvement in pre-processing over single use of impulse rejection filter and removal of abnormal beats for heart rate variability for the estimation of SDNN and Poncaré plot descriptors (SD1, SD2, and SD1/SD2) in detail. We have found the 22 ms value of SDNN and 36 ms value of SD2 descriptor of Poincaré plot as clinical indicators in discriminating the normal cases from CHF cases. The pre-processing is also useful in calculation of Lyapunov exponent which is a nonlinear index as Lyapunov exponents calculated after proposed pre-processing modified in a way that it start following the notion of less complex behaviour of diseased states.

Effect of packaging on physicochemical characteristics of irradiated pre-processed chicken

International Nuclear Information System (INIS)

Jiang Xiujie; Zhang Dongjie; Zhang Dequan; Li Shurong; Gao Meixu; Wang Zhidong

2011-01-01

To explore the effect of modified atmosphere packaging and antioxidants on the physicochemical characteristics of irradiated pre-processed chicken, the pre-processed chicken was added antioxidants first, and then packaged in common, vacuum and gas respectively, and finally irradiated at 5 kGy dosage. All samples was stored at 4 ℃. The pH, TBA, TVB-N and color deviation were evaluated after 0, 3, 7, 10, 14, 18 and 21 d of storage. The results showed that pH value of pre-processed chicken with antioxidants and vacuum packaged increased with the storage time but not significantly among different treatments. The TBA value was also increased but not significantly (P > 0.05), which indicated that vacuum package inhibited the lipid oxidation. TVB-N value increased with storage time, TVB-N value of vacuum package samples reached 14.29 mg/100 g at 21 d storage, which did not exceeded the reference indexes of fresh meat. a * value of the pre-processed chicken of vacuum package and non-oxygen package samples increased significantly during storage (P > 0.05), and chicken color kept bright red after 21 d storage with vacuum package It is concluded that vacuum packaging of irradiated pre-processed chicken is effective on ensuring its physical and chemical properties during storage. (authors)

Optimization of Pre-Treatment Process Parameters to Generate Biodiesel from Microalga

Directory of Open Access Journals (Sweden)

Chukwuma Onumaegbu

2018-03-01

Full Text Available Cell disruption is an integral part of microalga production process, which improves the release of intracellular products that are essential for biofuel production. In this work, pre-treatment parameters that will enhance the efficiency of lipid production using high-pressure homogenizer on microalgae biomass will be investigated. The high-pressure homogenizer that is considered is a GYB40-10S/GY60-6S; with a pre-treatment pressure of 1000 psi, 2000 psi, and 3000 psi, the number of passes; 1, 2, and 3, a reaction time of 3, 3.5, and 4 h. Pressure and cavitation increase the efficiency of the pre-treatment process of the homogenizer. In addition, homogenization shear force and pressure are the basic significant factors that enhance the efficiency of microalgae cell rupture. Also, the use of modelling to simulate pre-treatment processes (Response Surface Methodology (RSM, Box-Behnken Designs (BBD, and design of experiment (DOE for process optimization will be adopted in this study. The results clearly demonstrate that high-pressure homogenization pre-treatment can effectively disrupt microalga cell walls to enhance lipid recovery efficiency, with a relatively short extraction time, both that are essential for maintaining a good quality of lipids for biofuel production. A maximum of 18% lipid yields were obtained after 3 h of HPH pre-treatment at 3000 psi.

Comparing Binaural Pre-processing Strategies II

Directory of Open Access Journals (Sweden)

Regina M. Baumgärtel

2015-12-01

Full Text Available Several binaural audio signal enhancement algorithms were evaluated with respect to their potential to improve speech intelligibility in noise for users of bilateral cochlear implants (CIs. 50% speech reception thresholds (SRT50 were assessed using an adaptive procedure in three distinct, realistic noise scenarios. All scenarios were highly nonstationary, complex, and included a significant amount of reverberation. Other aspects, such as the perfectly frontal target position, were idealized laboratory settings, allowing the algorithms to perform better than in corresponding real-world conditions. Eight bilaterally implanted CI users, wearing devices from three manufacturers, participated in the study. In all noise conditions, a substantial improvement in SRT50 compared to the unprocessed signal was observed for most of the algorithms tested, with the largest improvements generally provided by binaural minimum variance distortionless response (MVDR beamforming algorithms. The largest overall improvement in speech intelligibility was achieved by an adaptive binaural MVDR in a spatially separated, single competing talker noise scenario. A no-pre-processing condition and adaptive differential microphones without a binaural link served as the two baseline conditions. SRT50 improvements provided by the binaural MVDR beamformers surpassed the performance of the adaptive differential microphones in most cases. Speech intelligibility improvements predicted by instrumental measures were shown to account for some but not all aspects of the perceptually obtained SRT50 improvements measured in bilaterally implanted CI users.

Organotypic slice cultures containing the preBötzinger complex generate respiratory-like rhythms

DEFF Research Database (Denmark)

Phillips, Wiktor S; Herly, Mikkel; Del Negro, Christopher A

2016-01-01

containing the preBötzinger complex (preBötC), the core inspiratory rhythm generator of the ventrolateral brainstem. We measured bilateral synchronous network oscillations, using calcium-sensitive fluorescent dyes, in both ventrolateral (presumably the preBötC) and dorsomedial regions of 7-43 days in vitro......Acute brainstem slice preparations in vitro have advanced understanding of the cellular and synaptic mechanisms of respiratory rhythm generation, but their inherent limitations preclude long-term manipulation and recording experiments. Here, we developed an organotypic slice culture preparation...... of the brainstem displayed up to 193% faster burst frequency (22.4 ± 8.3 bursts/min) and higher signal amplitude (340%) compared to acute slices. We conclude that preBötC-containing slice cultures retain inspiratory-like rhythmic function and therefore may facilitate lines of experimentation that involve extended...

Pre-processing for Triangulation of Probabilistic Networks

NARCIS (Netherlands)

Bodlaender, H.L.; Koster, A.M.C.A.; Eijkhof, F. van den; Gaag, L.C. van der

2001-01-01

The currently most efficient algorithm for inference with a probabilistic network builds upon a triangulation of a networks graph. In this paper, we show that pre-processing can help in finding good triangulations for probabilistic networks, that is, triangulations with a minimal maximum

Efficient mRNA delivery with graphene oxide-polyethylenimine for generation of footprint-free human induced pluripotent stem cells.

Science.gov (United States)

Choi, Hye Yeon; Lee, Tae-Jin; Yang, Gwang-Mo; Oh, Jaesur; Won, Jihye; Han, Jihae; Jeong, Gun-Jae; Kim, Jongpil; Kim, Jin-Hoi; Kim, Byung-Soo; Cho, Ssang-Goo

2016-08-10

Clinical applications of induced pluripotent stem cells (iPSCs) require development of technologies for the production of "footprint-free" (gene integration-free) iPSCs, which avoid the potential risk of insertional mutagenesis in humans. Previously, several studies have shown that mRNA transfer can generate "footprint-free" iPSCs, but these studies did not use a delivery vehicle and thus repetitive daily transfection was required because of mRNA degradation. Here, we report an mRNA delivery system employing graphene oxide (GO)-polyethylenimine (PEI) complexes for the efficient generation of "footprint-free" iPSCs. GO-PEI complexes were found to be very effective for loading mRNA of reprogramming transcription factors and protection from mRNA degradation by RNase. Dynamic suspension cultures of GO-PEI/RNA complexes-treated cells dramatically increased the reprogramming efficiency and successfully generated rat and human iPSCs from adult adipose tissue-derived fibroblasts without repetitive daily transfection. The iPSCs showed all the hallmarks of pluripotent stem cells including expression of pluripotency genes, epigenetic reprogramming, and differentiation into the three germ layers. These results demonstrate that mRNA delivery using GO-PEI-RNA complexes can efficiently generate "footprint-free" iPSCs, which may advance the translation of iPSC technology into the clinical settings. Copyright © 2016. Published by Elsevier B.V.

Time-course of 5-HT(6) receptor mRNA expression during memory consolidation and amnesia.

Science.gov (United States)

Huerta-Rivas, A; Pérez-García, G; González-Espinosa, C; Meneses, A

2010-01-01

Growing evidence indicates that antagonists of the 5-hydroxytryptamine (serotonin) receptor(6) (5-HT(6)) improve memory and reverse amnesia although the mechanisms involved are poorly understood. Hence, in this paper RT-PCR was used to evaluate changes in mRNA expression of 5-HT(6) receptor in trained and untrained rats treated with the 5-HT(6) receptor antagonist SB-399885 and amnesic drugs scopolamine or dizocilpine. Changes in mRNA expression of 5-HT(6) receptor were investigated at different times in prefrontal cortex, hippocampus and striatum. Data indicated that memory in the Pavlovian/instrumental autoshaping task was a progressive process associated to reduced mRNA expression of 5-HT(6) receptor in the three structures examined. SB-399885 improved long-term memory at 48h, while the muscarinic receptor antagonist scopolamine or the non-competitive NMDA receptor antagonist dizocilpine impaired it at 24h. Autoshaping training and treatment with SB-399885 increased 5-HT(6) receptor mRNA expression in (maximum increase) prefrontal cortex and striatum, 24 or 48h. The scopolamine-induced amnesia suppressed 5-HT(6) receptor mRNA expression while the dizocilpine-induced amnesia did not modify 5-HT(6) receptor mRNA expression. SB-399885 and scopolamine or dizocilpine were able to reestablish memory and 5-HT(6) receptor mRNA expression. These data confirmed previous memory evidence and of more interest is the observation that training, SB-399885 and amnesic drugs modulated 5-HT(6) receptor mRNA expression in prefrontal cortex, hippocampus and striatum. Further investigation in different memory tasks, times and amnesia models together with more complex control groups might provide further clues. Copyright 2009 Elsevier Inc. All rights reserved.

The Effects of Pre-Task Planning and On-line Planning on Fluency, Complexity, and Accuracy in L2 Monologic Oral Production.

Science.gov (United States)

Yuan, Fangyuan; Ellis, Rod

2003-01-01

Investigated the effects of both pre-task and on-line planning on second language (L2) oral production. Results show that pre-task planning enhances grammatical complexity while on-line planning positively influences accuracy and grammatical complexity. Pre-task planners also produced more fluent and lexically varied language than the on-line…

HIV-1 matrix dependent membrane targeting is regulated by Gag mRNA trafficking.

Directory of Open Access Journals (Sweden)

Jing Jin

Full Text Available Retroviral Gag polyproteins are necessary and sufficient for virus budding. Productive HIV-1 Gag assembly takes place at the plasma membrane. However, little is known about the mechanisms by which thousands of Gag molecules are targeted to the plasma membrane. Using a bimolecular fluorescence complementation (BiFC assay, we recently reported that the cellular sites and efficiency of HIV-1 Gag assembly depend on the precise pathway of Gag mRNA export from the nucleus, known to be mediated by Rev. Here we describe an assembly deficiency in human cells for HIV Gag whose expression depends on hepatitis B virus (HBV post-transcriptional regulatory element (PRE mediated-mRNA nuclear export. PRE-dependent HIV Gag expressed well in human cells, but assembled with slower kinetics, accumulated intracellularly, and failed to associate with a lipid raft compartment where the wild-type Rev-dependent HIV-1 Gag efficiently assembles. Surprisingly, assembly and budding of PRE-dependent HIV Gag in human cells could be rescued in trans by co-expression of Rev-dependent Gag that provides correct membrane targeting signals, or in cis by replacing HIV matrix (MA with other membrane targeting domains. Taken together, our results demonstrate deficient membrane targeting of PRE-dependent HIV-1 Gag and suggest that HIV MA function is regulated by the trafficking pathway of the encoding mRNA.

Learners’ processes during pre-task planning and Working Memory Capacity

Directory of Open Access Journals (Sweden)

Maria da Gloria Tavares

2016-01-01

Full Text Available http://dx.doi.org/10.5007/2175-8026.2016v69n1p79 The present study is part of a larger scale research (Guará-Tavares, 2011, 2013 that investigates the relationship among working memory capacity, pre-task planning, and L2 speech performance. The aim of the study was to analyze 1 what processes learners engage during pre-task planning, and 2 whether higher and lower working memory spans engage in different processes during pre-task planning. Learners’ processes were accessed by means of think aloud protocols and a retrospective interview. Working memory capacity was measured by the Speaking Span Test. Results show that learners engage mainly in organization of ideas, rehearsal, lexical searches, and monitoring.. Moreover, higher spans employ significantly more metacognitive strategies during planning when compared to lower spans.

Purification of ribonucleoproteins by a novel approach: isolation of the SSB1 ribonucleoprotein from yeast and demonstration that it has no role in mRNA splicing.

Science.gov (United States)

Cusick, M E

1992-12-29

A novel approach is described to purify potential ribonucleoproteins (RNP) of yeast. The method assays a yeast RNP complex, assembled in vitro on actin pre-mRNA, by low-ionic strength acrylamide gel electrophoresis. The minimal protein components of this RNP complex were three proteins, one of 30 kDa and two at 42-44 kDa, defined by formation of the complex on biotinylated-RNA, binding of this complex to avidin-agarose, and salt elution of the protein in the biotinylated-RNP complex. Using the assay for RNP complex formation, an RNP protein was purified to homogeneity on the basis of its affinity towards single-stranded DNA and RNA. This RNP protein turned out to be identical to a known RNP protein, the single-stranded binding protein 1 (ssb1) of yeast, on the basis of identical gel electrophoretic migration, antibody cross-reactivity, and identical properties on the gel complex formation assay. In vitro mRNA splicing was normal in extracts made from a yeast strain missing ssb1 (ssb1- strain). Addition of anti-ssb1 antibody to splicing extracts made from a wild type strain did not inhibit or diminish splicing. Instead, mRNA splicing was reproducibly stimulated several fold, indicating competition between ssb1 and splicing factors for binding to single-stranded RNA in the extracts. RNP complexes still formed in the ssb1- strain, demonstrating that it would be possible to purify other RNP proteins from this strain using the gel complex formation assay.

The Mediator complex and transcription regulation

Science.gov (United States)

Poss, Zachary C.; Ebmeier, Christopher C.

2013-01-01

The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module. PMID:24088064

THE SPATIAL DISTRIBUTION OF COMPLEX ORGANIC MOLECULES IN THE L1544 PRE-STELLAR CORE

Energy Technology Data Exchange (ETDEWEB)

Jiménez-Serra, Izaskun [Astronomy Unit, School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London E1 4NS (United Kingdom); Vasyunin, Anton I.; Caselli, Paola [Max-Planck-Institut für extraterrestrische Physik (MPE), Gießenbachstr., D-85741 Garching (Germany); Marcelino, Nuria [INAF, Osservatorio di Radioastronomia, Via P. Gobetti 101, I-40129 Bologna (Italy); Billot, Nicolas [Instituto de Radioastronomía Milimétrica, Avenida Divina Pastora 7, E-18012 Granada (Spain); Viti, Serena [Department of Physics and Astronomy, University College London, 132 Hampstead Road, London NW1 2PS (United Kingdom); Testi, Leonardo [European Southern Observatory (ESO), Karl-Schwarzschild-Str. 2, D-85748 Garching (Germany); Vastel, Charlotte [Université de Toulouse, UPS-OMP, IRAP, F-31400 Toulouse (France); Lefloch, Bertrand [Univ. Grenoble Alpes, IPAG, F-38000 Grenoble (France); Bachiller, Rafael, E-mail: i.jimenez-serra@qmul.ac.uk [Observatorio Astronómico Nacional (OAN, IGN), Calle Alfonso XII 3, E-28014 Madrid (Spain)

2016-10-10

The detection of complex organic molecules (COMs) toward cold sources such as pre-stellar cores (with T < 10 K) has challenged our understanding of the formation processes of COMs in the interstellar medium. Recent modeling on COM chemistry at low temperatures has provided new insight into these processes predicting that COM formation depends strongly on parameters such as visual extinction and the level of CO freeze out. We report deep observations of COMs toward two positions in the L1544 pre-stellar core: the dense, highly extinguished continuum peak with A{sub V}≥ 30 mag within the inner 2700 au; and a low-density shell with average A{sub V}∼ 7.5–8 mag located at 4000 au from the core’s center and bright in CH{sub 3}OH. Our observations show that CH{sub 3}O, CH{sub 3}OCH{sub 3}, and CH{sub 3}CHO are more abundant (by factors of ∼2–10) toward the low-density shell than toward the continuum peak. Other COMs such as CH{sub 3}OCHO, c-C{sub 3}H{sub 2}O, HCCCHO, CH{sub 2}CHCN, and HCCNC show slight enhancements (by factors ≤3), but the associated uncertainties are large. This suggests that COMs are actively formed and already present in the low-density shells of pre-stellar cores. The modeling of the chemistry of O-bearing COMs in L1544 indicates that these species are enhanced in this shell because (i) CO starts freezing out onto dust grains driving an active surface chemistry; (ii) the visual extinction is sufficiently high to prevent the UV photo-dissociation of COMs by the external interstellar radiation field; and (iii) the density is still moderate to prevent severe depletion of COMs onto grains.

THE SPATIAL DISTRIBUTION OF COMPLEX ORGANIC MOLECULES IN THE L1544 PRE-STELLAR CORE

International Nuclear Information System (INIS)

Jiménez-Serra, Izaskun; Vasyunin, Anton I.; Caselli, Paola; Marcelino, Nuria; Billot, Nicolas; Viti, Serena; Testi, Leonardo; Vastel, Charlotte; Lefloch, Bertrand; Bachiller, Rafael

2016-01-01

The detection of complex organic molecules (COMs) toward cold sources such as pre-stellar cores (with T < 10 K) has challenged our understanding of the formation processes of COMs in the interstellar medium. Recent modeling on COM chemistry at low temperatures has provided new insight into these processes predicting that COM formation depends strongly on parameters such as visual extinction and the level of CO freeze out. We report deep observations of COMs toward two positions in the L1544 pre-stellar core: the dense, highly extinguished continuum peak with A_V≥ 30 mag within the inner 2700 au; and a low-density shell with average A_V∼ 7.5–8 mag located at 4000 au from the core’s center and bright in CH_3OH. Our observations show that CH_3O, CH_3OCH_3, and CH_3CHO are more abundant (by factors of ∼2–10) toward the low-density shell than toward the continuum peak. Other COMs such as CH_3OCHO, c-C_3H_2O, HCCCHO, CH_2CHCN, and HCCNC show slight enhancements (by factors ≤3), but the associated uncertainties are large. This suggests that COMs are actively formed and already present in the low-density shells of pre-stellar cores. The modeling of the chemistry of O-bearing COMs in L1544 indicates that these species are enhanced in this shell because (i) CO starts freezing out onto dust grains driving an active surface chemistry; (ii) the visual extinction is sufficiently high to prevent the UV photo-dissociation of COMs by the external interstellar radiation field; and (iii) the density is still moderate to prevent severe depletion of COMs onto grains.

Coordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells.

KAUST Repository

Arae, Toshihiro

2017-04-18

Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. The actual level of individual mRNAs is determined by a balance between mRNA synthesis and degradation. Therefore, it is important to assess the regulatory steps to increase our understanding of gene regulation. Here, we analyzed temporal changes in mRNA amounts and half-lives in response to cold stress in Arabidopsis cell cultures based on genome-wide analysis. In this mRNA decay array method, mRNA half-life measurements and microarray analyses were combined. In addition, temporal changes in the integrated value of transcription rates were estimated from the above two parameters using a mathematical approach. Our results showed that several cold-responsive genes, including Cold-regulated 15a, were relatively destabilized, whereas the mRNA amounts were increased during cold treatment by accelerating the transcription rate to overcome the destabilization. Considering the kinetics of mRNA synthesis and degradation, this apparently contradictory result supports that mRNA destabilization is advantageous for the swift increase in CBF-responsive genes in response to cold stress.

Quality assessment of baby food made of different pre-processed organic raw materials under industrial processing conditions.

Science.gov (United States)

Seidel, Kathrin; Kahl, Johannes; Paoletti, Flavio; Birlouez, Ines; Busscher, Nicolaas; Kretzschmar, Ursula; Särkkä-Tirkkonen, Marjo; Seljåsen, Randi; Sinesio, Fiorella; Torp, Torfinn; Baiamonte, Irene

2015-02-01

The market for processed food is rapidly growing. The industry needs methods for "processing with care" leading to high quality products in order to meet consumers' expectations. Processing influences the quality of the finished product through various factors. In carrot baby food, these are the raw material, the pre-processing and storage treatments as well as the processing conditions. In this study, a quality assessment was performed on baby food made from different pre-processed raw materials. The experiments were carried out under industrial conditions using fresh, frozen and stored organic carrots as raw material. Statistically significant differences were found for sensory attributes among the three autoclaved puree samples (e.g. overall odour F = 90.72, p processed from frozen carrots show increased moisture content and decrease of several chemical constituents. Biocrystallization identified changes between replications of the cooking. Pre-treatment of raw material has a significant influence on the final quality of the baby food.

Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA.

Directory of Open Access Journals (Sweden)

Carlus Deneke

Full Text Available Experimental studies on mRNA stability have established several, qualitatively distinct decay patterns for the amount of mRNA within the living cell. Furthermore, a variety of different and complex biochemical pathways for mRNA degradation have been identified. The central aim of this paper is to bring together both the experimental evidence about the decay patterns and the biochemical knowledge about the multi-step nature of mRNA degradation in a coherent mathematical theory. We first introduce a mathematical relationship between the mRNA decay pattern and the lifetime distribution of individual mRNA molecules. This relationship reveals that the mRNA decay patterns at steady state expression level must obey a general convexity condition, which applies to any degradation mechanism. Next, we develop a theory, formulated as a Markov chain model, that recapitulates some aspects of the multi-step nature of mRNA degradation. We apply our theory to experimental data for yeast and explicitly derive the lifetime distribution of the corresponding mRNAs. Thereby, we show how to extract single-molecule properties of an mRNA, such as the age-dependent decay rate and the residual lifetime. Finally, we analyze the decay patterns of the whole translatome of yeast cells and show that yeast mRNAs can be grouped into three broad classes that exhibit three distinct decay patterns. This paper provides both a method to accurately analyze non-exponential mRNA decay patterns and a tool to validate different models of degradation using decay data.

Wig1 prevents cellular senescence by regulating p21 mRNA decay through control of RISC recruitment.

Science.gov (United States)

Kim, Bong Cho; Lee, Hyung Chul; Lee, Je-Jung; Choi, Chang-Min; Kim, Dong-Kwan; Lee, Jae Cheol; Ko, Young-Gyu; Lee, Jae-Seon

2012-11-14

Premature senescence, a key strategy used to suppress carcinogenesis, can be driven by p53/p21 proteins in response to various stresses. Here, we demonstrate that Wig1 plays a critical role in this process through regulation of p21 mRNA stability. Wig1 controls the association of Argonaute2 (Ago2), a central component of the RNA-induced silencing complex (RISC), with target p21 mRNA via binding of the stem-loop structure near the microRNA (miRNA) target site. Depletion of Wig1 prohibited miRNA-mediated p21 mRNA decay and resulted in premature senescence. Wig1 plays an essential role in cell proliferation, as demonstrated in tumour xenografts in mice, and Wig1 and p21 mRNA levels are inversely correlated in human normal and cancer tissues. Together, our data indicate a novel role of Wig1 in RISC target accessibility, which is a key step in RNA-mediated gene silencing. In addition, these findings indicate that fine-tuning of p21 levels by Wig1 is essential for the prevention of cellular senescence.

The role of the amygdala during emotional processing in Huntington's disease: from pre-manifest to late stage disease.

Science.gov (United States)

Mason, Sarah L; Zhang, Jiaxiang; Begeti, Faye; Guzman, Natalie Valle; Lazar, Alpar S; Rowe, James B; Barker, Roger A; Hampshire, Adam

2015-04-01

Deficits in emotional processing can be detected in the pre-manifest stage of Huntington's disease and negative emotion recognition has been identified as a predictor of clinical diagnosis. The underlying neuropathological correlates of such deficits are typically established using correlative structural MRI studies. This approach does not take into consideration the impact of disruption to the complex interactions between multiple brain circuits on emotional processing. Therefore, exploration of the neural substrates of emotional processing in pre-manifest HD using fMRI connectivity analysis may be a useful way of evaluating the way brain regions interrelate in the period prior to diagnosis. We investigated the impact of predicted time to disease onset on brain activation when participants were exposed to pictures of faces with angry and neutral expressions, in 20 pre-manifest HD gene carriers and 23 healthy controls. On the basis of the results of this initial study went on to look at amygdala dependent cognitive performance in 79 Huntington's disease patients from a cross-section of disease stages (pre-manifest to late disease) and 26 healthy controls, using a validated theory of mind task: "the Reading the Mind in the Eyes Test" which has been previously been shown to be amygdala dependent. Psychophysiological interaction analysis identified reduced connectivity between the left amygdala and right fusiform facial area in pre-manifest HD gene carriers compared to controls when viewing angry compared to neutral faces. Change in PPI connectivity scores correlated with predicted time to disease onset (r=0.45, pneural networks underlying social cognition and emotional processing can be detected prior to clinical diagnosis in Huntington's disease. Connectivity between the amygdala and other brain regions is impacted by the disease process in pre-manifest HD and may therefore be a useful way of identifying participants who are approaching a clinical diagnosis

Is a pre-analytical process for urinalysis required?

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Petit, Morgane; Beaudeux, Jean-Louis; Majoux, Sandrine; Hennequin, Carole

2017-10-01

For the reliable urinary measurement of calcium, phosphate and uric acid, a pre-analytical process by adding acid or base to urine samples at laboratory is recommended in order to dissolve precipitated solutes. Several studies on different kind of samples and analysers have previously shown that a such pre-analytical treatment is useless. The objective was to study the necessity of pre-analytical treatment of urine on samples collected using the V-Monovette ® (Sarstedt) system and measured on the analyser Architect C16000 (Abbott Diagnostics). Sixty urinary samples of hospitalized patients were selected (n=30 for calcium and phosphate, and n=30 for uric acid). After acidification of urine samples for measurement of calcium and phosphate, and alkalinisation for measurement of uric acid respectively, differences between results before and after the pre-analytical treatment were compared to acceptable limits recommended by the French society of clinical biology (SFBC). No difference in concentration between before and after pre-analytical treatment of urine samples exceeded acceptable limits from SFBC for measurement of calcium and uric acid. For phosphate, only one sample exceeded these acceptable limits, showing a result paradoxically lower after acidification. In conclusion, in agreement with previous study, our results show that acidification or alkalinisation of urine samples from 24 h urines or from urination is not a pre-analytical necessity for measurement of calcium, phosphate and uric acid.

Labeled EF-Tus for rapid kinetic studies of pretranslocation complex formation

DEFF Research Database (Denmark)

Liu, Wei; Kavaliauskas, Darius; Schrader, Jared

2014-01-01

The universally conserved translation elongation factor EF-Tu delivers aminoacyl(aa)-tRNA in the form of an aa-tRNA·EF-Tu·GTP ternary complex (TC) to the ribosome where it binds to the cognate mRNA codon within the ribosomal A-site, leading to formation of a pretranslocation (PRE) complex. Here we...... describe preparation of QSY9 and Cy5 derivatives of the variant E348C-EF-Tu that are functional in translation elongation. Together with fluorophore derivatives of aa-tRNA and of ribosomal protein L11, located within the GTPase associated center (GAC), these labeled EF-Tus allow development of two new FRET...... assays that permit the dynamics of distance changes between EF-Tu and both L11 (Tu-L11 assay) and aa-tRNA (Tu-tRNA assay) to be determined during the decoding process. We use these assays to examine: (i) the relative rates of EF-Tu movement away from the GAC and from aa-tRNA during decoding, (ii...

How Pre-Service Teachers' Understand and Perform Science Process Skills

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Chabalengula, Vivien Mweene; Mumba, Frackson; Mbewe, Simeon

2012-01-01

This study explored pre-service teachers' conceptual understanding and performance on science process skills. A sample comprised 91 elementary pre-service teachers at a university in the Midwest of the USA. Participants were enrolled in two science education courses; introductory science teaching methods course and advanced science methods course.…

Structures of transcription pre-initiation complex with TFIIH and Mediator.

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Schilbach, S; Hantsche, M; Tegunov, D; Dienemann, C; Wigge, C; Urlaub, H; Cramer, P

2017-11-09

For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.

Consequences of metaphase II oocyte cryopreservation on mRNA content.

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Chamayou, S; Bonaventura, G; Alecci, C; Tibullo, D; Di Raimondo, F; Guglielmino, A; Barcellona, M L

2011-04-01

We studied the consequences of freezing/thawing processes on mRNA contents in MII oocytes after slow-freezing/rapid thawing (SF/RT) and vitrification/warming (V/W) protocols, and compared the results to fresh MII oocytes. We quantified the nuclear transcript mRNA responsible for the translation of proteins belonging either to trans-regulatory protein family or to functional structural proteins such as proteins involved in DNA structural organization (NAP1L1, TOP1, H1F0H1), chromosomal structure maintenance (SMC, SCC3, RAD21, SMC1A, SMC1B, STAG3, REC8), mitochondrial energetic pathways (ATP5GJ, SDHC), cell cycle regulation and processes (CLTA, MAPK6, CKS2) and staminal cell potency-development competence stage (DPPA3, OCT4, FOXJ2). Surplus MII oocytes were donated from patients in IVF cycles and divided in three groups of 15 oocytes. Group 1 was comprised of non-cryopreserved oocytes and Groups 2 and 3 underwent SF/RT and V/W procedures, respectively. There was an overall decrease of mRNA extracted from cryopreserved oocytes compared to control group. Only 39.4% of mRNA content were preserved after SF/RT while 63.3% of mRNA content were maintained after V/W. Oocyte cryopreservation is associated with molecular injury associated with the decrease of stored mRNA. However the V/W protocol is more conservative than SF/RT resulting in a level of mRNA sufficient to maintain biologic functions in the subsequent fertilized oocyte. Copyright © 2011 Elsevier Inc. All rights reserved.

Modulation of respiratory frequency by peptidergic input to rhythmogenic neurons in the preBötzinger complex

DEFF Research Database (Denmark)

Gray, P A; Rekling, J C; Bocchiaro, C M

1999-01-01

Neurokinin-1 receptor (NK1R) and mu-opioid receptor (muOR) agonists affected respiratory rhythm when injected directly into the preBötzinger Complex (preBötC), the hypothesized site for respiratory rhythmogenesis in mammals. These effects were mediated by actions on preBötC rhythmogenic neurons....... The distribution of NK1R+ neurons anatomically defined the preBötC. Type 1 neurons in the preBötC, which have rhythmogenic properties, expressed both NK1Rs and muORs, whereas type 2 neurons expressed only NK1Rs. These findings suggest that the preBötC is a definable anatomic structure with unique physiological...... function and that a subpopulation of neurons expressing both NK1Rs and muORs generate respiratory rhythm and modulate respiratory frequency....

Pre-Processing and Modeling Tools for Bigdata

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Hashem Hadi

2016-09-01

Full Text Available Modeling tools and operators help the user / developer to identify the processing field on the top of the sequence and to send into the computing module only the data related to the requested result. The remaining data is not relevant and it will slow down the processing. The biggest challenge nowadays is to get high quality processing results with a reduced computing time and costs. To do so, we must review the processing sequence, by adding several modeling tools. The existing processing models do not take in consideration this aspect and focus on getting high calculation performances which will increase the computing time and costs. In this paper we provide a study of the main modeling tools for BigData and a new model based on pre-processing.

Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.

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Judith Somekh

2012-12-01

Full Text Available We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM, a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure-the objects that comprise the system, and behavior-how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point-the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model.

Auto-Regulatory RNA Editing Fine-Tunes mRNA Re-Coding and Complex Behaviour in Drosophila

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Savva, Yiannis A.; Jepson, James E.C; Sahin, Asli; Sugden, Arthur U.; Dorsky, Jacquelyn S.; Alpert, Lauren; Lawrence, Charles; Reenan, Robert A.

2014-01-01

Auto-regulatory feedback loops are a common molecular strategy used to optimize protein function. In Drosophila many mRNAs involved in neuro-transmission are re-coded at the RNA level by the RNA editing enzyme dADAR, leading to the incorporation of amino acids that are not directly encoded by the genome. dADAR also re-codes its own transcript, but the consequences of this auto-regulation in vivo are unclear. Here we show that hard-wiring or abolishing endogenous dADAR auto-regulation dramatically remodels the landscape of re-coding events in a site-specific manner. These molecular phenotypes correlate with altered localization of dADAR within the nuclear compartment. Furthermore, auto-editing exhibits sexually dimorphic patterns of spatial regulation and can be modified by abiotic environmental factors. Finally, we demonstrate that modifying dAdar auto-editing affects adaptive complex behaviors. Our results reveal the in vivo relevance of auto-regulatory control over post-transcriptional mRNA re-coding events in fine-tuning brain function and organismal behavior. PMID:22531175

Visfatin mRNA expression in human subcutaneous adipose tissue is regulated by exercise

DEFF Research Database (Denmark)

Frydelund-Larsen, Lone; Åkerström, Thorbjörn; Nielsen, Søren

2006-01-01

in abdominal subcutaneous adipose tissue and skeletal muscle biopsies obtained from healthy young men at time points 0, 3, 4.5, 6, 9, and 24 h in relation to either 3 h of ergometer cycle exercise at 60% of Vo(2 max) or rest. Adipose tissue visfatin mRNA expression increased threefold at the time points 3, 4......Visfatin [pre-beta-cell colony-enhancing factor (PBEF)] is a novel adipokine that is produced by adipose tissue, skeletal muscle, and liver and has insulin-mimetic actions. Regular exercise enhances insulin sensitivity. In the present study, we therefore examined visfatin mRNA expression.......5, and 6 h in response to exercise (n = 8) compared with preexercise samples and compared with the resting control group (n = 7, P = 0.001). Visfatin mRNA expression in skeletal muscle was not influenced by exercise. The exercise-induced increase in adipose tissue visfatin was, however, not accompanied...

Postage for the messenger: Designating routes for Nuclear mRNA Export

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Natalizio, Barbara J.; Wente, Susan R.

2013-01-01

Transcription of messenger(m) RNA occurs in the nucleus, making the translocation of mRNA across the nuclear envelope (NE) boundary a critical determinant of proper gene expression and cell survival. A major mRNA export route occurs via the NXF1-dependent pathway through the nuclear pore complexes (NPCs) embedded in the NE. However, recent findings have discovered new evidence supporting the existence of multiple mechanisms for crossing the NE, including both NPC-mediated and NE budding-mediated pathways. An analysis of the trans-acting factors and cis components that define these pathways reveals shared elements as well as mechanistic differences. We review here the current understanding of the mechanisms that characterize each pathway and highlight the determinants that influence mRNA transport fate. PMID:23583578

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

International Nuclear Information System (INIS)

Kurkcuoglu, Ozge; Doruker, Pemra; Jernigan, Robert L; Sen, Taner Z; Kloczkowski, Andrzej

2008-01-01

The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3' end forming the Shine–Dalgarno complex at the initiation step; the 3' end may act as a 'hook' to reel in the mRNA to facilitate its exit

A novel link between Sus1 and the cytoplasmic mRNA decay machinery suggests a broad role in mRNA metabolism

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Llopis Ana

2010-03-01

Full Text Available Abstract Background Gene expression is achieved by the coordinated action of multiple factors to ensure a perfect synchrony from chromatin epigenetic regulation through to mRNA export. Sus1 is a conserved mRNA export/transcription factor and is a key player in coupling transcription initiation, elongation and mRNA export. In the nucleus, Sus1 is associated to the transcriptional co-activator SAGA and to the NPC associated complex termed TREX2/THSC. Through these associations, Sus1 mediates the nuclear dynamics of different gene loci and facilitate the export of the new transcripts. Results In this study, we have investigated whether the yeast Sus1 protein is linked to factors involved in mRNA degradation pathways. We provide evidence for genetic interactions between SUS1 and genes coding for components of P-bodies such as PAT1, LSM1, LSM6 and DHH1. We demonstrate that SUS1 deletion is synthetic lethal with 5'→3' decay machinery components LSM1 and PAT1 and has a strong genetic interaction with LSM6 and DHH1. Interestingly, Sus1 overexpression led to an accumulation of Sus1 in cytoplasmic granules, which can co-localise with components of P-bodies and stress granules. In addition, we have identified novel physical interactions between Sus1 and factors associated to P-bodies/stress granules. Finally, absence of LSM1 and PAT1 slightly promotes the Sus1-TREX2 association. Conclusions In this study, we found genetic and biochemical association between Sus1 and components responsible for cytoplasmic mRNA metabolism. Moreover, Sus1 accumulates in discrete cytoplasmic granules, which partially co-localise with P-bodies and stress granules under specific conditions. These interactions suggest a role for Sus1 in gene expression during cytoplasmic mRNA metabolism in addition to its nuclear function.

[Variation of water DOC during the process of pre-pressure and coagulation sedimentation treatment].

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Chen, Wen-Jing; Cong, Hai-Bing; Xu, Ya-Jun; Wang, Wei; Jiang, Xin-Yue; Liu, Yu-Jiao

2014-07-01

The aim of the study was to explore whether the pre-pressure and coagulation sedimentation process would result in algal cell disruption, leading to increased dissolved organic carbon (DOC) in water, based on which, the pressure application mode would be optimized and safe and efficient pre-pressure algae removal process would be obtained. The changes in DOC during the process of pre-pressure and preoxidation treatment, the distribution of molecular weight in water as well as the removal efficiency of algae, turbidity and DOC after coagulation and sedimentation were investigated. The results showed that the DOC in water did not increase but decreased, and the molecular weight decreased after treated with 0.5-0.8 MPa pressure. While KMnO4 and NaClO pre-oxidation both increased the DOC, in the meanwhile, the distribution of molecular weight showed no obvious change. After the pre-pressure coagulation and sedimentation process, the removal rate of algae was 96.23% and that of DOC was 29. 11%, which was by 10% - 30% higher than the rate of pre-oxidation coagulation and sedimentation process.

Simultaneous data pre-processing and SVM classification model selection based on a parallel genetic algorithm applied to spectroscopic data of olive oils.

Science.gov (United States)

Devos, Olivier; Downey, Gerard; Duponchel, Ludovic

2014-04-01

Classification is an important task in chemometrics. For several years now, support vector machines (SVMs) have proven to be powerful for infrared spectral data classification. However such methods require optimisation of parameters in order to control the risk of overfitting and the complexity of the boundary. Furthermore, it is established that the prediction ability of classification models can be improved using pre-processing in order to remove unwanted variance in the spectra. In this paper we propose a new methodology based on genetic algorithm (GA) for the simultaneous optimisation of SVM parameters and pre-processing (GENOPT-SVM). The method has been tested for the discrimination of the geographical origin of Italian olive oil (Ligurian and non-Ligurian) on the basis of near infrared (NIR) or mid infrared (FTIR) spectra. Different classification models (PLS-DA, SVM with mean centre data, GENOPT-SVM) have been tested and statistically compared using McNemar's statistical test. For the two datasets, SVM with optimised pre-processing give models with higher accuracy than the one obtained with PLS-DA on pre-processed data. In the case of the NIR dataset, most of this accuracy improvement (86.3% compared with 82.8% for PLS-DA) occurred using only a single pre-processing step. For the FTIR dataset, three optimised pre-processing steps are required to obtain SVM model with significant accuracy improvement (82.2%) compared to the one obtained with PLS-DA (78.6%). Furthermore, this study demonstrates that even SVM models have to be developed on the basis of well-corrected spectral data in order to obtain higher classification rates. Copyright © 2013 Elsevier Ltd. All rights reserved.

Integrating microRNA and mRNA expression profiles in response to radiation-induced injury in rat lung

International Nuclear Information System (INIS)

Xie, Ling; Zhou, Jundong; Zhang, Shuyu; Chen, Qing; Lai, Rensheng; Ding, Weiqun; Song, ChuanJun; Meng, XingJun; Wu, Jinchang

2014-01-01

Exposure to radiation provokes cellular responses, which are likely regulated by gene expression networks. MicroRNAs are small non-coding RNAs, which regulate gene expression by promoting mRNA degradation or inhibiting protein translation. The expression patterns of both mRNA and miRNA during the radiation-induced lung injury (RILI) remain less characterized and the role of miRNAs in the regulation of this process has not been studied. The present study sought to evaluate miRNA and mRNA expression profiles in the rat lung after irradiation. Male Wistar rats were subjected to single dose irradiation with 20 Gy using 6 MV x-rays to the right lung. (A dose rate of 5 Gy/min was applied). Rats were sacrificed at 3, 12 and 26 weeks after irradiation, and morphological changes in the lung were examined by haematoxylin and eosin. The miRNA and mRNA expression profiles were evaluated by microarrays and followed by quantitative RT-PCR analysis. A cDNA microarray analysis found 2183 transcripts being up-regulated and 2917 transcripts down-regulated (P ≤ 0.05, ≥2.0 fold change) in the lung tissues after irradiation. Likewise, a miRNAs microarray analysis indicated 15 miRNA species being up-regulated and 8 down-regulated (P ≤ 0.05). Subsequent bioinformatics anal -yses of the differentially expressed mRNA and miRNAs revealed that alterations in mRNA expression following irradiation were negatively correlated with miRNAs expression. Our results provide evidence indicating that irradiation induces alterations of mRNA and miRNA expression in rat lung and that there is a negative correlation of mRNA and miRNA expression levels after irradiation. These findings significantly advance our understanding of the regulatory mechanisms underlying the pathophysiology of radiation-induced lung injury. In summary, RILI does not develop gradually in a linear process. In fact, different cell types interact via cytokines in a very complex network. Furthermore, this study suggests that

Degradation of YRA1 Pre-mRNA in the cytoplasm requires translational repression, multiple modular intronic elements, Edc3p, and Mex67p.

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Shuyun Dong

2010-04-01

Full Text Available Intron-containing pre-mRNAs are normally retained and processed in the nucleus but are sometimes exported to the cytoplasm and degraded by the nonsense-mediated mRNA decay (NMD pathway as a consequence of their inclusion of intronic in-frame termination codons. When shunted to the cytoplasm by autoregulated nuclear export, the intron-containing yeast YRA1 pre-mRNA evades NMD and is targeted by a cytoplasmic decay pathway mediated by the decapping activator Edc3p. Here, we have elucidated this transcript-specific decay mechanism, showing that Edc3p-mediated YRA1 pre-mRNA degradation occurs independently of translation and is controlled through five structurally distinct but functionally interdependent modular elements in the YRA1 intron. Two of these elements target the pre-mRNA as an Edc3p substrate and the other three mediate transcript-specific translational repression. Translational repression of YRA1 pre-mRNA also requires the heterodimeric Mex67p/Mtr2p general mRNA export receptor, but not Edc3p, and serves to enhance Edc3p substrate specificity by inhibiting the susceptibility of this pre-mRNA to NMD. Collectively, our data indicate that YRA1 pre-mRNA degradation is a highly regulated process that proceeds through translational repression, substrate recognition by Edc3p, recruitment of the Dcp1p/Dcp2p decapping enzyme, and activation of decapping.

Consequences of daily corticosteroid dosing with or without pre-treatment with quinidine on the in vivo cytochrome P450 2D (CYP2D) enzyme in rats: effect on O-demethylation activity of dextromethorphan and expression levels of CYP2D1 mRNA.

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Giri, Poonam; Delvadia, Prashant; Gupta, Laxmikant; Patel, Nirmal; Trivedi, Priyal; Lad, Krishna; Patel, Hiren M; Srinivas, Nuggehally R

2018-01-01

1. Present investigation was carried out in rats to study influence of corticosteroids after repeated dosing with/without pre-treatment with CYP2D inhibitor quinidine on the CYP2D1 mRNA levels and CYP2D enzyme activity using dextromethorphan as probe substrate. 2. CYP2D1 mRNA was measured in liver homogenate using quantitative real-time polymerase chain reaction [qRT-PCR] and enzymatic reaction was studied ex vivo in liver S-9 fractions of rats treated with oral 10 mg/kg dexamethasone or prednisolone for five days or pre-treated with quinidine and followed by treatment with oral 10 mg/kg corticosteroids for five days. 3. Five days repeat dosing of dexamethasone or prednisolone decreased the activity of the rat liver CYP2D by 37% and 34%, at 30 min incubation and decreased CYP2D1 mRNA levels by 62% and 61%, respectively. 4. Pre-treatment of quinidine decreased the enzymatic activity of rat CYP2D by 58% and did not potentiate CYP2D inhibition by corticosteroids. This observation was further complemented by qRT-PCR data. 5. Corticosteroids caused CYP2D inhibition in rats vs. literature evidence of CYP2D induction in human hepatocytes/pregnant humans demonstrating lack of concordance. In vivo inhibition should be factored for interpretation of pharmacokinetic data of CYP2D substrates when treated with corticosteroids in rats.

The involvement of mRNA processing factors TIA-1, TIAR, and PABP-1 during mammalian hibernation.

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Tessier, Shannon N; Audas, Timothy E; Wu, Cheng-Wei; Lee, Stephen; Storey, Kenneth B

2014-11-01

Mammalian hibernators survive low body temperatures, ischemia-reperfusion, and restricted nutritional resources via global reductions in energy-expensive cellular processes and selective increases in stress pathways. Consequently, studies that analyze hibernation uncover mechanisms which balance metabolism and support survival by enhancing stress tolerance. We hypothesized processing factors that influence messenger ribonucleic acid (mRNA) maturation and translation may play significant roles in hibernation. We characterized the amino acid sequences of three RNA processing proteins (T cell intracellular antigen 1 (TIA-1), TIA1-related (TIAR), and poly(A)-binding proteins (PABP-1)) from thirteen-lined ground squirrels (Ictidomys tridecemlineatus), which all displayed a high degree of sequence identity with other mammals. Alternate Tia-1 and TiaR gene variants were found in the liver with higher expression of isoform b versus a in both cases. The localization of RNA-binding proteins to subnuclear structures was assessed by immunohistochemistry and confirmed by subcellular fractionation; TIA-1 was identified as a major component of subnuclear structures with up to a sevenfold increase in relative protein levels in the nucleus during hibernation. By contrast, there was no significant difference in the relative protein levels of TIARa/TIARb in the nucleus, and a decrease was observed for TIAR isoforms in cytoplasmic fractions of torpid animals. Finally, we used solubility tests to analyze the formation of reversible aggregates that are associated with TIA-1/R function during stress; a shift towards the soluble fraction (TIA-1a, TIA-1b) was observed during hibernation suggesting enhanced protein aggregation was not present during torpor. The present study identifies novel posttranscriptional regulatory mechanisms that may play a role in reducing translational rates and/or mRNA processing under unfavorable environmental conditions.

Abnormal emotional processing in maltreated children diagnosed of Complex Posttraumatic Stress Disorder.

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Bertó, Clara; Ferrin, Maite; Barberá, María; Livianos, Lorenzo; Rojo, Luis; García-Blanco, Ana

2017-11-01

Maltreated children usually show a specific pattern of emotional and behavioral symptoms that exceed those relating to posttraumatic stress disorder (PTSD). These symptoms have been defined as Complex PTSD (CPTSD). The underlying attentional mechanisms of abnormal emotional processing and their relation to the clinical presentation of CPTSD are not well understood. A visual dot-probe paradigm involving pre-attentive (i.e., 500ms) and attentive (i.e., 1500ms) presentation rates of neutral versus emotional (i.e., angry, happy or sad) facial expressions was applied. Twenty-one maltreated CPTSD children were compared with twenty-six controls. The results are as follows: an attention bias away from threatening faces and an attentional bias towards sad faces were observed in maltreated CPTSD children during pre-attentive and attentive processing. Whereas the attentional bias away from angry faces was associated with social problems, the attentional bias towards sad faces was associated with depressive and withdrawn symptoms. Therefore, CPTSD children develop maladaptive negative cognitive styles, which may underlie not only social problems (by a cognitive avoidance of threatening stimuli) but also depressive symptoms (by a cognitive approach to sad stimuli). Attention processing abnormalities should be considered as therapeutic targets for new treatment approaches in this population. Copyright © 2017 Elsevier Ltd. All rights reserved.

An adaptive deep-coupled GNSS/INS navigation system with hybrid pre-filter processing

Science.gov (United States)

Wu, Mouyan; Ding, Jicheng; Zhao, Lin; Kang, Yingyao; Luo, Zhibin

2018-02-01

The deep-coupling of a global navigation satellite system (GNSS) with an inertial navigation system (INS) can provide accurate and reliable navigation information. There are several kinds of deeply-coupled structures. These can be divided mainly into coherent and non-coherent pre-filter based structures, which have their own strong advantages and disadvantages, especially in accuracy and robustness. In this paper, the existing pre-filters of the deeply-coupled structures are analyzed and modified to improve them firstly. Then, an adaptive GNSS/INS deeply-coupled algorithm with hybrid pre-filters processing is proposed to combine the advantages of coherent and non-coherent structures. An adaptive hysteresis controller is designed to implement the hybrid pre-filters processing strategy. The simulation and vehicle test results show that the adaptive deeply-coupled algorithm with hybrid pre-filters processing can effectively improve navigation accuracy and robustness, especially in a GNSS-challenged environment.

CCL5 promotes proliferation of MCF-7 cells through mTOR-dependent mRNA translation

International Nuclear Information System (INIS)

Murooka, Thomas T.; Rahbar, Ramtin; Fish, Eleanor N.

2009-01-01

The proliferative capacity of cancer cells is regulated by factors intrinsic to cancer cells and by secreted factors in the microenvironment. Here, we investigated the proto-oncogenic potential of the chemokine receptor, CCR5, in MCF-7 breast cancer cell lines. At physiological levels, CCL5, a ligand for CCR5, enhanced MCF-7.CCR5 proliferation. Treatment with the mTOR inhibitor, rapamycin, inhibited this CCL5-inducible proliferation. Because mTOR directly modulates mRNA translation, we investigated whether CCL5 activation of CCR5 leads to increased translation. CCL5 induced the formation of the eIF4F translation initiation complex through an mTOR-dependent process. Indeed, CCL5 initiated mRNA translation, shown by an increase in high-molecular-weight polysomes. Specifically, we show that CCL5 mediated a rapid up-regulation of protein expression for cyclin D1, c-Myc and Dad-1, without affecting their mRNA levels. Taken together, we describe a mechanism by which CCL5 influences translation of rapamycin-sensitive mRNAs, thereby providing CCR5-positive breast cancer cells with a proliferative advantage.

Crimean-Congo Hemorrhagic Fever Virus Nucleocapsid Protein Augments mRNA Translation.

Science.gov (United States)

Jeeva, Subbiah; Cheng, Erdong; Ganaie, Safder S; Mir, Mohammad A

2017-08-01

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne Nairovirus of the Bunyaviridae family, causing severe illness with high mortality rates in humans. Here, we demonstrate that CCHFV nucleocapsid protein (CCHFV-NP) augments mRNA translation. CCHFV-NP binds to the viral mRNA 5' untranslated region (UTR) with high affinity. It facilitates the translation of reporter mRNA both in vivo and in vitro with the assistance of the viral mRNA 5' UTR. CCHFV-NP equally favors the translation of both capped and uncapped mRNAs, demonstrating the independence of this translation strategy on the 5' cap. Unlike the canonical host translation machinery, inhibition of eIF4F complex, an amalgam of three initiation factors, eIF4A, eIF4G, and eIF4E, by the chemical inhibitor 4E1RCat did not impact the CCHFV-NP-mediated translation mechanism. However, the proteolytic degradation of eIF4G alone by the human rhinovirus 2A protease abrogated this translation strategy. Our results demonstrate that eIF4F complex formation is not required but eIF4G plays a critical role in this translation mechanism. Our results suggest that CCHFV has adopted a unique translation mechanism to facilitate the translation of viral mRNAs in the host cell cytoplasm where cellular transcripts are competing for the same translation apparatus. IMPORTANCE Crimean-Congo hemorrhagic fever, a highly contagious viral disease endemic to more than 30 countries, has limited treatment options. Our results demonstrate that NP favors the translation of a reporter mRNA harboring the viral mRNA 5' UTR. It is highly likely that CCHFV uses an NP-mediated translation strategy for the rapid synthesis of viral proteins during the course of infection. Shutdown of this translation mechanism might selectively impact viral protein synthesis, suggesting that an NP-mediated translation strategy is a target for therapeutic intervention against this viral disease. Copyright © 2017 American Society for Microbiology.

Carbenoxolone induced depression of rhythmogenesis in the pre-Bötzinger Complex

Directory of Open Access Journals (Sweden)

VanDam Richard J

2008-05-01

Full Text Available Abstract Background Carbenoxolone (CBX, a gap junction uncoupler, alters the functioning of the pre-Bötzinger Complex (preBötC, a central pattern generating neuronal network important for the production of respiratory rhythm in mammals. Even when isolated in a 1/2 mm-thick slice of medulla oblongata from neonatal mouse the preBötC continues producing periodic bursts of action potentials, termed population bursts that are thought to be important in generating various patterns of inspiration, in vivo. Whether gap junction communication contributes to preBötC rhythmogenesis remains unresolved, largely because existing gap junction uncouplers exert numerous non-specific effects (e.g., inhibition of active transport, alteration of membrane conductances. Here, we determined whether CBX alters preBötC rhythmogenesis by altering membrane properties including input resistance (Rin, voltage-gated Na+ current (INa, and/or voltage-gated K+ current (IK, rather than by blocking gap junction communication. To do so we used a medullary slice preparation, network-level recordings, whole-cell voltage clamp, and glycyrrhizic acid (GZA; a substance used as a control for CBX, since it is similar in structure and does not block gap junctions. Results Whereas neither of the control treatments [artificial cerebrospinal fluid (aCSF or GZA (50 μM] noticeably affected preBötC rhythmogenesis, CBX (50 μM decreased the frequency, area and amplitude of population bursts, eventually terminating population burst production after 45–60 min. Both CBX and GZA decreased neuronal Rin and induced an outward holding current. Although neither agent altered the steady state component of IK evoked by depolarizing voltage steps, CBX, but not GZA, increased peak INa. Conclusion The data presented herein are consistent with the notion that gap junction communication is important for preBötC rhythmogenesis. By comparing the effects of CBX and GZA on membrane properties our data a

Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants

DEFF Research Database (Denmark)

Rougemaille, Mathieu; Gudipati, Rajani Kanth; Olesen, Jens Raabjerg

2007-01-01

by appending oligo(A)-tails onto structured substrates. Another role of the nuclear exosome is that of mRNA surveillance. In strains harboring a mutated THO/Sub2p system, involved in messenger ribonucleoprotein particle biogenesis and nuclear export, the exosome-associated 3' 5' exonuclease Rrp6p is required...

mRNA: From a chemical blueprint for protein production to an off-the-shelf therapeutic.

Science.gov (United States)

Van Lint, Sandra; Heirman, Carlo; Thielemans, Kris; Breckpot, Karine

2013-02-01

Two decades ago, mRNA became the focus of research in molecular medicine and was proposed as an active pharmaceutical ingredient for the therapy of cancer. In this regard, mRNA has been mainly used for ex vivo modification of antigen-presenting cells (APCs), such as dendritic cells (DCs). This vaccination strategy has proven to be safe, well tolerated and capable of inducing tumor antigen-specific immune responses. Recently, the direct application of mRNA for in situ modification of APCs, hence immunization was shown to be feasible and at least as effective as DC-based immunization in pre-clinical models. It is believed that application of mRNA as an off-the-shelf vaccine represents an important step in the development of future cancer immunotherapeutic strategies. Here, we will discuss the use of ex vivo mRNA-modified DCs and "naked mRNA" for cancer immunotherapy focusing on parameters such as the employed DC subtype, DC activation stimulus and route of immunization. In addition, we will provide an overview on the clinical trials published so far, trying to link their outcome to the aforementioned parameters.

Spatial Organization and Dynamics of Transcription Elongation and Pre-mRNA Processing in Live Cells

Directory of Open Access Journals (Sweden)

Miguel Sánchez-Álvarez

2011-01-01

Full Text Available During the last 30 years, systematic biochemical and functional studies have significantly expanded our knowledge of the transcriptional molecular components and the pre-mRNA processing machinery of the cell. However, our current understanding of how these functions take place spatiotemporally within the highly compartmentalized eukaryotic nucleus remains limited. Moreover, it is increasingly clear that “the whole is more than the sum of its parts” and that an understanding of the dynamic coregulation of genes is essential for fully characterizing complex biological phenomena and underlying diseases. Recent technological advances in light microscopy in addition to novel cell and molecular biology approaches have led to the development of new tools, which are being used to address these questions and may contribute to achieving an integrated and global understanding of how the genome works at a cellular level. Here, we review major hallmarks and novel insights in RNA polymerase II activity and pre-mRNA processing in the context of nuclear organization, as well as new concepts and challenges arising from our ability to gather extensive dynamic information at the single-cell resolution.

The 1992 ENDF Pre-processing codes

International Nuclear Information System (INIS)

Cullen, D.E.

1992-01-01

This document summarizes the 1992 version of the ENDF pre-processing codes which are required for processing evaluated nuclear data coded in the format ENDF-4, ENDF-5, or ENDF-6. Included are the codes CONVERT, MERGER, LINEAR, RECENT, SIGMA1, LEGEND, FIXUP, GROUPIE, DICTION, MIXER, VIRGIN, COMPLOT, EVALPLOT, RELABEL. Some of the functions of these codes are: to calculate cross-sections from resonance parameters; to calculate angular distributions, group average, mixtures of cross-sections, etc; to produce graphical plottings and data comparisons. The codes are designed to operate on virtually any type of computer including PC's. They are available from the IAEA Nuclear Data Section, free of charge upon request, on magnetic tape or a set of HD diskettes. (author)

Pre-aggregation for Probability Distributions

DEFF Research Database (Denmark)

Timko, Igor; Dyreson, Curtis E.; Pedersen, Torben Bach

Motivated by the increasing need to analyze complex uncertain multidimensional data (e.g., in order to optimize and personalize location-based services), this paper proposes novel types of {\\em probabilistic} OLAP queries that operate on aggregate values that are probability distributions...... and the techniques to process these queries. The paper also presents the methods for computing the probability distributions, which enables pre-aggregation, and for using the pre-aggregated distributions for further aggregation. In order to achieve good time and space efficiency, the methods perform approximate...... multidimensional data analysis that is considered in this paper (i.e., approximate processing of probabilistic OLAP queries over probability distributions)....

Pre-processing by data augmentation for improved ellipse fitting.

Science.gov (United States)

Kumar, Pankaj; Belchamber, Erika R; Miklavcic, Stanley J

2018-01-01

Ellipse fitting is a highly researched and mature topic. Surprisingly, however, no existing method has thus far considered the data point eccentricity in its ellipse fitting procedure. Here, we introduce the concept of eccentricity of a data point, in analogy with the idea of ellipse eccentricity. We then show empirically that, irrespective of ellipse fitting method used, the root mean square error (RMSE) of a fit increases with the eccentricity of the data point set. The main contribution of the paper is based on the hypothesis that if the data point set were pre-processed to strategically add additional data points in regions of high eccentricity, then the quality of a fit could be improved. Conditional validity of this hypothesis is demonstrated mathematically using a model scenario. Based on this confirmation we propose an algorithm that pre-processes the data so that data points with high eccentricity are replicated. The improvement of ellipse fitting is then demonstrated empirically in real-world application of 3D reconstruction of a plant root system for phenotypic analysis. The degree of improvement for different underlying ellipse fitting methods as a function of data noise level is also analysed. We show that almost every method tested, irrespective of whether it minimizes algebraic error or geometric error, shows improvement in the fit following data augmentation using the proposed pre-processing algorithm.

Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle.

Science.gov (United States)

Shock, Jennifer L; Fischer, Kael F; DeRisi, Joseph L

2007-01-01

The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms. Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression. We used a genome-wide approach to characterize mRNA decay in Plasmodium falciparum. We found that, globally, rates of mRNA decay increase dramatically during the asexual intra-erythrocytic developmental cycle. During the ring stage of the cycle, the average mRNA half-life was 9.5 min, but this was extended to an average of 65 min during the late schizont stage of development. Thus, a major determinant of mRNA decay rate appears to be linked to the stage of intra-erythrocytic development. Furthermore, we found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening. These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes. Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies. Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intra-erythrocytic development. This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum.

Endurance exercise induces mRNA expression of oxidative enzymes in human skeletal muscle late in recovery

DEFF Research Database (Denmark)

Leick, Lotte; Plomgaard, Peter S.; Grønløkke, L.

2010-01-01

exercise. To test the hypothesis that mRNA expression of many oxidative enzymes is up-regulated late in recovery (10-24 h) after exercise, male subjects (n=8) performed a 90-min cycling exercise (70% VO(2-max)), with muscle biopsies obtained before exercise (pre), and after 10, 18 and 24 h of recovery....... The mRNA expression of carnitine-palmitoyltransferase (CPT)I, CD36, 3-hydroxyacyl-CoA-dehydrogenase (HAD), cytochrome (Cyt)c, aminolevulinate-delta-synthase (ALAS)1 and GLUT4 was 100-200% higher at 10-24 h of recovery from exercise than in a control trial. Exercise induced a 100-300% increase...... in peroxisome proliferator-activated receptor gamma co-activator (PGC)-1alpha, citrate synthase (CS), CPTI, CD36, HAD and ALAS1 mRNA contents at 10-24 h of recovery relative to before exercise. No protein changes were detected in Cytc, ALAS1 or GLUT4. This shows that mRNA expression of several training...

Complex sound processing during human REM sleep by recovering information from long-term memory as revealed by the mismatch negativity (MMN).

Science.gov (United States)

Atienza, M; Cantero, J L

2001-05-18

Perceptual learning is thought to be the result of neural changes that take place over a period of several hours or days, allowing information to be transferred to long-term memory. Evidence suggests that contents of long-term memory may improve attentive and pre-attentive sensory processing. Therefore, it is plausible to hypothesize that learning-induced neural changes that develop during wakefulness could improve automatic information processing during human REM sleep. The MMN, an objective measure of the automatic change detection in auditory cortex, was used to evaluate long-term learning effects on pre-attentive processing during wakefulness and REM sleep. When subjects learned to discriminate two complex auditory patterns in wakefulness, an increase in the MMN was obtained in both wake and REM states. The automatic detection of the infrequent complex auditory pattern may therefore be improved in both brain states by reactivating information from long-term memory. These findings suggest that long-term learning-related neural changes are accessible during REM sleep as well.

Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

Directory of Open Access Journals (Sweden)

Hoefsloot Huub CJ

2009-05-01

Full Text Available Abstract Background Mass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Results Two in-house generated clinical SELDI-TOF MS datasets are used in this study as an example of high throughput mass-spectrometry data. We perform a systematic comparison of two commonly used pre-processing methods as implemented in Ciphergen ProteinChip Software and in the Cromwell package. With respect to reproducibility, Ciphergen and Cromwell pre-processing are largely comparable. We find that the overlap between peaks detected by either Ciphergen ProteinChip Software or Cromwell is large. This is especially the case for the more stringent peak detection settings. Moreover, similarity of the estimated intensities between matched peaks is high. We evaluate the pre-processing methods using five different classification methods. Classification is done in a double cross-validation protocol using repeated random sampling to obtain an unbiased estimate of classification accuracy. No pre-processing method significantly outperforms the other for all peak detection settings evaluated. Conclusion We use classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Both pre-processing methods lead to similar classification results on an ovarian cancer and a Gaucher disease dataset. However, the settings for pre-processing

Selective catalytic reduction system and process using a pre-sulfated zirconia binder

Science.gov (United States)

Sobolevskiy, Anatoly; Rossin, Joseph A.

2010-06-29

A selective catalytic reduction (SCR) process with a palladium catalyst for reducing NOx in a gas, using hydrogen as a reducing agent is provided. The process comprises contacting the gas stream with a catalyst system, the catalyst system comprising (ZrO.sub.2)SO.sub.4, palladium, and a pre-sulfated zirconia binder. The inclusion of a pre-sulfated zirconia binder substantially increases the durability of a Pd-based SCR catalyst system. A system for implementing the disclosed process is further provided.

Anaerobic digestion of organic by-products from meat-processing industry. The effect of pre-treatments and co-digestion

Energy Technology Data Exchange (ETDEWEB)

Luste, S.

2011-07-01

suitable for anaerobic co-digestion. The co-digestion of the ABPs with sewage sludge and cattle slurry resulted improved methane production and reusability of the digestate. These enhancements were further improved by the pre-treatments studied. The most suitable (ultrasound and bacterial product addition) and synergistically beneficial (pre-hygienisation) pretreatments were found to enhance the complex degradation of materials. Pre-treatments effects on the whole process and on the end-products were depended on the hydrolysis values, but especially on the content of the materials and qualities of the solubilised compounds. Economical feasibility of ultrasound and hygienisation pre-treatments is attainable. Materials and process methods studied in this thesis offer required new information and aspects about the case- and material-specific factors of process requirements, process optimisation according to the requirements in practice, degradability of the ABP materials, hygienic matters and mechanisms involved in pre-treatments and co-digestion of ABPs. The information produced could be directly utilised in the practical implementations of the anaerobic digestion of studied or corresponding materials and feed mixtures. (orig.)

Pre-processing of input files for the AZTRAN code; Pre procesamiento de archivos de entrada para el codigo AZTRAN

Energy Technology Data Exchange (ETDEWEB)

Vargas E, S. [ININ, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico); Ibarra, G., E-mail: samuel.vargas@inin.gob.mx [IPN, Av. Instituto Politecnico Nacional s/n, 07738 Ciudad de Mexico (Mexico)

2017-09-15

The AZTRAN code began to be developed in the Nuclear Engineering Department of the Escuela Superior de Fisica y Matematicas (ESFM) of the Instituto Politecnico Nacional (IPN) with the purpose of numerically solving various models arising from the physics and engineering of nuclear reactors. The code is still under development and is part of the AZTLAN platform: Development of a Mexican platform for the analysis and design of nuclear reactors. Due to the complexity to generate an input file for the code, a script based on D language is developed, with the purpose of making its elaboration easier, based on a new input file format which includes specific cards, which have been divided into two blocks, mandatory cards and optional cards, including a pre-processing of the input file to identify possible errors within it, as well as an image generator for the specific problem based on the python interpreter. (Author)

Low ERCC1 mRNA and protein expression are associated with worse survival in cervical cancer patients treated with radiation alone

International Nuclear Information System (INIS)

Doll, Corinne M.; Prystajecky, Michael; Eliasziw, Misha; Klimowicz, Alexander C.; Petrillo, Stephanie K.; Craighead, Peter S.; Hao, Desiree; Diaz, Roman; Lees-Miller, Susan P.; Magliocco, Anthony M.

2010-01-01

Purpose: To evaluate the association of excision repair cross-complementation group 1 (ERCC1) expression, using both mRNA and protein expression analysis, with clinical outcome in cervical cancer patients treated with radical radiation therapy (RT). Experimental design: Patients (n = 186) with locally advanced cervical cancer, treated with radical RT alone from a single institution were evaluated. Pre-treatment FFPE biopsy specimens were retrieved from 112 patients. ERCC1 mRNA level was determined by real-time PCR, and ERCC1 protein expression (FL297, 8F1) was measured using quantitative immunohistochemistry (AQUA (registered) ). The association of ERCC1 status with local response, 10-year disease-free (DFS) and overall survival (OS) was analyzed. Results: ERCC1 protein expression levels using both FL297 and 8F1 antibodies were determined for 112 patients; mRNA analysis was additionally performed in 32 patients. Clinical and outcome factors were comparable between the training and validation sets. Low ERCC1 mRNA expression status was associated with worse OS (17.9% vs 50.1%, p = 0.046). ERCC1 protein expression using the FL297 antibody, but not the 8F1 antibody, was significantly associated with both OS (p = 0.002) and DFS (p = 0.010). After adjusting for pre-treatment hemoglobin in a multivariate analysis, ERCC1 FL297 expression status remained statistically significant for OS [HR 1.9 (1.1-3.3), p = 0.031]. Conclusions: Pre-treatment tumoral ERCC1 mRNA and protein expression, using the FL297 antibody, are predictive factors for survival in cervical cancer patients treated with RT, with ERCC1 FL297 expression independently associated with survival. These results identify a subset of patients who may derive the greatest benefit from the addition of cisplatin chemotherapy.

Minimized state complexity of quantum-encoded cryptic processes

Science.gov (United States)

Riechers, Paul M.; Mahoney, John R.; Aghamohammadi, Cina; Crutchfield, James P.

2016-05-01

The predictive information required for proper trajectory sampling of a stochastic process can be more efficiently transmitted via a quantum channel than a classical one. This recent discovery allows quantum information processing to drastically reduce the memory necessary to simulate complex classical stochastic processes. It also points to a new perspective on the intrinsic complexity that nature must employ in generating the processes we observe. The quantum advantage increases with codeword length: the length of process sequences used in constructing the quantum communication scheme. In analogy with the classical complexity measure, statistical complexity, we use this reduced communication cost as an entropic measure of state complexity in the quantum representation. Previously difficult to compute, the quantum advantage is expressed here in closed form using spectral decomposition. This allows for efficient numerical computation of the quantum-reduced state complexity at all encoding lengths, including infinite. Additionally, it makes clear how finite-codeword reduction in state complexity is controlled by the classical process's cryptic order, and it allows asymptotic analysis of infinite-cryptic-order processes.

Nuclear data for fusion: Validation of typical pre-processing methods for radiation transport calculations

International Nuclear Information System (INIS)

Hutton, T.; Sublet, J.C.; Morgan, L.; Leadbeater, T.W.

2015-01-01

Highlights: • We quantify the effect of processing nuclear data from ENDF to ACE format. • We consider the differences between fission and fusion angular distributions. • C-nat(n,el) at 2.0 MeV has a 0.6% deviation between original and processed data. • Fe-56(n,el) at 14.1 MeV has a 11.0% deviation between original and processed data. • Processed data do not accurately depict ENDF distributions for fusion energies. - Abstract: Nuclear data form the basis of the radiation transport codes used to design and simulate the behaviour of nuclear facilities, such as the ITER and DEMO fusion reactors. Typically these data and codes are biased towards fission and high-energy physics applications yet are still applied to fusion problems. With increasing interest in fusion applications, the lack of fusion specific codes and relevant data libraries is becoming increasingly apparent. Industry standard radiation transport codes require pre-processing of the evaluated data libraries prior to use in simulation. Historically these methods focus on speed of simulation at the cost of accurate data representation. For legacy applications this has not been a major concern, but current fusion needs differ significantly. Pre-processing reconstructs the differential and double differential interaction cross sections with a coarse binned structure, or more recently as a tabulated cumulative distribution function. This work looks at the validity of applying these processing methods to data used in fusion specific calculations in comparison to fission. The relative effects of applying this pre-processing mechanism, to both fission and fusion relevant reaction channels are demonstrated, and as such the poor representation of these distributions for the fusion energy regime. For the nat C(n,el) reaction at 2.0 MeV, the binned differential cross section deviates from the original data by 0.6% on average. For the 56 Fe(n,el) reaction at 14.1 MeV, the deviation increases to 11.0%. We

The Effects of Pre-Task, On-Line, and Both Pre-Task and On-Line Planning on Fluency, Complexity, and Accuracy--The Case of Iranian EFL Learners' Written Production

Science.gov (United States)

Piri, Faramarz; Barati, Hossein; Ketabi, Saeed

2012-01-01

Previous studies on the effect of planning on language production have revealed that planning does have a positive effect on language performance in terms of fluency, complexity, and accuracy. The present study was an attempt to investigate the effects of pre-task, on-line, and both pre-task and on-line planning on fluency, accuracy, and…

Expression of mRNA for galanin, galanin-like peptide and galanin receptors 1-3 in the ovine hypothalamus and pituitary gland: effects of age and gender.

Science.gov (United States)

Whitelaw, Christine Margaret; Robinson, Jane Elizabeth; Chambers, George Ballantine; Hastie, Peter; Padmanabhan, Vasantha; Thompson, Robert Charles; Evans, Neil Price

2009-01-01

The neurotransmitters/neuromodulators galanin (GAL) and galanin-like peptide (GALP) are known to operate through three G protein-coupled receptors, GALR1, GALR2 and GALR3. The aim of this study was to investigate changes in expression of mRNA for galanin, GALP and GALR1-3 in the hypothalamus and pituitary gland, of male and female sheep, to determine how expression changed in association with growth and the attainment of reproductive competence. Tissue samples from the hypothalami and pituitary glands were analysed from late foetal and pre-pubertal lambs and adult sheep. Although mRNA for galanin and GALR1-3 was present in both tissues, at all ages and in both genders, quantification of GALP mRNA was not possible due to its low levels of expression. mRNA expression for both galanin and its receptors was seen to change significantly in both tissues as a function of age. Specifically, hypothalamic galanin mRNA expression increased with age in the male, but decreased with age in the female pituitary gland. mRNA expression for all receptors increased between foetal and pre-pubertal age groups and decreased significantly between pre-pubertal and adult animals. The results indicate that the expression of mRNA for galanin and its receptors changes dynamically with age and those significant differences exist with regard to tissue type and gender. These changes suggest that galaninergic neuroendocrine systems could be involved in the regulation of ovine growth and or the development of reproductive competence. The roles played by these systems in the sheep, however, may differ from other species, in particular the neuroendocrine link between nutrition and reproduction and GALR1's role in pituitary signalling.

Implication of Ccr4-Not complex function in mRNA quality control in Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Assenholt, Jannie; Mouaikel, John; Saguez, Cyril

2011-01-01

RNPs are exported to the cytoplasm. The Ccr4-Not complex, which constitutes the major S. cerevisiae cytoplasmic deadenylase, has recently been implied in nuclear exosome–related processes. Consistent with a possible nuclear function of the complex, the deletion or mutation of Ccr4-Not factors also elicits...

An interdisciplinary approach to study Pre-Earthquake processes

Science.gov (United States)

Ouzounov, D.; Pulinets, S. A.; Hattori, K.; Taylor, P. T.

2017-12-01

We will summarize a multi-year research effort on wide-ranging observations of pre-earthquake processes. Based on space and ground data we present some new results relevant to the existence of pre-earthquake signals. Over the past 15-20 years there has been a major revival of interest in pre-earthquake studies in Japan, Russia, China, EU, Taiwan and elsewhere. Recent large magnitude earthquakes in Asia and Europe have shown the importance of these various studies in the search for earthquake precursors either for forecasting or predictions. Some new results were obtained from modeling of the atmosphere-ionosphere connection and analyses of seismic records (foreshocks /aftershocks), geochemical, electromagnetic, and thermodynamic processes related to stress changes in the lithosphere, along with their statistical and physical validation. This cross - disciplinary approach could make an impact on our further understanding of the physics of earthquakes and the phenomena that precedes their energy release. We also present the potential impact of these interdisciplinary studies to earthquake predictability. A detail summary of our approach and that of several international researchers will be part of this session and will be subsequently published in a new AGU/Wiley volume. This book is part of the Geophysical Monograph series and is intended to show the variety of parameters seismic, atmospheric, geochemical and historical involved is this important field of research and will bring this knowledge and awareness to a broader geosciences community.

Dis3- and exosome subunit-responsive 3′ mRNA instability elements

International Nuclear Information System (INIS)

Kiss, Daniel L.; Hou, Dezhi; Gross, Robert H.; Andrulis, Erik D.

2012-01-01

Highlights: ► Successful use of a novel RNA-specific bioinformatic tool, RNA SCOPE. ► Identified novel 3′ UTR cis-acting element that destabilizes a reporter mRNA. ► Show exosome subunits are required for cis-acting element-mediated mRNA instability. ► Define precise sequence requirements of novel cis-acting element. ► Show that microarray-defined exosome subunit-regulated mRNAs have novel element. -- Abstract: Eukaryotic RNA turnover is regulated in part by the exosome, a nuclear and cytoplasmic complex of ribonucleases (RNases) and RNA-binding proteins. The major RNase of the complex is thought to be Dis3, a multi-functional 3′–5′ exoribonuclease and endoribonuclease. Although it is known that Dis3 and core exosome subunits are recruited to transcriptionally active genes and to messenger RNA (mRNA) substrates, this recruitment is thought to occur indirectly. We sought to discover cis-acting elements that recruit Dis3 or other exosome subunits. Using a bioinformatic tool called RNA SCOPE to screen the 3′ untranslated regions of up-regulated transcripts from our published Dis3 depletion-derived transcriptomic data set, we identified several motifs as candidate instability elements. Secondary screening using a luciferase reporter system revealed that one cassette—harboring four elements—destabilized the reporter transcript. RNAi-based depletion of Dis3, Rrp6, Rrp4, Rrp40, or Rrp46 diminished the efficacy of cassette-mediated destabilization. Truncation analysis of the cassette showed that two exosome subunit-sensitive elements (ESSEs) destabilized the reporter. Point-directed mutagenesis of ESSE abrogated the destabilization effect. An examination of the transcriptomic data from exosome subunit depletion-based microarrays revealed that mRNAs with ESSEs are found in every up-regulated mRNA data set but are underrepresented or missing from the down-regulated data sets. Taken together, our findings imply a potentially novel mechanism of mRNA

Domain general sequence operations contribute to pre-SMA involvement in visuo-spatial processing

Directory of Open Access Journals (Sweden)

E. Charles eLeek

2016-01-01

Full Text Available This study used 3T MRI to elucidate the functional role of supplementary motor area (SMA in relation to visuo-spatial processing. A localizer task contrasting sequential number subtraction and repetitive button pressing was used to functionally delineate non-motor sequence processing in pre-SMA, and activity in SMA-proper associated with motor sequencing. Patterns of BOLD responses in these regions were then contrasted to those from two tasks of visuo-spatial processing. In one task participants performed mental rotation in which recognition memory judgments were made to previously memorized 2D novel patterns across image-plane rotations. The other task involved abstract grid navigation in which observers computed a series of imagined location shifts in response to directional (arrow cues around a mental grid. The results showed overlapping activation in pre-SMA for sequential subtraction and both visuo-spatial tasks. These results suggest that visuo-spatial processing is supported by non-motor sequence operations that involve pre-SMA. More broadly, these data further highlight the functional heterogeneity of pre-SMA, and show that its role extends to processes beyond the planning and online control of movement.

Parallel finite elements with domain decomposition and its pre-processing

International Nuclear Information System (INIS)

Yoshida, A.; Yagawa, G.; Hamada, S.

1993-01-01

This paper describes a parallel finite element analysis using a domain decomposition method, and the pre-processing for the parallel calculation. Computer simulations are about to replace experiments in various fields, and the scale of model to be simulated tends to be extremely large. On the other hand, computational environment has drastically changed in these years. Especially, parallel processing on massively parallel computers or computer networks is considered to be promising techniques. In order to achieve high efficiency on such parallel computation environment, large granularity of tasks, a well-balanced workload distribution are key issues. It is also important to reduce the cost of pre-processing in such parallel FEM. From the point of view, the authors developed the domain decomposition FEM with the automatic and dynamic task-allocation mechanism and the automatic mesh generation/domain subdivision system for it. (author)

Inner nuclear envelope protein SUN1 plays a prominent role in mammalian mRNA export.

Science.gov (United States)

Li, Ping; Noegel, Angelika A

2015-11-16

Nuclear export of messenger ribonucleoproteins (mRNPs) through the nuclear pore complex (NPC) can be roughly classified into two forms: bulk and specific export, involving an nuclear RNA export factor 1 (NXF1)-dependent pathway and chromosome region maintenance 1 (CRM1)-dependent pathway, respectively. SUN proteins constitute the inner nuclear envelope component of the l I: nker of N: ucleoskeleton and C: ytoskeleton (LINC) complex. Here, we show that mammalian cells require SUN1 for efficient nuclear mRNP export. The results indicate that both SUN1 and SUN2 interact with heterogeneous nuclear ribonucleoprotein (hnRNP) F/H and hnRNP K/J. SUN1 depletion inhibits the mRNP export, with accumulations of both hnRNPs and poly(A)+RNA in the nucleus. Leptomycin B treatment indicates that SUN1 functions in mammalian mRNA export involving the NXF1-dependent pathway. SUN1 mediates mRNA export through its association with mRNP complexes via a direct interaction with NXF1. Additionally, SUN1 associates with the NPC through a direct interaction with Nup153, a nuclear pore component involved in mRNA export. Taken together, our results reveal that the inner nuclear envelope protein SUN1 has additional functions aside from being a central component of the LINC complex and that it is an integral component of the mammalian mRNA export pathway suggesting a model whereby SUN1 recruits NXF1-containing mRNP onto the nuclear envelope and hands it over to Nup153. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Epidemic processes in complex networks

OpenAIRE

Pastor Satorras, Romualdo; Castellano, Claudio; Van Mieghem, Piet; Vespignani, Alessandro

2015-01-01

In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world networks have a profound impact on the behavior of equilibrium and nonequilibrium phenomena occurring in various systems, and the study of epidemic spreading is central to our understanding of the unfolding of dynamical processes in complex networks. The t...

Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data

Directory of Open Access Journals (Sweden)

Katharina Stoecker

2017-03-01

Full Text Available The process of adipogenesis is controlled in a highly orchestrated manner, including transcriptional and post-transcriptional events. In developing 3T3-L1 pre-adipocytes, this program can be interrupted by all-trans retinoic acid (ATRA. To examine this inhibiting impact by ATRA, we generated large-scale transcriptomic data on the microRNA and mRNA level. Non-coding RNAs such as microRNAs represent a field in RNA turnover, which is very important for understanding the regulation of mRNA gene expression. High throughput mRNA and microRNA expression profiling was performed using mRNA hybridisation microarray technology and multiplexed expression assay for microRNA quantification. After quantitative measurements we merged expression data sets, integrated the results and analysed the molecular regulation of in vitro adipogenesis. For this purpose, we applied local enrichment analysis on the integrative microRNA-mRNA network determined by a linear regression approach. This approach includes the target predictions of TargetScan Mouse 5.2 and 23 pre-selected, significantly regulated microRNAs as well as Affymetrix microarray mRNA data. We found that the cellular lipid metabolism is negatively affected by ATRA. Furthermore, we were able to show that microRNA 27a and/or microRNA 96 are important regulators of gap junction signalling, the rearrangement of the actin cytoskeleton as well as the citric acid cycle, which represent the most affected pathways with regard to inhibitory effects of ATRA in 3T3-L1 preadipocytes. In conclusion, the experimental workflow and the integrative microRNA–mRNA data analysis shown in this study represent a possibility for illustrating interactions in highly orchestrated biological processes. Further the applied global microRNA–mRNA interaction network may also be used for the pre-selection of potential new biomarkers with regard to obesity or for the identification of new pharmaceutical targets.

Yeast eIF4B binds to the head of the 40S ribosomal subunit and promotes mRNA recruitment through its N-terminal and internal repeat domains.

Science.gov (United States)

Walker, Sarah E; Zhou, Fujun; Mitchell, Sarah F; Larson, Victoria S; Valasek, Leos; Hinnebusch, Alan G; Lorsch, Jon R

2013-02-01

Eukaryotic translation initiation factor (eIF)4B stimulates recruitment of mRNA to the 43S ribosomal pre-initiation complex (PIC). Yeast eIF4B (yeIF4B), shown previously to bind single-stranded (ss) RNA, consists of an N-terminal domain (NTD), predicted to be unstructured in solution; an RNA-recognition motif (RRM); an unusual domain comprised of seven imperfect repeats of 26 amino acids; and a C-terminal domain. Although the mechanism of yeIF4B action has remained obscure, most models have suggested central roles for its RRM and ssRNA-binding activity. We have dissected the functions of yeIF4B's domains and show that the RRM and its ssRNA-binding activity are dispensable in vitro and in vivo. Instead, our data indicate that the 7-repeats and NTD are the most critical domains, which mediate binding of yeIF4B to the head of the 40S ribosomal subunit via interaction with Rps20. This interaction induces structural changes in the ribosome's mRNA entry channel that could facilitate mRNA loading. We also show that yeIF4B strongly promotes productive interaction of eIF4A with the 43S•mRNA PIC in a manner required for efficient mRNA recruitment.

Conversation on data mining strategies in LC-MS untargeted metabolomics: pre-processing and pre-treatment steps

CSIR Research Space (South Africa)

Tugizimana, F

2016-11-01

Full Text Available -MS)-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter. Data obtained in positive mode...

Mucin gene mRNA levels in broilers challenged with eimeria and/or Clostridium perfringens.

Science.gov (United States)

Kitessa, Soressa M; Nattrass, Gregory S; Forder, Rebecca E A; McGrice, Hayley A; Wu, Shu-Biao; Hughes, Robert J

2014-09-01

The effects of Eimeria (EM) and Clostridium perfringens (CP) challenges on the mRNA levels of genes involved in mucin (Muc) synthesis (Muc2, Muc5ac, Muc13, and trefoil family factor-2 [TFF2]), inflammation (tumor necrosis factor alpha [TNF-alpha] and interleukin-18 [IL-18]), and metabolic processes (cluster of differentiation [CD]36) in the jejunum of broilers were investigated. Two parallel experiments involving 1) EM challenge and 2) EM and CP challenges were conducted. The first experiment was a 2 X 2 study with 12 birds per treatment (N = 48) involving fishmeal substitution (25%) in the diet (FM) and EM challenge. The treatments were: Control (FM-, EM-), Fishmeal (FM+, EM-), EM challenge (FM-, EM+), and fishmeal substitution and EM challenge (FM+, EM+). The second experiment was a 2 X 2 X 2 experiment with six birds per treatment (N = 48) involving fishmeal (FM-, FM+), Eimeria (EM-, EM+), and C perfringens (CP-, CP+). In both arms of the study, male broilers were given a starter diet for the whole period of 16 days, except those assigned to FM+, where 25% of the starter ration was replaced with fishmeal from days 8 to 14. EM inoculation was performed on day 9 and CP inoculation on days 14 and 15. The EM challenge birds were euthanatized for sampling on day 13; postmortem examination and sampling for the Eimeria plus C perfringens challenge arm of the study were on day 16. In the Eimeria challenge arm of the study, fishmeal supplementation significantly suppressed the mRNA levels of TNF-alpha, TFF2, and IL-18 pre-CP inoculation but simultaneously increased the levels of Muc13 and CD36 mRNAs. Birds challenged with Eimeria exhibited increased mRNA levels of Muc13, Muc5ac, TNF-alpha, and IL-18. In the Eimeria and C. perfringens challenge arm, birds exposed to EM challenge exhibited significantly lower mRNA levels of Muc2 and CD36. The mRNA levels of CD36 were also significantly suppressed by CP challenge. Our results showed that the transcription of mucin synthesis

Summary of ENDF/B pre-processing codes

International Nuclear Information System (INIS)

Cullen, D.E.

1981-12-01

This document contains the summary documentation for the ENDF/B pre-processing codes: LINEAR, RECENT, SIGMA1, GROUPIE, EVALPLOT, MERGER, DICTION, CONVERT. This summary documentation is merely a copy of the comment cards that appear at the beginning of each programme; these comment cards always reflect the latest status of input options, etc. For the latest published documentation on the methods used in these codes see UCRL-50400, Vol.17 parts A-E, Lawrence Livermore Laboratory (1979)

CUP promotes deadenylation and inhibits decapping of mRNA targets

Science.gov (United States)

Igreja, Catia; Izaurralde, Elisa

2011-01-01

CUP is an eIF4E-binding protein (4E-BP) that represses the expression of specific maternal mRNAs prior to their posterior localization. Here, we show that CUP employs multiple mechanisms to repress the expression of target mRNAs. In addition to inducing translational repression, CUP maintains mRNA targets in a repressed state by promoting their deadenylation and protects deadenylated mRNAs from further degradation. Translational repression and deadenylation are independent of eIF4E binding and require both the middle and C-terminal regions of CUP, which collectively we termed the effector domain. This domain associates with the deadenylase complex CAF1–CCR4–NOT and decapping activators. Accordingly, in isolation, the effector domain is a potent trigger of mRNA degradation and promotes deadenylation, decapping and decay. However, in the context of the full-length CUP protein, the decapping and decay mediated by the effector domain are inhibited, and target mRNAs are maintained in a deadenylated, repressed form. Remarkably, an N-terminal regulatory domain containing a noncanonical eIF4E-binding motif is required to protect CUP-associated mRNAs from decapping and further degradation, suggesting that this domain counteracts the activity of the effector domain. Our findings indicate that the mode of action of CUP is more complex than previously thought and provide mechanistic insight into the regulation of mRNA expression by 4E-BPs. PMID:21937713

mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay.

Directory of Open Access Journals (Sweden)

Jennifer L Anderson

2017-11-01

Full Text Available As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of adaptations that can occur may inform the strategies of mutant generation.

Effective Complexity of Stationary Process Realizations

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Arleta Szkoła

2011-06-01

Full Text Available The concept of effective complexity of an object as the minimal description length of its regularities has been initiated by Gell-Mann and Lloyd. The regularities are modeled by means of ensembles, which is the probability distributions on finite binary strings. In our previous paper [1] we propose a definition of effective complexity in precise terms of algorithmic information theory. Here we investigate the effective complexity of binary strings generated by stationary, in general not computable, processes. We show that under not too strong conditions long typical process realizations are effectively simple. Our results become most transparent in the context of coarse effective complexity which is a modification of the original notion of effective complexity that needs less parameters in its definition. A similar modification of the related concept of sophistication has been suggested by Antunes and Fortnow.

Cisplatin binds to pre-miR-200b and impairs its processing to mature microRNA.

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Mezencev, R; Wartell, R M

2018-01-01

Cisplatin is an important anticancer drug with a complex mode of action, a variety of possible targets, and numerous resistance mechanisms. While genomic DNA has traditionally been considered to be its most critical anticancer target, several lines of evidence suggest that various RNAs and other biomolecules may play a role in its anticancer mode of action. In this report we demonstrate that cisplatin modifies pre-miR-200b, impairs its processing to mature miRNA, and decreases miR-200b expression in ovarian cancer cells. Considering the role of miR-200b in epithelial-to-mesenchymal transition and cancer chemosensitivity, cisplatin-induced modification of pre-miR-200b and subsequent deregulation of mature miR-200b may, depending on cell context, limit anticancer activity of this important anticancer drug. More gener- ally, precursor miRNAs may be important targets of cisplatin and play a role in this drug's anticancer activity or modulate cell responses to this drug.

Pre-movement planning processes in people with congenital mirror movements.

Science.gov (United States)

Franz, E A; Fu, Y

2017-10-01

Pre-movement processes were investigated in people with Congenital mirrormovement (CMM), a rare disorder in which bilateral movement (mirroring) occurs in the upper distal extremities (primarily the hands and fingers) during intended unilateral movements. Abnormal density of ipsilateral corticospinal projections is an established hallmark of CMM. This study tested whether the Lateralised Readiness Potential (LRP), which reflects movement planning and readiness, is also abnormal in people with CMM. Twenty-eight neurologically-normal controls and 8 people with CMM were tested on a unimanual Go/No-go task while electroencephalography (EEG) was recorded to assess the LRP. No significant group differences were found in reaction time (RT). However, significantly smaller LRP amplitudes were found, on average, in the CMM group compared to Controls at central-motor (C3,C4) sites in stimulus-locked and response-locked epochs; similar group differences were also found at further frontal sites (F3,F4) during response-locked epochs. Abnormal brain activity in pre-movement processes associated with response planning and preparation is present in people with CMM. Aberrant bilateral activity during pre-movement processes is clearly implicated; whether part of the etiology of CMM, or as a mechanism of neuro-compensation, is not yet known. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Viperin mRNA is a novel target for the human RNase MRP/RNase P endoribonuclease.

Science.gov (United States)

Mattijssen, Sandy; Hinson, Ella R; Onnekink, Carla; Hermanns, Pia; Zabel, Bernhard; Cresswell, Peter; Pruijn, Ger J M

2011-07-01

RNase MRP is a conserved endoribonuclease, in humans consisting of a 267-nucleotide RNA associated with 7-10 proteins. Mutations in its RNA component lead to several autosomal recessive skeletal dysplasias, including cartilage-hair hypoplasia (CHH). Because the known substrates of mammalian RNase MRP, pre-ribosomal RNA, and RNA involved in mitochondrial DNA replication are not likely involved in CHH, we analyzed the effects of RNase MRP (and the structurally related RNase P) depletion on mRNAs using DNA microarrays. We confirmed the upregulation of the interferon-inducible viperin mRNA by RNAi experiments and this appeared to be independent of the interferon response. We detected two cleavage sites for RNase MRP/RNase P in the coding sequence of viperin mRNA. This is the first study providing direct evidence for the cleavage of a mRNA by RNase MRP/RNase P in human cells. Implications for the involvement in the pathophysiology of CHH are discussed.

Phonological Processes in Complex and Compound Words

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Alieh Kord Zaferanlu Kambuziya

2016-02-01

Full Text Available Abstract This research at making a comparison between phonological processes in complex and compound Persian words. Data are gathered from a 40,000-word Persian dictionary. To catch some results, 4,034 complex words and 1,464 compound ones are chosen. To count the data, "excel" software is used. Some results of the research are: 1- "Insertion" is the usual phonological process in complex words. More than half of different insertions belongs to the consonant /g/. Then /y/ and // are in the second and the third order. The consonant /v/ has the least percentage of all. The most percentage of vowel insertion belongs to /e/. The vowels /a/ and /o/ are in the second and third order. Deletion in complex words can only be seen in consonant /t/ and vowel /e/. 2- The most frequent phonological processes in compounds is consonant deletion. In this process, seven different consonants including /t/, //, /m/, /r/, / ǰ/, /d, and /c/. The only deleted vowel is /e/. In both groups of complex and compound, /t/ deletion can be observed. A sequence of three consonants paves the way for the deletion of one of the consonants, if one of the sequences is a sonorant one like /n/, the deletion process rarely happens. 3- In complex words, consonant deletion causes a lighter syllable weight, whereas vowel deletion causes a heavier syllable weight. So, both of the processes lead to bi-moraic weight. 4- The production of bi-moraic syllable in Persian is preferable to Syllable Contact Law. So, Specific Rules have precedence to Universals. 5- Vowel insertion can be seen in both groups of complex and compound words. In complex words, /e/ insertion has the most fundamental part. The vowels /a/ and /o/ are in the second and third place. Whenever there are two sequences of ultra-heavy syllables. By vowel insertion, the first syllable is broken into two light syllables. The compounds that are influenced by vowel insertion, can be and are pronounced without any insertion

Regulation of mRNA Translation Is a Novel Mechanism for Phthalate Toxicity.

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Jun Ling

Full Text Available Phthalates are a group of plasticizers that are widely used in many consumer products and medical devices, thus generating a huge burden to human health. Phthalates have been known to cause a number of developmental and reproductive disorders functioning as endocrine modulators. They are also involved in carcinogenesis with mechanisms less understood. To further understand the molecular mechanisms of phthalate toxicity, in this study we reported a new effect of phthalates on mRNA translation/protein synthesis, a key regulatory step of gene expression. Butyl benzyl phthalate (BBP was found to directly inhibit mRNA translation in vitro but showed a complicated pattern of affecting mRNA translation in cells. In human kidney embryonic cell (HEK-293T, BBP increased cap-dependent mRNA translation at lower concentrations but showed inhibitory effect at higher concentrations. Cap-independent translation was not affected. On the other hand, mono (2-ethylhexyl phthalate (MEHP as a major metabolite of another important phthalate di (2-ethylhexyl phthalate (DEHP inhibited both can-dependent and -independent mRNA translation in vivo. In contrast, BBP and MEHP exhibited an overall promoting effect on mRNA translation in cancer cells. Mechanistic studies identified that the level and phosphorylation of eIF4E-BP (eIF4E binding protein and the amount of eIF4GI in eIF4F complex were altered in accordance with the effect of BBP on translation. BBP was also identified to directly bind to eIF4E, providing a further mechanism underlying the regulation of mRNA by phthalate. At the cellular level BBP inhibited normal cell growth but slightly promoted cancer cells (HT29 growth. Overall, this study provides the first evidence that phthalates can directly regulate mRNA translation as a novel mechanism to mediate their biological toxicities.

Image Processing of Welding Procedure Specification and Pre-process program development for Finite Element Modelling

International Nuclear Information System (INIS)

Kim, K. S.; Lee, H. J.

2009-11-01

PRE-WELD program, which generates automatically the input file for the finite element analysis on the 2D butt welding at the dissimilar metal weld part, was developed. This program is pre-process program of the FEM code for analyzing the residual stress at the welding parts. Even if the users have not the detail knowledge for the FEM modelling, the users can make the ABAQUS INPUT easily by inputting the shape data of welding part, the weld current and voltage of welding parameters. By using PRE-WELD program, we can save the time and the effort greatly for preparing the ABAQUS INPUT for the residual stress analysis at the welding parts, and make the exact input without the human error

Arc mRNA induction in striatal efferent neurons associated with response learning.

Science.gov (United States)

Daberkow, D P; Riedy, M D; Kesner, R P; Keefe, K A

2007-07-01

The dorsal striatum is involved in motor-response learning, but the extent to which distinct populations of striatal efferent neurons are differentially involved in such learning is unknown. Activity-regulated, cytoskeleton-associated (Arc) protein is an effector immediate-early gene implicated in synaptic plasticity. We examined arc mRNA expression in striatopallidal vs. striatonigral efferent neurons in dorsomedial and dorsolateral striatum of rats engaged in reversal learning on a T-maze motor-response task. Male Sprague-Dawley rats learned to turn right or left for 3 days. Half of the rats then underwent reversal training. The remaining rats were yoked to rats undergoing reversal training, such that they ran the same number of trials but ran them as continued-acquisition trials. Brains were removed and processed using double-label fluorescent in situ hybridization for arc and preproenkephalin (PPE) mRNA. In the reversal, but not the continued-acquisition, group there was a significant relation between the overall arc mRNA signal in dorsomedial striatum and the number of trials run, with rats reaching criterion in fewer trials having higher levels of arc mRNA expression. A similar relation was seen between the numbers of PPE(+) and PPE(-) neurons in dorsomedial striatum with cytoplasmic arc mRNA expression. Interestingly, in behaviourally activated animals significantly more PPE(-) neurons had cytoplasmic arc mRNA expression. These data suggest that Arc in both striatonigral and striatopallidal efferent neurons is involved in striatal synaptic plasticity mediating motor-response learning in the T-maze and that there is differential processing of arc mRNA in distinct subpopulations of striatal efferent neurons.

The structure of the Myo4p globular tail and its function in ASH1 mRNA localization.

Science.gov (United States)

Heuck, Alexander; Fetka, Ingrid; Brewer, Daniel N; Hüls, Daniela; Munson, Mary; Jansen, Ralf-Peter; Niessing, Dierk

2010-05-03

Type V myosin (MyoV)-dependent transport of cargo is an essential process in eukaryotes. Studies on yeast and vertebrate MyoV showed that their globular tails mediate binding to the cargo complexes. In Saccharomyces cerevisiae, the MyoV motor Myo4p interacts with She3p to localize asymmetric synthesis of HO 1 (ASH1) mRNA into the bud of dividing cells. A recent study showed that localization of GFP-MS2-tethered ASH1 particles does not require the Myo4p globular tail, challenging the supposed role of this domain. We assessed ASH1 mRNA and Myo4p distribution more directly and found that their localization is impaired in cells expressing globular tail-lacking Myo4p. In vitro studies further show that the globular tail together with a more N-terminal linker region is required for efficient She3p binding. We also determined the x-ray structure of the Myo4p globular tail and identify a conserved surface patch important for She3p binding. The structure shows pronounced similarities to membrane-tethering complexes and indicates that Myo4p may not undergo auto-inhibition of its motor domain.

Increased IL-10 mRNA and IL-23 mRNA expression in multiple sclerosis: interferon-beta treatment increases IL-10 mRNA expression while reducing IL-23 mRNA expression

DEFF Research Database (Denmark)

Krakauer, M.; Sorensen, P.; Khademi, M.

2008-01-01

volunteers served to confirm initial findings. mRNA was analyzed by real-time reverse transcriptase polymerase chain reaction (PCR). RESULTS: We found elevated expression of interleukin (IL)-23 and IL-10 in untreated MS patients. IFN-beta therapy increased IL-10 and decreased IL-23 expression independently...... of the regulatory cytokine IL-10. The elevated IL-23 mRNA levels in MS patients are noteworthy in view of the newly discovered IL-23-driven Th17 T-cell subset, which is crucial in animal models of MS. Since IFN-beta therapy resulted in decreased IL-23 mRNA levels, the Th17 axis could be another target of IFN...

Individual microRNAs (miRNAs) display distinct mRNA targeting "rules".

Science.gov (United States)

Wang, Wang-Xia; Wilfred, Bernard R; Xie, Kevin; Jennings, Mary H; Hu, Yanling Hu; Stromberg, Arnold J; Nelson, Peter T

2010-01-01

MicroRNAs (miRNAs) guide Argonaute (AGO)-containing microribonucleoprotein (miRNP) complexes to target mRNAs.It has been assumed that miRNAs behave similarly to each other with regard to mRNA target recognition. The usual assumptions, which are based on prior studies, are that miRNAs target preferentially sequences in the 3'UTR of mRNAs,guided by the 5' "seed" portion of the miRNAs. Here we isolated AGO- and miRNA-containing miRNPs from human H4 tumor cells by co-immunoprecipitation (co-IP) with anti-AGO antibody. Cells were transfected with miR-107, miR-124,miR-128, miR-320, or a negative control miRNA. Co-IPed RNAs were subjected to downstream high-density Affymetrix Human Gene 1.0 ST microarray analyses using an assay we validated previously-a "RIP-Chip" experimental design. RIP-Chip data provided a list of mRNAs recruited into the AGO-miRNP in correlation to each miRNA. These experimentally identified miRNA targets were analyzed for complementary six nucleotide "seed" sequences within the transfected miRNAs. We found that miR-124 targets tended to have sequences in the 3'UTR that would be recognized by the 5' seed of miR-124, as described in previous studies. By contrast, miR-107 targets tended to have 'seed' sequences in the mRNA open reading frame, but not the 3' UTR. Further, mRNA targets of miR-128 and miR-320 are less enriched for 6-mer seed sequences in comparison to miR-107 and miR-124. In sum, our data support the importance of the 5' seed in determining binding characteristics for some miRNAs; however, the "binding rules" are complex, and individual miRNAs can have distinct sequence determinants that lead to mRNA targeting.

Electrical coupling and excitatory synaptic transmission between rhythmogenic respiratory neurons in the preBötzinger complex

DEFF Research Database (Denmark)

Rekling, J C; Shao, X M; Feldman, J L

2000-01-01

Breathing pattern is postulated to be generated by brainstem neurons. However, determination of the underlying cellular mechanisms, and in particular the synaptic interactions between respiratory neurons, has been difficult. Here we used dual recordings from two distinct populations of brainstem...... respiratory neurons, hypoglossal (XII) motoneurons, and rhythmogenic (type-1) neurons in the preBötzinger complex (preBötC), the hypothesized site for respiratory rhythm generation, to determine whether electrical and chemical transmission is present. Using an in vitro brainstem slice preparation from newborn...... mice, we found that intracellularly recorded pairs of XII motoneurons and pairs of preBötC inspiratory type-1 neurons showed bidirectional electrical coupling. Coupling strength was low (neurons was heavily filtered (corner frequency,

Predicting prices of agricultural commodities in Thailand using combined approach emphasizing on data pre-processing technique

Directory of Open Access Journals (Sweden)

Thoranin Sujjaviriyasup

2018-02-01

Full Text Available In this research, a combined approach emphasizing on data pre-processing technique is developed to forecast prices of agricultural commodities in Thailand. The future prices play significant role in decision making to cultivate crops in next year. The proposed model takes ability of MODWT to decompose original time series data into more stable and explicit subseries, and SVR model to formulate complex function of forecasting. The experimental results indicated that the proposed model outperforms traditional forecasting models based on MAE and MAPE criteria. Furthermore, the proposed model reveals that it is able to be a useful forecasting tool for prices of agricultural commodities in Thailand

Adaptive Beamforming Based on Complex Quaternion Processes

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Jian-wu Tao

2014-01-01

Full Text Available Motivated by the benefits of array signal processing in quaternion domain, we investigate the problem of adaptive beamforming based on complex quaternion processes in this paper. First, a complex quaternion least-mean squares (CQLMS algorithm is proposed and its performance is analyzed. The CQLMS algorithm is suitable for adaptive beamforming of vector-sensor array. The weight vector update of CQLMS algorithm is derived based on the complex gradient, leading to lower computational complexity. Because the complex quaternion can exhibit the orthogonal structure of an electromagnetic vector-sensor in a natural way, a complex quaternion model in time domain is provided for a 3-component vector-sensor array. And the normalized adaptive beamformer using CQLMS is presented. Finally, simulation results are given to validate the performance of the proposed adaptive beamformer.

The impact of pre-existing anxiety on affective and cognitive processing of a Virtual Reality analogue trauma.

Science.gov (United States)

Schweizer, Tina; Schmitz, Julian; Plempe, Laura; Sun, Dali; Becker-Asano, Christian; Leonhart, Rainer; Tuschen-Caffier, Brunna

2017-01-01

Dysfunctional processing of traumatic events may be in particular related to high trait anxiety as a pre-traumatic risk factor for the development of post-traumatic stress disorder (PTSD). However, as this has rarely been investigated in prospective, experimental studies, we aimed to analyse the association between high trait anxiety and affective as well as cognitive processing of stress using a new prospective Virtual Reality analogue trauma paradigm to overcome limitations of retrospective or current analogue designs. Individuals with high and low trait anxiety (N = 80) were exposed to a multi-sensory Virtual Reality emergency scenario while psychophysiological stress response, emotion regulation and intrusive memories were assessed. Our results showed that high trait anxiety individuals display increased (i) subjective stress responses, (ii) emotion dysregulation and (iii) intrusive memories upon VR analogue trauma exposure. In particular, our sample of high trait anxiety individuals displayed limited access to different emotion regulation strategies as well as increased worry and rumination regarding perceived intrusive memories. Considering the complex interplay of multiple risk factors, our findings suggests that peri-traumatic affective processing seems to mediate high trait anxiety and post-traumatic intrusive memories thereby pointing out the central role of peri-traumatic processes for intrusion development. In addition, HA as a modulating pre-traumatic risk factor might further increase the risk of later dysfunctional processing of an analogue trauma by interacting with factors of affective processing during analogue trauma exposure. Implications of these findings which may contribute to a higher risk to develop PTSD are discussed.

The impact of pre-existing anxiety on affective and cognitive processing of a Virtual Reality analogue trauma.

Directory of Open Access Journals (Sweden)

Tina Schweizer

Full Text Available Dysfunctional processing of traumatic events may be in particular related to high trait anxiety as a pre-traumatic risk factor for the development of post-traumatic stress disorder (PTSD. However, as this has rarely been investigated in prospective, experimental studies, we aimed to analyse the association between high trait anxiety and affective as well as cognitive processing of stress using a new prospective Virtual Reality analogue trauma paradigm to overcome limitations of retrospective or current analogue designs. Individuals with high and low trait anxiety (N = 80 were exposed to a multi-sensory Virtual Reality emergency scenario while psychophysiological stress response, emotion regulation and intrusive memories were assessed. Our results showed that high trait anxiety individuals display increased (i subjective stress responses, (ii emotion dysregulation and (iii intrusive memories upon VR analogue trauma exposure. In particular, our sample of high trait anxiety individuals displayed limited access to different emotion regulation strategies as well as increased worry and rumination regarding perceived intrusive memories. Considering the complex interplay of multiple risk factors, our findings suggests that peri-traumatic affective processing seems to mediate high trait anxiety and post-traumatic intrusive memories thereby pointing out the central role of peri-traumatic processes for intrusion development. In addition, HA as a modulating pre-traumatic risk factor might further increase the risk of later dysfunctional processing of an analogue trauma by interacting with factors of affective processing during analogue trauma exposure. Implications of these findings which may contribute to a higher risk to develop PTSD are discussed.

A novel pre-oxidation method for elemental mercury removal utilizing a complex vaporized absorbent

International Nuclear Information System (INIS)

Zhao, Yi; Hao, Runlong; Guo, Qing

2014-01-01

Graphical abstract: - Highlights: • An innovative liquid-phase complex absorbent (LCA) for Hg 0 removal was prepared. • A novel integrative process for Hg 0 removal was proposed. • The simultaneous removal efficiencies of SO 2 , NO and Hg 0 were 100%, 79.5% and 80.4%, respectively. • The reaction mechanism of simultaneous removal of SO 2 , NO and Hg 0 was proposed. - Abstract: A novel semi-dry integrative method for elemental mercury (Hg 0 ) removal has been proposed in this paper, in which Hg 0 was initially pre-oxidized by a vaporized liquid-phase complex absorbent (LCA) composed of a Fenton reagent, peracetic acid (CH 3 COOOH) and sodium chloride (NaCl), after which Hg 2+ was absorbed by the resultant Ca(OH) 2 . The experimental results indicated that CH 3 COOOH and NaCl were the best additives for Hg 0 oxidation. Among the influencing factors, the pH of the LCA and the adding rate of the LCA significantly affected the Hg 0 removal. The coexisting gases, SO 2 and NO, were characterized as either increasing or inhibiting in the removal process, depending on their concentrations. Under optimal reaction conditions, the efficiency for the single removal of Hg 0 was 91%. Under identical conditions, the efficiencies of the simultaneous removal of SO 2 , NO and Hg 0 were 100%, 79.5% and 80.4%, respectively. Finally, the reaction mechanism for the simultaneous removal of SO 2 , NO and Hg 0 was proposed based on the characteristics of the removal products as determined by X-ray diffraction (XRD), atomic fluorescence spectrometry (AFS), the analysis of the electrode potentials, and through data from related research references

ALS Associated Mutations in Matrin 3 Alter Protein-Protein Interactions and Impede mRNA Nuclear Export.

Science.gov (United States)

Boehringer, Ashley; Garcia-Mansfield, Krystine; Singh, Gurkaran; Bakkar, Nadine; Pirrotte, Patrick; Bowser, Robert

2017-11-06

Mutations in Matrin 3 have recently been linked to ALS, though the mechanism that induces disease in these patients is unknown. To define the protein interactome of wild-type and ALS-linked MATR3 mutations, we performed immunoprecipitation followed by mass spectrometry using NSC-34 cells expressing human wild-type or mutant Matrin 3. Gene ontology analysis identified a novel role for Matrin 3 in mRNA transport centered on proteins in the TRanscription and EXport (TREX) complex, known to function in mRNA biogenesis and nuclear export. ALS-linked mutations in Matrin 3 led to its re-distribution within the nucleus, decreased co-localization with endogenous Matrin 3 and increased co-localization with specific TREX components. Expression of disease-causing Matrin 3 mutations led to nuclear mRNA export defects of both global mRNA and more specifically the mRNA of TDP-43 and FUS. Our findings identify a potential pathogenic mechanism attributable to MATR3 mutations and further link cellular transport defects to ALS.

Curcumin complexation with cyclodextrins by the autoclave process: Method development and characterization of complex formation.

Science.gov (United States)

Hagbani, Turki Al; Nazzal, Sami

2017-03-30

One approach to enhance curcumin (CUR) aqueous solubility is to use cyclodextrins (CDs) to form inclusion complexes where CUR is encapsulated as a guest molecule within the internal cavity of the water-soluble CD. Several methods have been reported for the complexation of CUR with CDs. Limited information, however, is available on the use of the autoclave process (AU) in complex formation. The aims of this work were therefore to (1) investigate and evaluate the AU cycle as a complex formation method to enhance CUR solubility; (2) compare the efficacy of the AU process with the freeze-drying (FD) and evaporation (EV) processes in complex formation; and (3) confirm CUR stability by characterizing CUR:CD complexes by NMR, Raman spectroscopy, DSC, and XRD. Significant differences were found in the saturation solubility of CUR from its complexes with CD when prepared by the three complexation methods. The AU yielded a complex with expected chemical and physical fingerprints for a CUR:CD inclusion complex that maintained the chemical integrity and stability of CUR and provided the highest solubility of CUR in water. Physical and chemical characterizations of the AU complexes confirmed the encapsulated of CUR inside the CD cavity and the transformation of the crystalline CUR:CD inclusion complex to an amorphous form. It was concluded that the autoclave process with its short processing time could be used as an alternate and efficient methods for drug:CD complexation. Copyright © 2017 Elsevier B.V. All rights reserved.

The effect of dilute acid pre-treatment process in bioethanol production from durian (Durio zibethinus) seeds waste

Science.gov (United States)

Ghazali, K. A.; Salleh, S. F.; Riayatsyah, T. M. I.; Aditiya, H. B.; Mahlia, T. M. I.

2016-03-01

Lignocellulosic biomass is one of the promising feedstocks for bioethanol production. The process starts from pre-treatment, hydrolysis, fermentation, distillation and finally obtaining the final product, ethanol. The efficiency of enzymatic hydrolysis of cellulosic biomass depends heavily on the effectiveness of the pre-treatment step which main function is to break the lignin structure of the biomass. This work aims to investigate the effects of dilute acid pre-treatment on the enzymatic hydrolysis of durian seeds waste to glucose and the subsequent bioethanol fermentation process. The yield of glucose from dilute acid pre-treated sample using 0.6% H2SO4 and 5% substrate concentration shows significant value of 23.4951 g/L. Combination of dilute acid pre-treatment and enzymatic hydrolysis using 150U of enzyme able to yield 50.0944 g/L of glucose content higher compared to normal pre-treated sample of 8.1093 g/L. Dilute acid pre-treatment sample also shows stable and efficient yeast activity during fermentation process with lowest glucose content at 2.9636 g/L compared to 14.7583g/L for normal pre-treated sample. Based on the result, it can be concluded that dilute acid pre-treatment increase the yield of ethanol from bioethanol production process.

Epidemic processes in complex networks

Science.gov (United States)

Pastor-Satorras, Romualdo; Castellano, Claudio; Van Mieghem, Piet; Vespignani, Alessandro

2015-07-01

In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world networks have a profound impact on the behavior of equilibrium and nonequilibrium phenomena occurring in various systems, and the study of epidemic spreading is central to our understanding of the unfolding of dynamical processes in complex networks. The theoretical analysis of epidemic spreading in heterogeneous networks requires the development of novel analytical frameworks, and it has produced results of conceptual and practical relevance. A coherent and comprehensive review of the vast research activity concerning epidemic processes is presented, detailing the successful theoretical approaches as well as making their limits and assumptions clear. Physicists, mathematicians, epidemiologists, computer, and social scientists share a common interest in studying epidemic spreading and rely on similar models for the description of the diffusion of pathogens, knowledge, and innovation. For this reason, while focusing on the main results and the paradigmatic models in infectious disease modeling, the major results concerning generalized social contagion processes are also presented. Finally, the research activity at the forefront in the study of epidemic spreading in coevolving, coupled, and time-varying networks is reported.

Reproducible cancer biomarker discovery in SELDI-TOF MS using different pre-processing algorithms.

Directory of Open Access Journals (Sweden)

Jinfeng Zou

Full Text Available BACKGROUND: There has been much interest in differentiating diseased and normal samples using biomarkers derived from mass spectrometry (MS studies. However, biomarker identification for specific diseases has been hindered by irreproducibility. Specifically, a peak profile extracted from a dataset for biomarker identification depends on a data pre-processing algorithm. Until now, no widely accepted agreement has been reached. RESULTS: In this paper, we investigated the consistency of biomarker identification using differentially expressed (DE peaks from peak profiles produced by three widely used average spectrum-dependent pre-processing algorithms based on SELDI-TOF MS data for prostate and breast cancers. Our results revealed two important factors that affect the consistency of DE peak identification using different algorithms. One factor is that some DE peaks selected from one peak profile were not detected as peaks in other profiles, and the second factor is that the statistical power of identifying DE peaks in large peak profiles with many peaks may be low due to the large scale of the tests and small number of samples. Furthermore, we demonstrated that the DE peak detection power in large profiles could be improved by the stratified false discovery rate (FDR control approach and that the reproducibility of DE peak detection could thereby be increased. CONCLUSIONS: Comparing and evaluating pre-processing algorithms in terms of reproducibility can elucidate the relationship among different algorithms and also help in selecting a pre-processing algorithm. The DE peaks selected from small peak profiles with few peaks for a dataset tend to be reproducibly detected in large peak profiles, which suggests that a suitable pre-processing algorithm should be able to produce peaks sufficient for identifying useful and reproducible biomarkers.

Data pre-processing: a case study in predicting student's retention in ...

African Journals Online (AJOL)

dataset with features that are ready for data mining task. The study also proposed a process model and suggestions, which can be applied to support more comprehensible tools for educational domain who is the end user. Subsequently, the data pre-processing become more efficient for predicting student's retention in ...

How does a scanning ribosomal particle move along the 5'-untranslated region of eukaryotic mRNA? Brownian Ratchet model.

Science.gov (United States)

Spirin, Alexander S

2009-11-17

A model of the ATP-dependent unidirectional movement of the 43S ribosomal initiation complex (=40S ribosomal subunit + eIF1 + eIF1A + eIF2.GTP.Met-tRNA(i) + eIF3) during scanning of the 5'-untranslated region of eukaryotic mRNA is proposed. The model is based on the principles of molecular Brownian ratchet machines and explains several enigmatic data concerning the scanning complex. In this model, the one-dimensional diffusion of the ribosomal initiation complex along the mRNA chain is rectified into the net-unidirectional 5'-to-3' movement by the Feynman ratchet-and-pawl mechanism. The proposed mechanism is organized by the heterotrimeric protein eIF4F (=eIF4A + eIF4E + eIF4G), attached to the scanning ribosomal particle via eIF3, and the RNA-binding protein eIF4B that is postulated to play the role of the pawl. The energy for the useful work of the ratchet-and-pawl mechanism is supplied from ATP hydrolysis induced by the eIF4A subunit: ATP binding and its hydrolysis alternately change the affinities of eIF4A for eIF4B and for mRNA, resulting in the restriction of backward diffusional sliding of the 43S ribosomal complex along the mRNA chain, while stochastic movements ahead are allowed.

Presence of albumin mRNA precursors in nuclei of analbuminemic rat liver lacking cytoplasmic albumin mRNA.

OpenAIRE

Esumi, H; Takahashi, Y; Sekiya, T; Sato, S; Nagase, S; Sugimura, T

1982-01-01

Analbuminemic rats, which lack serum albumin, were previously found to have no albumin mRNA in the cytoplasm of the liver. In the present study, the existence of nuclear albumin mRNA precursors in the liver of analbuminemic rats was examined by RNA X cDNA hybridization kinetics. Albumin mRNA precursors were present in the nuclei of analbuminemic rat liver at almost normal levels, despite the absence of albumin mRNA from the cytoplasm. Nuclear RNA of analbuminemic rat liver was subjected to el...

Summary of ENDF/B Pre-Processing Codes June 1983

International Nuclear Information System (INIS)

Cullen, D.E.

1983-06-01

This is the summary documentation for the 1983 version of the ENDF/B Pre-Processing Codes LINEAR, RECENT, SIGMA1, GROUPIE, EVALPLOT, MERGER, DICTION, COMPLOT, CONVERT. This summary documentation is merely a copy of the comment cards that appear at the beginning of each programme; these comment cards always reflect the latest status of input options, etc

Heritability in the efficiency of nonsense-mediated mRNA decay in humans.

LENUS (Irish Health Repository)

Seoighe, Cathal

2010-01-01

BACKGROUND: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. PRINCIPAL FINDINGS: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. CONCLUSIONS: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3.

Heritability in the efficiency of nonsense-mediated mRNA decay in humans

KAUST Repository

Seoighe, Cathal

2010-07-21

Background: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. Principal Findings: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. Conclusions: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3. © 2010 Seoighe, Gehring.

Improvement of Haramay Fiber by Pre-treatment of Retting Process withPhosphoric Acid

International Nuclear Information System (INIS)

Kuntari-Sasas; Neni-Rustini Eriawati

2000-01-01

Haramay as bast fiber contains of cellulose fiber as the main part, mixedwith hemi cellulose, pectin, and lignin as binding material for cellulosefiber to keep it together in the bundle form. For textile material, this bastfiber has to be freed from its binding material, called as retting process,before subjecting to scouring, dyeing and finishing process in textileindustry. In the retting process the dissolve of binding material can be doneeither by using enzyme in bio technology or extraction with strong alkalinecondition in common technology. Using sodium hydroxide for dissolving thebinding material can be carried out easily with good dissolving ability, butcan render the strength retention of the cellulose fiber. Pre-treatment ofthe bast fiber with phosphoric acid (H 3 PO 4 ), is expected to hydrolyze someof the binding materials that can not be dissolved in alkaline condition,including natural pigment that colored the fiber with creamy white. In thisstudy, the pre-treatment process before retting with phosphoric acid wascarried out in various condition, such as concentration of phosphoric acid (5ml/l- 25 ml/l), time and temperature of pre-treatment (1-3 hours at 50 o C or12-24 hours at room temperature), followed by neutralization in dilutealkaline. The retting process was carried out by means of scouring in variousconcentration of sodium hydroxide (NaOH 38 o Be, 10 ml/l-30 m/l), and then wascontinued with bleaching process in hydrogen peroxide solution. Aftercarrying out those experiment, the bast fiber that called haramay wassubjected to testing for weight reduction, strength retention and degree ofwhiteness. From the testing results it is concluded that pre-treatment withphosphoric acid can increase the weight reduction, strength retention ortenacity and degree of whiteness of haramay fiber compared to the oneswithout pre-treatment with phosphoric acid. The best result was obtained bypre-treatment with 5 ml/l H 3 PO 4 at 50 o C for 2 hours, continued by

LARP6 Meets Collagen mRNA: Specific Regulation of Type I Collagen Expression

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Yujie Zhang

2016-03-01

Full Text Available Type I collagen is the most abundant structural protein in all vertebrates, but its constitutive rate of synthesis is low due to long half-life of the protein (60–70 days. However, several hundred fold increased production of type I collagen is often seen in reparative or reactive fibrosis. The mechanism which is responsible for this dramatic upregulation is complex, including multiple levels of regulation. However, posttranscriptional regulation evidently plays a predominant role. Posttranscriptional regulation comprises processing, transport, stabilization and translation of mRNAs and is executed by RNA binding proteins. There are about 800 RNA binding proteins, but only one, La ribonucleoprotein domain family member 6 (LARP6, is specifically involved in type I collagen regulation. In the 5′untranslated region (5’UTR of mRNAs encoding for type I and type III collagens there is an evolutionally conserved stem-loop (SL structure; this structure is not found in any other mRNA, including any other collagen mRNA. LARP6 binds to the 5′SL in sequence specific manner to regulate stability of collagen mRNAs and their translatability. Here, we will review current understanding of how is LARP6 involved in posttranscriptional regulation of collagen mRNAs. We will also discuss how other proteins recruited by LARP6, including nonmuscle myosin, vimentin, serine threonine kinase receptor associated protein (STRAP, 25 kD FK506 binding protein (FKBP25 and RNA helicase A (RHA, contribute to this process.

Triage of Women with Low-Grade Cervical Lesions - HPV mRNA Testing versus Repeat Cytology

Science.gov (United States)

Sørbye, Sveinung Wergeland; Arbyn, Marc; Fismen, Silje; Gutteberg, Tore Jarl; Mortensen, Elin Synnøve

2011-01-01

Background In Norway, women with low-grade squamous intraepithelial lesions (LSIL) are followed up after six months in order to decide whether they should undergo further follow-up or be referred back to the screening interval of three years. A high specificity and positive predictive value (PPV) of the triage test is important to avoid unnecessary diagnostic and therapeutic procedures. Materials and Methods At the University Hospital of North Norway, repeat cytology and the HPV mRNA test PreTect HPV-Proofer, detecting E6/E7 mRNA from HPV types 16, 18, 31, 33 and 45, are used in triage of women with ASC-US and LSIL. In this study, women with LSIL cytology in the period 2005–2008 were included (n = 522). Two triage methods were evaluated in two separate groups: repeat cytology only (n = 225) and HPV mRNA testing in addition to repeat cytology (n = 297). Histologically confirmed cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) was used as the study endpoint. Results Of 522 women with LSIL, 207 had biopsies and 125 of them had CIN2+. The sensitivity and specificity of repeat cytology (ASC-US or worse) were 85.7% (95% confidence interval (CI): 72.1, 92.2) and 54.4 % (95% CI: 46.9, 61.9), respectively. The sensitivity and specificity of the HPV mRNA test were 94.2% (95% CI: 88.7, 99.7) and 86.0% (95% CI: 81.5, 90.5), respectively. The PPV of repeat cytology was 38.4% (95% CI: 29.9, 46.9) compared to 67.0% (95% CI: 57.7, 76.4) of the HPV mRNA test. Conclusion HPV mRNA testing was more sensitive and specific than repeat cytology in triage of women with LSIL cytology. In addition, the HPV mRNA test showed higher PPV. These data indicate that the HPV mRNA test is a better triage test for women with LSIL than repeat cytology. PMID:21918682

Targeted siRNA Delivery and mRNA Knockdown Mediated by Bispecific Digoxigenin-binding Antibodies

Directory of Open Access Journals (Sweden)

Britta Schneider

2012-01-01

Full Text Available Bispecific antibodies (bsAbs that bind to cell surface antigens and to digoxigenin (Dig were used for targeted small interfering RNA (siRNA delivery. They are derivatives of immunoglobulins G (IgGs that bind tumor antigens, such as Her2, IGF1-R, CD22, and LeY, with stabilized Dig-binding variable domains fused to the C-terminal ends of the heavy chains. siRNA that was digoxigeninylated at its 3′end was bound in a 2:1 ratio to the bsAbs. These bsAb–siRNA complexes delivered siRNAs specifically to cells that express the corresponding antigen as demonstrated by flow cytometry and confocal microscopy. The complexes internalized into endosomes and Dig-siRNAs separated from bsAbs, but Dig-siRNA was not released into the cytoplasm; bsAb-targeting alone was thus not sufficient for effective mRNA knockdown. This limitation was overcome by formulating the Dig-siRNA into nanoparticles consisting of dynamic polyconjugates (DPCs or into lipid-based nanoparticles (LNPs. The resulting complexes enabled bsAb-targeted siRNA-specific messenger RNA (mRNA knockdown with IC50 siRNA values in the low nanomolar range for a variety of bsAbs, siRNAs, and target cells. Furthermore, pilot studies in mice bearing tumor xenografts indicated mRNA knockdown in endothelial cells following systemic co-administration of bsAbs and siRNA formulated in LNPs that were targeted to the tumor vasculature.

CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast.

Science.gov (United States)

Nguyen, Thi Hoang Duong; Galej, Wojciech P; Fica, Sebastian M; Lin, Pei-Chun; Newman, Andrew J; Nagai, Kiyoshi

2016-02-01

The spliceosome is formed on pre-mRNA substrates from five small nuclear ribonucleoprotein particles (U1, U2, U4/U6 and U5 snRNPs), and numerous non-snRNP factors. Saccharomyces cerevisiae U4/U6.U5 tri-snRNP comprises U5 snRNA, U4/U6 snRNA duplex and approximately 30 proteins and represents a substantial part of the spliceosome before activation. Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex is a post-catalytic intron lariat spliceosome containing U2 and U5 snRNPs, NTC (nineteen complex), NTC-related proteins (NTR), U6 snRNA, and an RNA intron lariat. Two recent papers describe near-complete atomic structures of these complexes based on cryoEM single-particle analysis. The U4/U6.U5 tri-snRNP structure provides crucial insight into the activation mechanism of the spliceosome. The U2.U6.U5 complex reveals the striking architecture of NTC and NTR and important features of the group II intron-like catalytic RNA core remaining after spliced mRNA is released. These two structures greatly advance our understanding of the mechanism of pre-mRNA splicing. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Repeated exposure to cat urine induces complex behavioral, hormonal, and c-fos mRNA responses in Norway rats ( Rattus norvegicus)

Science.gov (United States)

Yin, Baofa; Gu, Chen; Lu, Yi; Hegab, Ibrahim M.; Yang, Shengmei; Wang, Aiqin; Wei, Wanhong

2017-08-01

Prey species show specific adaptations that allow recognition, avoidance, and defense against predators. This study was undertaken to investigate the processing of a chronic, life-threatening stimulus to Norway rats ( Rattus norvegicus). One hundred forty-four Norway rats were tested by repeated presentation of cat urine for 1 h at different days in a defensive withdrawal apparatus. Rats exposed to urine for short periods showed significantly larger defensive behavioral and medial hypothalamic c-fos messenger RNA (mRNA) responses than other groups. These defensive responses habituated shortly after the presentation of cat urine. Serum levels of adrenocorticotropic hormone and corticosterone increased significantly when animals were repeatedly exposed to cat urine. However, the hormonal responses took longer to habituate than the behavioral and molecular responses did. We conclude that the behavioral and c-fos mRNA responses are "primed" for habituation to repeated exposures to cat urine, while the hormonal responses show "resistance." The results support our hypothesis that the strongest anti-predator responses at three levels would occur during short-term exposure to cat urine and that these responses would subsequently disappear on prolonged exposure. This study assists understanding the way in which the different levels of defensive responses are integrated and react during chronic stress.

A novel pre-oxidation method for elemental mercury removal utilizing a complex vaporized absorbent

Energy Technology Data Exchange (ETDEWEB)

Zhao, Yi, E-mail: zhaoyi9515@163.com; Hao, Runlong; Guo, Qing

2014-09-15

Graphical abstract: - Highlights: • An innovative liquid-phase complex absorbent (LCA) for Hg{sup 0} removal was prepared. • A novel integrative process for Hg{sup 0} removal was proposed. • The simultaneous removal efficiencies of SO{sub 2}, NO and Hg{sup 0} were 100%, 79.5% and 80.4%, respectively. • The reaction mechanism of simultaneous removal of SO{sub 2}, NO and Hg{sup 0} was proposed. - Abstract: A novel semi-dry integrative method for elemental mercury (Hg{sup 0}) removal has been proposed in this paper, in which Hg{sup 0} was initially pre-oxidized by a vaporized liquid-phase complex absorbent (LCA) composed of a Fenton reagent, peracetic acid (CH{sub 3}COOOH) and sodium chloride (NaCl), after which Hg{sup 2+} was absorbed by the resultant Ca(OH){sub 2}. The experimental results indicated that CH{sub 3}COOOH and NaCl were the best additives for Hg{sup 0} oxidation. Among the influencing factors, the pH of the LCA and the adding rate of the LCA significantly affected the Hg{sup 0} removal. The coexisting gases, SO{sub 2} and NO, were characterized as either increasing or inhibiting in the removal process, depending on their concentrations. Under optimal reaction conditions, the efficiency for the single removal of Hg{sup 0} was 91%. Under identical conditions, the efficiencies of the simultaneous removal of SO{sub 2}, NO and Hg{sup 0} were 100%, 79.5% and 80.4%, respectively. Finally, the reaction mechanism for the simultaneous removal of SO{sub 2}, NO and Hg{sup 0} was proposed based on the characteristics of the removal products as determined by X-ray diffraction (XRD), atomic fluorescence spectrometry (AFS), the analysis of the electrode potentials, and through data from related research references.

Kinetin improves IKBKAP mRNA splicing in patients with familial dysautonomia

Science.gov (United States)

Axelrod, Felicia B.; Liebes, Leonard; Gold-von Simson, Gabrielle; Mendoza, Sandra; Mull, James; Leyne, Maire; Norcliffe-Kaufmann, Lucy; Kaufmann, Horacio; Slaugenhaupt, Susan A.

2011-01-01

Familial dysautonomia (FD) is caused by an intronic splice mutation in the IKBKAP gene that leads to partial skipping of exon 20 and tissue-specific reduction in I-κ-B kinase complex associated protein/ elongation protein 1 (IKAP/ELP-1) expression. Kinetin (6-furfurylaminopurine) has been shown to improve splicing and increase wild-type IKBKAP mRNA and IKAP protein expression in FD cell lines and carriers. To determine if oral kinetin treatment could alter mRNA splicing in FD subjects and was tolerable, we administered kinetin to eight FD individuals homozygous for the splice mutation. Subjects received 23.5 mg/Kg/day for 28 days. An increase in wild-type IKBKAP mRNA expression in leukocytes was noted after eight days in six of eight individuals; after 28 days the mean increase as compared to baseline was significant (p=0.002). We have demonstrated that kinetin is tolerable in this medically fragile population. Not only did kinetin produce the desired effect on splicing in FD patients, but also that effect appears to improve with time despite lack of dose change. This is the first report of a drug that produces in vivo mRNA splicing changes in individuals with FD and supports future long-term trials to determine if kinetin will prove therapeutic in FD patients. PMID:21775922

Poisson pre-processing of nonstationary photonic signals: Signals with equality between mean and variance.

Science.gov (United States)

Poplová, Michaela; Sovka, Pavel; Cifra, Michal

2017-01-01

Photonic signals are broadly exploited in communication and sensing and they typically exhibit Poisson-like statistics. In a common scenario where the intensity of the photonic signals is low and one needs to remove a nonstationary trend of the signals for any further analysis, one faces an obstacle: due to the dependence between the mean and variance typical for a Poisson-like process, information about the trend remains in the variance even after the trend has been subtracted, possibly yielding artifactual results in further analyses. Commonly available detrending or normalizing methods cannot cope with this issue. To alleviate this issue we developed a suitable pre-processing method for the signals that originate from a Poisson-like process. In this paper, a Poisson pre-processing method for nonstationary time series with Poisson distribution is developed and tested on computer-generated model data and experimental data of chemiluminescence from human neutrophils and mung seeds. The presented method transforms a nonstationary Poisson signal into a stationary signal with a Poisson distribution while preserving the type of photocount distribution and phase-space structure of the signal. The importance of the suggested pre-processing method is shown in Fano factor and Hurst exponent analysis of both computer-generated model signals and experimental photonic signals. It is demonstrated that our pre-processing method is superior to standard detrending-based methods whenever further signal analysis is sensitive to variance of the signal.

The Ratios of Pre-emulsified Duck Skin for Optimized Processing of Restructured Ham.

Science.gov (United States)

Shim, Jae-Yun; Kim, Tae-Kyung; Kim, Young-Boong; Jeon, Ki-Hong; Ahn, Kwang-Il; Paik, Hyun-Dong; Choi, Yun-Sang

2018-02-01

The purpose of this study was to investigate the quality of duck ham formulated with duck skin through the pre-emulsification process. The experiments to investigate the quality characteristics of duck ham were carried out to measure proximate composition, cooking loss, emulsion stability, pH, color, texture profile analysis, apparent viscosity, and sensory characteristics. Duck ham was prepared with various ratios of duck skin in pre-emulsion as follows: Control (duct skin 30%), T1 (duck skin 20% + pre-emulsified duck skin 10%), T2 (duck skin 15% + pre-emulsified duck skin 15%), T3 (duck skin 10% + pre-emulsified duck skin 20%), and T4 (pre-emulsified duck skin 30%). As the ratio of duck skin to pre-emulsified skin changed, the quality of duck ham in terms of moisture content, fat content, cooking loss, emulsion stability, lightness, textural analysis, apparent viscosity, and overall acceptability changed. The moisture content of T2 was the highest ( p ham and 1:1 ratio of duck skin and pre-emulsified skin was the proper ratio to improve the quality characteristics of duck ham.

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana.

Science.gov (United States)

Branco-Price, Cristina; Kaiser, Kayla A; Jang, Charles J H; Larive, Cynthia K; Bailey-Serres, Julia

2008-12-01

Cellular oxygen deprivation (hypoxia/anoxia) requires an acclimation response that enables survival during an energy crisis. To gain new insights into the processes that facilitate the endurance of transient oxygen deprivation, the dynamics of the mRNA translation state and metabolites were quantitatively monitored in Arabidopsis thaliana seedlings exposed to a short (2 h) or prolonged (9 h) period of oxygen and carbon dioxide deprivation and following 1 h of re-aeration. Hypoxia stress and reoxygenation promoted adjustments in the levels of polyribosomes (polysomes) that were highly coordinated with cellular ATP content. A quantitative comparison of steady-state and polysomal mRNA populations revealed that over half of the cellular mRNAs were restricted from polysome complexes during the stress, with little or no change in abundance. This selective repression of translation was rapidly reversed upon reoxygenation. Comparison of the adjustment in gene transcripts and metabolites demonstrated that profiling of polysomal mRNAs strongly augments the prediction of cellular processes that are altered during cellular oxygen deprivation. The selective translation of a subset of mRNAs promotes the conservation of ATP and facilitates the transition to anaerobic metabolism during low-oxygen stress.

How Do Pre-Service Teachers' Reflective Processes Differ in Relation to Different Contexts?

Science.gov (United States)

Kaasila, Raimo; Lauriala, Anneli

2012-01-01

Reflective practice represents a central theme in teacher education. The focus of this study is to look at pre-service teachers' reflection processes and their breadth and depth in four different contexts. Our research data consist of 53 pre-service teachers' mathematics portfolios, from which three were selected for closer scrutiny. The chosen…

The Problem-Based Learning Process: Reflections of Pre-Service Elementary School Teachers

Science.gov (United States)

Baysal, Zeliha Nurdan

2017-01-01

This study aims to identify the benefits acquired by third-year pre-service elementary school teachers participating in a problem-based learning process in social studies education, the issues they encountered in that process and those they are likely to encounter, and their feelings about the process. Semi-structured interviews were used as one…

Effectiveness acidic pre-cleaning for copper-gold ore

Directory of Open Access Journals (Sweden)

Antonio Clareti Pereira

Full Text Available Abstract The presence of copper-bearing minerals is known to bring on many challenges during the cyanidation of gold ore, like high consumption of cyanide and low extraction of metal, which are undesirable impacts on the auriferous recovery in the subsequent process step. The high copper solubility in cyanide prevents the direct use of classical hydrometallurgical processes for the extraction of gold by cyanidation. Additionally, the application of a conventional flotation process to extract copper is further complicated when it is oxidized. As a result, an acid pre-leaching process was applied in order to clean the ore of these copper minerals that are cyanide consumers. The objective was to evaluate the amount of soluble copper in cyanide before and after acidic cleaning. From a gold ore containing copper, the study selected four samples containing 0.22%, 0.55%, 1.00% and 1.36% of copper. For direct cyanidation of the ore without pre-treatment, copper extraction by cyanide complexing ranged from 8 to 83%. In contrast, the pre-treatment carried out with sulfuric acid extracted 24% to 99% of initial copper and subsequent cyanidation extracted 0.13 to 1.54% of initial copper. The study also showed that the copper contained in the secondary minerals is more easily extracted by cyanide (83%, being followed by the copper oxy-hydroxide minerals (60%, while the copper contained in the manganese oxide is less complexed by cyanide (8% a 12%. It was possible to observe that minerals with low acid solubility also have low solubility in cyanide. Cyanide consumption decreased by about 2.5 times and gold recovery increased to above 94% after acidic pre-cleaning.

A single bout of whole-leg, peristaltic pulse external pneumatic compression upregulates PGC-1α mRNA and endothelial nitric oxide sythase protein in human skeletal muscle tissue.

Science.gov (United States)

Kephart, Wesley C; Mobley, C Brooks; Fox, Carlton D; Pascoe, David D; Sefton, JoEllen M; Wilson, Trent J; Goodlett, Michael D; Kavazis, Andreas N; Roberts, Michael D; Martin, Jeffrey S

2015-07-01

What is the central question of this study? Does 60 min of peristaltic pulse external pneumatic compression (EPC) alter gene and protein expression patterns related to metabolism, vascular biology, redox balance and inflammation in vastus lateralis biopsy samples? What is the main finding and its importance? A single bout of EPC transiently upregulates PGC-1α mRNA, while also upregulating endothelial nitric oxide synthase protein and nitric oxide metabolite concentrations in vastus lateralis biopsy samples. We investigated whether a single 60 min bout of whole-leg, lower pressure external pneumatic compression (EPC) altered select vascular, metabolic, antioxidant and inflammation-related mRNAs. Ten participants (eight male, two female; aged 22.0 ± 0.4 years) reported to the laboratory 4 h postprandial, and vastus lateralis muscle biopsies were obtained before (PRE) and 1 and 4 h after EPC treatment. Messenger RNA expression was analysed using real-time RT-PCR, and significant mRNA findings were investigated further by Western blot analysis of respective protein concentrations. Peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) mRNA increased by 77% 1 h following EPC compared with PRE levels (P = 0.005), but no change in protein concentration 1 or 4 h post-EPC was observed. Increases in endothelial nitric oxide sythase (eNOS) mRNA (+44%) and superoxide dismutase 2 (SOD2) mRNA (+57%) 1 h post-EPC as well as an increase in interleukin-10 mRNA (+132%) 4 h post-EPC compared with PRE levels were observed, but only approached significance (P = 0.076, 0.077 and 0.074, respectively). Interestingly, eNOS protein (+40%, P = 0.025) and nitrate and nitrite (NOx) concentrations (+69%, P = 0.025) increased 1-4 h post-EPC. Moreover, SOD2 protein tended to increase from PRE to 4 h post-EPC (+43%, P = 0.074), although no changes in tissue 4-hydroxnonenal levels was observed. An acute bout of EPC transiently upregulates PGC-1α mRNA, while also upregulating e

Pre-processing data using wavelet transform and PCA based on ...

Indian Academy of Sciences (India)

Abazar Solgi

2017-07-14

Jul 14, 2017 ... Pre-processing data using wavelet transform and PCA based on support vector regression and gene expression programming for river flow simulation. Abazar Solgi1,*, Amir Pourhaghi1, Ramin Bahmani2 and Heidar Zarei3. 1. Department of Water Resources Engineering, Shahid Chamran University of ...

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

Science.gov (United States)

Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka-Weng; Wang, Jinfan; Petrov, Alexey; Prabhakar, Arjun; Rechavi, Gideon; Dominissini, Dan; He, Chuan; Ehrenberg, Måns; Puglisi, Joseph D

2018-03-01

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

The MARVEL domain protein, Singles Bar, is required for progression past the pre-fusion complex stage of myoblast fusion.

Science.gov (United States)

Estrada, Beatriz; Maeland, Anne D; Gisselbrecht, Stephen S; Bloor, James W; Brown, Nicholas H; Michelson, Alan M

2007-07-15

Multinucleated myotubes develop by the sequential fusion of individual myoblasts. Using a convergence of genomic and classical genetic approaches, we have discovered a novel gene, singles bar (sing), that is essential for myoblast fusion. sing encodes a small multipass transmembrane protein containing a MARVEL domain, which is found in vertebrate proteins involved in processes such as tight junction formation and vesicle trafficking where--as in myoblast fusion--membrane apposition occurs. sing is expressed in both founder cells and fusion competent myoblasts preceding and during myoblast fusion. Examination of embryos injected with double-stranded sing RNA or embryos homozygous for ethane methyl sulfonate-induced sing alleles revealed an identical phenotype: replacement of multinucleated myofibers by groups of single, myosin-expressing myoblasts at a stage when formation of the mature muscle pattern is complete in wild-type embryos. Unfused sing mutant myoblasts form clusters, suggesting that early recognition and adhesion of these cells are unimpaired. To further investigate this phenotype, we undertook electron microscopic ultrastructural studies of fusing myoblasts in both sing and wild-type embryos. These experiments revealed that more sing mutant myoblasts than wild-type contain pre-fusion complexes, which are characterized by electron-dense vesicles paired on either side of the fusing plasma membranes. In contrast, embryos mutant for another muscle fusion gene, blown fuse (blow), have a normal number of such complexes. Together, these results lead to the hypothesis that sing acts at a step distinct from that of blow, and that sing is required on both founder cell and fusion-competent myoblast membranes to allow progression past the pre-fusion complex stage of myoblast fusion, possibly by mediating fusion of the electron-dense vesicles to the plasma membrane.

Altered brain mechanisms of emotion processing in pre-manifest Huntington's disease.

Science.gov (United States)

Novak, Marianne J U; Warren, Jason D; Henley, Susie M D; Draganski, Bogdan; Frackowiak, Richard S; Tabrizi, Sarah J

2012-04-01

Huntington's disease is an inherited neurodegenerative disease that causes motor, cognitive and psychiatric impairment, including an early decline in ability to recognize emotional states in others. The pathophysiology underlying the earliest manifestations of the disease is not fully understood; the objective of our study was to clarify this. We used functional magnetic resonance imaging to investigate changes in brain mechanisms of emotion recognition in pre-manifest carriers of the abnormal Huntington's disease gene (subjects with pre-manifest Huntington's disease): 16 subjects with pre-manifest Huntington's disease and 14 control subjects underwent 1.5 tesla magnetic resonance scanning while viewing pictures of facial expressions from the Ekman and Friesen series. Disgust, anger and happiness were chosen as emotions of interest. Disgust is the emotion in which recognition deficits have most commonly been detected in Huntington's disease; anger is the emotion in which impaired recognition was detected in the largest behavioural study of emotion recognition in pre-manifest Huntington's disease to date; and happiness is a positive emotion to contrast with disgust and anger. Ekman facial expressions were also used to quantify emotion recognition accuracy outside the scanner and structural magnetic resonance imaging with voxel-based morphometry was used to assess the relationship between emotion recognition accuracy and regional grey matter volume. Emotion processing in pre-manifest Huntington's disease was associated with reduced neural activity for all three emotions in partially separable functional networks. Furthermore, the Huntington's disease-associated modulation of disgust and happiness processing was negatively correlated with genetic markers of pre-manifest disease progression in distributed, largely extrastriatal networks. The modulated disgust network included insulae, cingulate cortices, pre- and postcentral gyri, precunei, cunei, bilateral putamena

Fluorescence Correlation Spectroscopy to find the critical balance between extracellular association and intracellular dissociation of mRNA-complexes.

Science.gov (United States)

Zhang, Heyang; De Smedt, Stefaan C; Remaut, Katrien

2018-05-10

Fluorescence Correlation Spectroscopy (FCS) is a promising tool to study interactions on a single molecule level. The diffusion of fluorescent molecules in and out of the excitation volume of a confocal microscope leads to the fluorescence fluctuations that give information on the average number of fluorescent molecules present in the excitation volume and their diffusion coefficients. In this context, we complexed mRNA into lipoplexes and polyplexes and explored the association/dissociation degree of complexes by using gel electrophoresis and FCS. FCS enabled us to measure the association and dissociation degree of mRNA-based complexes both in buffer and protein-rich biological fluids such as human serum and ascitic fluid, which is a clear advantage over gel electrophoresis that was only applicable in protein-free buffer solutions. Furthermore, following the complex stability in buffer and biological fluids by FCS assisted to understand how complex characteristics, such as charge ratio and strength of mRNA binding, correlated to the transfection efficiency. We found that linear polyethyleneimine prevented efficient translation of mRNA, most likely due to a too strong mRNA binding, whereas the lipid based carrier Lipofectamine ® messengerMAX did succeed in efficient release and subsequent translation of mRNA in the cytoplasm of the cells. Overall, FCS is a reliable tool for the in depth characterization of mRNA complexes and can help us to find the critical balance keeping mRNA bound in complexes in the extracellular environment and efficient intracellular mRNA release leading to protein production. The delivery of messenger RNA (mRNA) to cells is promising to treat a variety of diseases. Therefore, the mRNA is typically packed in small lipid particles or polymer particles that help the mRNA to reach the cytoplasm of the cells. These particles should bind and carry the mRNA in the extracellular environment (e.g. blood, peritoneal fluid, ...), but should release

Process and device for automatically surveying complex installations

International Nuclear Information System (INIS)

Pekrul, P.J.; Thiele, A.W.

1976-01-01

A description is given of a process for automatically analysing separate signal processing channels in real time, one channel per signal, in a facility with significant background noise in signals varying in time and coming from transducers at selected points for the continuous monitoring of the operating conditions of the various components of the installation. The signals are intended to determine potential breakdowns, determine conclusions as to the severity of these potential breakdowns and indicate to an operator the measures to be taken in consequence. The feature of this process is that it comprises the automatic and successive selection of each channel for the purpose of spectral analysis, the automatic processing of the signal of each selected channel to show energy spectrum density data at pre-determined frequencies, the automatic comparison of the energy spectrum density data of each channel with pre-determined sets of limits varying with the frequency, and the automatic indication to the operator of the condition of the various components of the installation associated to each channel and the measures to be taken depending on the set of limits [fr

Reprogramming the Dynamin 2 mRNA by Spliceosome-mediated RNA Trans-splicing

Directory of Open Access Journals (Sweden)

Delphine Trochet

2016-01-01

Full Text Available Dynamin 2 (DNM2 is a large GTPase, ubiquitously expressed, involved in membrane trafficking and regulation of actin and microtubule cytoskeletons. DNM2 mutations cause autosomal dominant centronuclear myopathy which is a rare congenital myopathy characterized by skeletal muscle weakness and histopathological features including nuclear centralization in absence of regeneration. No curative treatment is currently available for the DNM2-related autosomal dominant centronuclear myopathy. In order to develop therapeutic strategy, we evaluated here the potential of Spliceosome-Mediated RNA Trans-splicing technology to reprogram the Dnm2-mRNA in vitro and in vivo in mice. We show that classical 3′-trans-splicing strategy cannot be considered as accurate therapeutic strategy regarding toxicity of the pre-trans-splicing molecules leading to low rate of trans-splicing in vivo. Thus, we tested alternative strategies devoted to prevent this toxicity and enhance frequency of trans-splicing events. We succeeded to overcome the toxicity through a 5′-trans-splicing strategy which also allows detection of trans-splicing events at mRNA and protein levels in vitro and in vivo. These results suggest that the Spliceosome-Mediated RNA Trans-splicing strategy may be used to reprogram mutated Dnm2-mRNA but highlight the potential toxicity linked to the molecular tools which have to be carefully investigated during preclinical development.

Scientific data products and the data pre-processing subsystem of the Chang'e-3 mission

International Nuclear Information System (INIS)

Tan Xu; Liu Jian-Jun; Li Chun-Lai; Feng Jian-Qing; Ren Xin; Wang Fen-Fei; Yan Wei; Zuo Wei; Wang Xiao-Qian; Zhang Zhou-Bin

2014-01-01

The Chang'e-3 (CE-3) mission is China's first exploration mission on the surface of the Moon that uses a lander and a rover. Eight instruments that form the scientific payloads have the following objectives: (1) investigate the morphological features and geological structures at the landing site; (2) integrated in-situ analysis of minerals and chemical compositions; (3) integrated exploration of the structure of the lunar interior; (4) exploration of the lunar-terrestrial space environment, lunar surface environment and acquire Moon-based ultraviolet astronomical observations. The Ground Research and Application System (GRAS) is in charge of data acquisition and pre-processing, management of the payload in orbit, and managing the data products and their applications. The Data Pre-processing Subsystem (DPS) is a part of GRAS. The task of DPS is the pre-processing of raw data from the eight instruments that are part of CE-3, including channel processing, unpacking, package sorting, calibration and correction, identification of geographical location, calculation of probe azimuth angle, probe zenith angle, solar azimuth angle, and solar zenith angle and so on, and conducting quality checks. These processes produce Level 0, Level 1 and Level 2 data. The computing platform of this subsystem is comprised of a high-performance computing cluster, including a real-time subsystem used for processing Level 0 data and a post-time subsystem for generating Level 1 and Level 2 data. This paper describes the CE-3 data pre-processing method, the data pre-processing subsystem, data classification, data validity and data products that are used for scientific studies

Enhancement of Pre-and Post-Processing Capability of the CUPID code

Energy Technology Data Exchange (ETDEWEB)

Kim, Jongtae; Park, Ik Kyu; Yoon, Hanyoung [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2014-05-15

To simulate heat transfer and fluid flow in a field with a complicated geometry, an unstructured mesh is popularly used. Most commercial CFD (Computational Fluid Dynamics) solvers are based on an unstructured mesh technology. An advantage of using unstructured meshes for a field simulation is reduced man-hours by automatic mesh generation compared to a traditional structured mesh generation, which requires a huge amount of man-hours to discretized a complex geometry. Initially, unstructured meshes that can be generated automatically are limited to regular cell elements such as tetrahedron, pyramid, prism, or hexahedron. The multi-dimensional multi-phase flow solver, CUPID, has been developed in the context of an unstructured mesh finite volume method (FVM). Its numerical formulation and programming structure is independent of the number of faces surrounding the computational cells. Thus, it can be easily extended into polyhedral unstructured meshes. In this study, new tools for enhancing the pre- and post-processing capabilities of CUPID are proposed. They are based on an open-source CFD tool box OpenFOAM. A goal of this study is an extension of the applicability of the CUPID code by improving the mesh and solution treatment of the code.

Complexity evaluation for the implementation of a pre-FFT equalizer in an OFDM receiver

OpenAIRE

Armour, SMD; Nix, AR

2000-01-01

A pre-FFT equalizer (PFE) has been shown to offer a significant throughput efficiency improvement when applied to an OFDM receiver. Alternatively, the PFE can be used to increase the maximum delay spread conditions under which the OFDM system can operate effectively. Due to the manner of its operation, the PFE requires the use of modified adaptation algorithms if iterative, decision directed, adaptation is required. The computational complexity required to implement a PFE and a suitable adapt...

Human papillomavirus mRNA and DNA testing in women with atypical squamous cells of undetermined significance

DEFF Research Database (Denmark)

Thomsen, Louise T; Dehlendorff, Christian; Junge, Jette

2016-01-01

In this prospective cohort study, we compared the performance of human papillomavirus (HPV) mRNA and DNA testing of women with atypical squamous cells of undetermined significance (ASC-US) during cervical cancer screening. Using a nationwide Danish pathology register, we identified women aged 30......-65 years with ASC-US during 2005-2011 who were tested for HPV16/18/31/33/45 mRNA using PreTect HPV-Proofer (n = 3,226) or for high-risk HPV (hrHPV) DNA using Hybrid Capture 2 (HC2) (n = 9,405) or Linear Array HPV-Genotyping test (LA) (n = 1,533). Women with ≥1 subsequent examination in the register (n = 13...... those testing HC2 negative (3.2% [95% CI: 2.2-4.2%] versus 0.5% [95% CI: 0.3-0.7%]). Patterns were similar after 18 months and 5 years'; follow-up; for CIN2+ and cancer as outcomes; across all age groups; and when comparing mRNA testing to hrHPV DNA testing using LA. In conclusion, the HPV16...

Increased shelterin mRNA expression in peripheral blood mononuclear cells and skeletal muscle following an ultra-long-distance running event

DEFF Research Database (Denmark)

Laye, Matthew J; Solomon, Thomas; Karstoft, Kristian

2012-01-01

. In this study, we examine the mRNA and protein levels of proteins within and associated with the shelterin complex in subjects (n = 8, mean age = 44 yr) who completed a physiological stress of seven marathons in 7 days. Twenty-two to 24 h after the last marathon, subjects had increased mRNA levels of DNA repair...

Real-time monitoring of clinical processes using complex event processing and transition systems.

Science.gov (United States)

Meinecke, Sebastian

2014-01-01

Dependencies between tasks in clinical processes are often complex and error-prone. Our aim is to describe a new approach for the automatic derivation of clinical events identified via the behaviour of IT systems using Complex Event Processing. Furthermore we map these events on transition systems to monitor crucial clinical processes in real-time for preventing and detecting erroneous situations.

Optimization of treaining process in pre-start fencing training on the base of out-of-training means’ of mobilization orientation application

Directory of Open Access Journals (Sweden)

G.O. Lopatenko

2016-04-01

Full Text Available Purpose: to show effectiveness of out-of- training means of mobilization orientation in pre-start preparation of elite fencers. Material: in the research 12 elite sportsmen-fencers participated. Results: it was found that under influence of the worked out pre-start complex (during 15-18 minutes, comparing with traditional warming up (40 minutes more expressed mobilization effect was registered. This effect also lasted longer time. Higher stimulating effects of pre-start complex are proved by confident differences in sportsmen’s special workability (p -0.05. Conclusions: the achieved stimulating effects reduced duration of general warming up to twenty minutes. It permits to more rationally organize pre-start training of fencers in comparison with application of traditional means.

Pre-writing Techniques In The Writing Process For The L2 Classroom

OpenAIRE

Gülşah Geyimci

2014-01-01

This study investigated pre-writing techniques in the learning process to improve written communication skills of learners using qualitative research methods. This study was performed in a public school, Suphi Öner Primary School in Turkey, in Mersin. Students were seventh grade class that their level was pre-intermediate. This class was made up of twenty students. It took three weeks, the students' samples, drawings and blogs were documented by the students. In order to examine the results, ...

The ApaH-like phosphatase TbALPH1 is the major mRNA decapping enzyme of trypanosomes.

Directory of Open Access Journals (Sweden)

Susanne Kramer

2017-06-01

Full Text Available 5'-3' decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5'-3' exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5'-3' degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1 as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding. A fraction of ALPH1 co-localises exclusively with the trypanosome 5'-3' exoribonuclease XRNA to a special granule at the posterior pole of the cell, indicating a connection between the two enzymes. RNAi depletion of ALPH1 is lethal and causes a massive increase in total mRNAs that are deadenylated, but have not yet started 5'-3' decay. These data suggest that ALPH1 acts downstream of deadenylation and upstream of mRNA degradation, consistent with a function in mRNA decapping. In vitro experiments show that recombinant, N-terminally truncated ALHP1 protein, but not a catalytically inactive mutant, sensitises the capped trypanosome spliced leader RNA to yeast Xrn1, but only if an RNA 5' polyphosphatase is included. This indicates that the decapping mechanism of ALPH1 differs from the decapping mechanism of Dcp2 by leaving more than one phosphate group at the mRNA's 5' end. This is the first reported function of a eukaryotic ApaH-like phosphatase, a bacterial-derived class of enzymes present in all phylogenetic super-groups of the eukaryotic kingdom. The substrates of eukaryotic ApaH-like phosphatases are unknown. However, the substrate of the related bacterial enzyme ApaH, diadenosine tetraphosphate, is highly reminiscent of a eukaryotic mRNA cap.

Discrete pre-processing step effects in registration-based pipelines, a preliminary volumetric study on T1-weighted images.

Science.gov (United States)

Muncy, Nathan M; Hedges-Muncy, Ariana M; Kirwan, C Brock

2017-01-01

Pre-processing MRI scans prior to performing volumetric analyses is common practice in MRI studies. As pre-processing steps adjust the voxel intensities, the space in which the scan exists, and the amount of data in the scan, it is possible that the steps have an effect on the volumetric output. To date, studies have compared between and not within pipelines, and so the impact of each step is unknown. This study aims to quantify the effects of pre-processing steps on volumetric measures in T1-weighted scans within a single pipeline. It was our hypothesis that pre-processing steps would significantly impact ROI volume estimations. One hundred fifteen participants from the OASIS dataset were used, where each participant contributed three scans. All scans were then pre-processed using a step-wise pipeline. Bilateral hippocampus, putamen, and middle temporal gyrus volume estimations were assessed following each successive step, and all data were processed by the same pipeline 5 times. Repeated-measures analyses tested for a main effects of pipeline step, scan-rescan (for MRI scanner consistency) and repeated pipeline runs (for algorithmic consistency). A main effect of pipeline step was detected, and interestingly an interaction between pipeline step and ROI exists. No effect for either scan-rescan or repeated pipeline run was detected. We then supply a correction for noise in the data resulting from pre-processing.

The design and development of a complex multifactorial falls assessment intervention for falls prevention: The Prevention of Falls Injury Trial (PreFIT).

Science.gov (United States)

Bruce, Julie; Ralhan, Shvaita; Sheridan, Ray; Westacott, Katharine; Withers, Emma; Finnegan, Susanne; Davison, John; Martin, Finbarr C; Lamb, Sarah E

2017-06-01

This paper describes the design and development of a complex multifactorial falls prevention (MFFP) intervention for implementation and testing within the framework of a large UK-based falls prevention randomised controlled trial (RCT). A complex intervention was developed for inclusion within the Prevention of Falls Injury Trial (PreFIT), a multicentre pragmatic RCT. PreFIT aims to compare the clinical and cost-effectiveness of three alternative primary care falls prevention interventions (advice, exercise and MFFP), on outcomes of fractures and falls. Community-dwelling adults, aged 70 years and older, were recruited from primary care in the National Health Service (NHS), England. Development of the PreFIT MFFP intervention was informed by the existing evidence base and clinical guidelines for the assessment and management of falls in older adults. After piloting and modification, the final MFFP intervention includes seven falls risk factors: a detailed falls history interview with consideration of 'red flags'; assessment of balance and gait; vision; medication screen; cardiac screen; feet and footwear screen and home environment assessment. This complex intervention has been fully manualised with clear, documented assessment and treatment pathways for each risk factor. Each risk factor is assessed in every trial participant referred for MFFP. Referral for assessment is based upon a screening survey to identify those with a history of falling or balance problems. Intervention delivery can be adapted to the local setting. This complex falls prevention intervention is currently being tested within the framework of a large clinical trial. This paper adheres to TIDieR and CONSORT recommendations for the comprehensive and explicit reporting of trial interventions. Results from the PreFIT study will be published in due course. The effectiveness and cost-effectiveness of the PreFIT MFFP intervention, compared to advice and exercise, on the prevention of falls and

Learning processes of students in competence based pre-vocational secondary education

NARCIS (Netherlands)

Koopman, M.; Teune, P.J.; Beijaard, D.; Brok, den P.J.

2009-01-01

The purpose of this study was to validate a causal and hierarchical model to elaborate on the relation between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education-students. This model can be used to describe students'

Learning processes of students in competence-based pre-vocational secondary education

NARCIS (Netherlands)

prof dr Douwe Beijaard; Dr. M. Koopman; P. den Brok; Dr P.J. Teune

2008-01-01

The purpose of this study was to validate a causal and hierarchical model that describes the relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education-students (n=719; 14 schools). Preferences of students for

Chronic intermittent hypoxia alters local respiratory circuit function at the level of the preBötzinger complex

Directory of Open Access Journals (Sweden)

Alfredo J Garcia

2016-02-01

Full Text Available Chronic intermittent hypoxia (CIH is a common state experienced in several breathing disorders, including obstructive sleep apnea (OSA and apneas of prematurity. Unraveling how CIH affects the CNS, and in turn how the CNS contributes to apneas is perhaps the most challenging task. The preBötzinger complex (preBötC is a pre-motor respiratory network critical for inspiratory rhythm generation. Here, we test the hypothesis that CIH increases irregular output from the isolated preBötC, which can be mitigated by antioxidant treatment. Electrophysiological recordings from brainstem slices revealed that CIH enhanced burst-to-burst irregularity in period and/or amplitude. Irregularities represented a change in individual fidelity among preBötC neurons, and changed transmission from preBötC to the hypoglossal motor nucleus (XIIn, which resulted in increased transmission failure to XIIn. CIH increased the degree of lipid peroxidation in the preBötC and treatment with the antioxidant, 5,10,15,20-Tetrakis (1-methylpyridinium-4-yl-21H,23H-porphyrin manganese(III pentachloride (MnTMPyP, reduced CIH-mediated irregularities on the network rhythm and improved transmission of preBötC to the XIIn. These findings suggest that CIH promotes a pro-oxidant state that destabilizes rhythmogenesis originating from the preBötC and changes the local rhythm generating circuit which in turn, can lead to intermittent transmission failure to the XIIn. We propose that these CIH-mediated effects represent a part of the central mechanism that may perpetuate apneas and respiratory instability, which are hallmark traits in several dysautonomic conditions.

Human apolipoprotein B (apoB) mRNA: Identification of two distinct apoB mRNAs, an mRNA with the apoB-100 sequence and an apoB mRNA containing a premature in-frame translational stop codon, in both liver and intestine

International Nuclear Information System (INIS)

Higuchi, K.; Hospattankar, A.V.; Law, S.W.; Meglin, N.; Cortright, J.; Brewer, H.B. Jr.

1988-01-01

Human apolipoprotein B (apoB) is present in plasma as two separate isoproteins, designated apoB-100 (512 kDa) and apoB-48 (250 kDa). ApoB is encoded by a single gene on chromosome 2, and a single nuclear mRNA is edited and processed into two separate apoB mRNAs. A 14.1-kilobase apoB mRNA codes for apoB-100, and the second mRNA, which codes for apoB-48, contains a premature stop codon generated by a single base substitution of cytosine to uracil at nucleotide 6,538, which converts the translated CAA codon coding for the amino acid glutamine at residue 2,153 in apoB-100 to a premature in-frame stop codon (UAA). Two 30-base synthetic oligonucleotides, designated apoB-Stop and apoB-Gln, were synthesized containing the complementary sequence to the stop codon (UAA) and glutamine codon (CAA), respectively. The combined results from these studies establish that both human intestine and liver contain the two distinct apoB mRNAs, an mRNA that codes for apoB-100 and an apoB mRNA that contains the premature stop codon, which codes for apoB-48. The premature in-frame stop codon is not tissue specific and is present in both human liver and intestine

A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons.

Science.gov (United States)

Vidaki, Marina; Drees, Frauke; Saxena, Tanvi; Lanslots, Erwin; Taliaferro, Matthew J; Tatarakis, Antonios; Burge, Christopher B; Wang, Eric T; Gertler, Frank B

2017-08-02

During neuronal development, local mRNA translation is required for axon guidance and synaptogenesis, and dysregulation of this process contributes to multiple neurodevelopmental and cognitive disorders. However, regulation of local protein synthesis in developing axons remains poorly understood. Here, we uncover a novel role for the actin-regulatory protein Mena in the formation of a ribonucleoprotein complex that involves the RNA-binding proteins HnrnpK and PCBP1 and regulates local translation of specific mRNAs in developing axons. We find that translation of dyrk1a, a Down syndrome- and autism spectrum disorders-related gene, is dependent on Mena, both in steady-state conditions and upon BDNF stimulation. We identify hundreds of additional mRNAs that associate with the Mena complex, suggesting that it plays broader role(s) in post-transcriptional gene regulation. Our work establishes a dual role for Mena in neurons, providing a potential link between regulation of actin dynamics and local translation. Copyright © 2017 Elsevier Inc. All rights reserved.

Pre-eruptive magmatic processes re-timed using a non-isothermal approach to magma chamber dynamics.

Science.gov (United States)

Petrone, Chiara Maria; Bugatti, Giuseppe; Braschi, Eleonora; Tommasini, Simone

2016-10-05

Constraining the timescales of pre-eruptive magmatic processes in active volcanic systems is paramount to understand magma chamber dynamics and the triggers for volcanic eruptions. Temporal information of magmatic processes is locked within the chemical zoning profiles of crystals but can be accessed by means of elemental diffusion chronometry. Mineral compositional zoning testifies to the occurrence of substantial temperature differences within magma chambers, which often bias the estimated timescales in the case of multi-stage zoned minerals. Here we propose a new Non-Isothermal Diffusion Incremental Step model to take into account the non-isothermal nature of pre-eruptive processes, deconstructing the main core-rim diffusion profiles of multi-zoned crystals into different isothermal steps. The Non-Isothermal Diffusion Incremental Step model represents a significant improvement in the reconstruction of crystal lifetime histories. Unravelling stepwise timescales at contrasting temperatures provides a novel approach to constraining pre-eruptive magmatic processes and greatly increases our understanding of magma chamber dynamics.

Comparison of HPV detection technologies: Hybrid capture 2, PreTect HPV-Proofer and analysis of HPV DNA viral load in HPV16, HPV18 and HPV33 E6/E7 mRNA positive specimens.

LENUS (Irish Health Repository)

Keegan, Helen

2012-02-01

Human papillomavirus (HPV) testing using molecular methods in liquid based cytology (LBC) specimens may be useful as an adjunct to cervical screening by cytology. We compared the positivity rate of the commercially available HPV DNA method hybrid capture 2 (hc2) and the commercially available E6\\/E7 mRNA method PreTect HPV-Proofer in cytological specimens (n=299). LBC specimens collected (n=299) represented the following cervical cytological disease categories: Normal (n=60), borderline nuclear abnormalities (BNA) (n=34), CIN1 (n=121), CIN2 (n=60), CIN3 (n=24). Overall, 69% (205\\/299) of the cases were positive by hc2 and 38% (112\\/299) of the cases were positive by PreTect HPV-Proofer. Concordance rates between the two tests were highest in the high-grade cytology cases (CIN2: 67% and CIN3: 83%) and the normal cytology cases (88%) and lowest in the BNA and CIN1 categories (56% and 52%). HPV DNA viral load analyses were carried out on HPV16 (n=55), HPV18 (n=9) and HPV33 (n=13) samples that were positive by PreTect HPV-Proofer. The sensitivity and specificity of PreTect HPV-Proofer and the hc2 DNA test for the detection of high-grade cytology (i.e. CIN2+) were 71.4% and 75.8% vs 100% and 43.7%, respectively. The relatively low detection rate observed by PreTect HPV-Proofer in the whole range of cytological positive cases, combined with a relatively higher specificity and PPV, suggests that PreTect HPV-Proofer may be more useful than hc2 for triage and in predicting high-grade disease.

Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA stabilization during T-cell activation

DEFF Research Database (Denmark)

Chen, C Y; Gherzi, R; Andersen, Jens S.

2000-01-01

Regulated mRNA turnover is a highly important process, but its mechanism is poorly understood. Using interleukin-2 (IL-2) mRNA as a model, we described a role for the JNK-signaling pathway in stabilization of IL-2 mRNA during T-cell activation, acting via a JNK response element (JRE) in the 5' un...

Modelling of information processes management of educational complex

Directory of Open Access Journals (Sweden)

Оксана Николаевна Ромашкова

2014-12-01

Full Text Available This work concerns information model of the educational complex which includes several schools. A classification of educational complexes formed in Moscow is given. There are also a consideration of the existing organizational structure of the educational complex and a suggestion of matrix management structure. Basic management information processes of the educational complex were conceptualized.

Visual perception of complex shape-transforming processes.

Science.gov (United States)

Schmidt, Filipp; Fleming, Roland W

2016-11-01

Morphogenesis-or the origin of complex natural form-has long fascinated researchers from practically every branch of science. However, we know practically nothing about how we perceive and understand such processes. Here, we measured how observers visually infer shape-transforming processes. Participants viewed pairs of objects ('before' and 'after' a transformation) and identified points that corresponded across the transformation. This allowed us to map out in spatial detail how perceived shape and space were affected by the transformations. Participants' responses were strikingly accurate and mutually consistent for a wide range of non-rigid transformations including complex growth-like processes. A zero-free-parameter model based on matching and interpolating/extrapolating the positions of high-salience contour features predicts the data surprisingly well, suggesting observers infer spatial correspondences relative to key landmarks. Together, our findings reveal the operation of specific perceptual organization processes that make us remarkably adept at identifying correspondences across complex shape-transforming processes by using salient object features. We suggest that these abilities, which allow us to parse and interpret the causally significant features of shapes, are invaluable for many tasks that involve 'making sense' of shape. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Natural selection and algorithmic design of mRNA.

Science.gov (United States)

Cohen, Barry; Skiena, Steven

2003-01-01

Messenger RNA (mRNA) sequences serve as templates for proteins according to the triplet code, in which each of the 4(3) = 64 different codons (sequences of three consecutive nucleotide bases) in RNA either terminate transcription or map to one of the 20 different amino acids (or residues) which build up proteins. Because there are more codons than residues, there is inherent redundancy in the coding. Certain residues (e.g., tryptophan) have only a single corresponding codon, while other residues (e.g., arginine) have as many as six corresponding codons. This freedom implies that the number of possible RNA sequences coding for a given protein grows exponentially in the length of the protein. Thus nature has wide latitude to select among mRNA sequences which are informationally equivalent, but structurally and energetically divergent. In this paper, we explore how nature takes advantage of this freedom and how to algorithmically design structures more energetically favorable than have been built through natural selection. In particular: (1) Natural Selection--we perform the first large-scale computational experiment comparing the stability of mRNA sequences from a variety of organisms to random synonymous sequences which respect the codon preferences of the organism. This experiment was conducted on over 27,000 sequences from 34 microbial species with 36 genomic structures. We provide evidence that in all genomic structures highly stable sequences are disproportionately abundant, and in 19 of 36 cases highly unstable sequences are disproportionately abundant. This suggests that the stability of mRNA sequences is subject to natural selection. (2) Artificial Selection--motivated by these biological results, we examine the algorithmic problem of designing the most stable and unstable mRNA sequences which code for a target protein. We give a polynomial-time dynamic programming solution to the most stable sequence problem (MSSP), which is asymptotically no more complex

Quantitative analysis of ribosome–mRNA complexes at different translation stages

Science.gov (United States)

Shirokikh, Nikolay E.; Alkalaeva, Elena Z.; Vassilenko, Konstantin S.; Afonina, Zhanna A.; Alekhina, Olga M.; Kisselev, Lev L.; Spirin, Alexander S.

2010-01-01

Inhibition of primer extension by ribosome–mRNA complexes (toeprinting) is a proven and powerful technique for studying mechanisms of mRNA translation. Here we have assayed an advanced toeprinting approach that employs fluorescently labeled DNA primers, followed by capillary electrophoresis utilizing standard instruments for sequencing and fragment analysis. We demonstrate that this improved technique is not merely fast and cost-effective, but also brings the primer extension inhibition method up to the next level. The electrophoretic pattern of the primer extension reaction can be characterized with a precision unattainable by the common toeprint analysis utilizing radioactive isotopes. This method allows us to detect and quantify stable ribosomal complexes at all stages of translation, including initiation, elongation and termination, generated during the complete translation process in both the in vitro reconstituted translation system and the cell lysate. We also point out the unique advantages of this new methodology, including the ability to assay sites of the ribosomal complex assembly on several mRNA species in the same reaction mixture. PMID:19910372

Investigating Pre-service Mathematics Teachers’ Geometric Problem Solving Process in Dynamic Geometry Environment

Directory of Open Access Journals (Sweden)

Deniz Özen

2013-03-01

Full Text Available The aim of this study is to investigate pre-service elementary mathematics teachers’ open geometric problem solving process in a Dynamic Geometry Environment. With its qualitative inquiry based research design employed, the participants of the study are three pre-service teachers from 4th graders of the Department of Elementary Mathematics Teaching. In this study, clinical interviews, screencaptures of the problem solving process in the Cabri Geomery Environment, and worksheets included 2 open geometry problems have been used to collect the data. It has been investigated that all the participants passed through similar recursive phases as construction, exploration, conjecture, validate, and justification in the problem solving process. It has been thought that this study provide a new point of view to curriculum developers, teachers and researchers

A pp32-retinoblastoma protein complex modulates androgen receptor-mediated transcription and associates with components of the splicing machinery

International Nuclear Information System (INIS)

Adegbola, Onikepe; Pasternack, Gary R.

2005-01-01

We have previously shown pp32 and the retinoblastoma protein interact. pp32 and the retinoblastoma protein are nuclear receptor transcriptional coregulators: the retinoblastoma protein is a coactivator for androgen receptor, the major regulator of prostate cancer growth, while pp32, which is highly expressed in prostate cancer, is a corepressor of the estrogen receptor. We now show pp32 increases androgen receptor-mediated transcription and the retinoblastoma protein modulates this activity. Using affinity purification and mass spectrometry, we identify members of the pp32-retinoblastoma protein complex as PSF and nonO/p54nrb, proteins implicated in coordinate regulation of nuclear receptor-mediated transcription and splicing. We show that the pp32-retinoblastoma protein complex is modulated during TPA-induced K562 differentiation. Present evidence suggests that nuclear receptors assemble multiprotein complexes to coordinately regulate transcription and mRNA processing. Our results suggest that pp32 and the retinoblastoma protein may be part of a multiprotein complex that coordinately regulates nuclear receptor-mediated transcription and mRNA processing

The modification of siRNA with 3' cholesterol to increase nuclease protection and suppression of native mRNA by select siRNA polyplexes.

Science.gov (United States)

Ambardekar, Vishakha V; Han, Huai-Yun; Varney, Michelle L; Vinogradov, Serguei V; Singh, Rakesh K; Vetro, Joseph A

2011-02-01

Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3' cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. Copyright © 2010 Elsevier Ltd. All rights reserved.

Effect of pre-processing on the physico-chemical properties of ...

African Journals Online (AJOL)

The findings indicated that the pre-processing treatments produced significant differences (p < 0.05) in protein (1.50 ± 0.18g/100g) and carbohydrate (1.09 ± 0.94g/100g) composition of the baking soda blanched milk sample. The viscosity of the baking soda blanched milk (18.91 ± 3.38cps) was significantly higher than that ...

Gradation of complexity and predictability of hydrological processes

Science.gov (United States)

Sang, Yan-Fang; Singh, Vijay P.; Wen, Jun; Liu, Changming

2015-06-01

Quantification of the complexity and predictability of hydrological systems is important for evaluating the impact of climate change on hydrological processes, and for guiding water activities. In the literature, the focus seems to have been on describing the complexity of spatiotemporal distribution of hydrological variables, but little attention has been paid to the study of complexity gradation, because the degree of absolute complexity of hydrological systems cannot be objectively evaluated. Here we show that complexity and predictability of hydrological processes can be graded into three ranks (low, middle, and high). The gradation is based on the difference in the energy distribution of hydrological series and that of white noise under multitemporal scales. It reflects different energy concentration levels and contents of deterministic components of the hydrological series in the three ranks. Higher energy concentration level reflects lower complexity and higher predictability, but scattered energy distribution being similar to white noise has the highest complexity and is almost unpredictable. We conclude that the three ranks (low, middle, and high) approximately correspond to deterministic, stochastic, and random hydrological systems, respectively. The result of complexity gradation can guide hydrological observations and modeling, and identification of similarity patterns among different hydrological systems.

Pre-analytic process control: projecting a quality image.

Science.gov (United States)

Serafin, Mark D

2006-09-26

Within the health-care system, the term "ancillary department" often describes the laboratory. Thus, laboratories may find it difficult to define their image and with it, customer perception of department quality. Regulatory requirements give laboratories who so desire an elegant way to address image and perception issues--a comprehensive pre-analytic system solution. Since large laboratories use such systems--laboratory service manuals--I describe and illustrate the process for the benefit of smaller facilities. There exist resources to help even small laboratories produce a professional service manual--an elegant solution to image and customer perception of quality.

[Effects of lipopolysaccharides extracted from Porphyromonas endodontalis on the expression of IL-1beta mRNA and IL-6 mRNA in osteoblasts].

Science.gov (United States)

Yang, Di; Li, Ren; Qiu, Li-Hong; Li, Chen

2009-04-01

To quantify the IL-1 beta mRNA and IL-6 mRNA expression induced by lipopolysaccharides (LPS)extracted from Porphyromonas endodontalis(P.e) in osteoblasts, and to relate P.e-LPS to bone absorption pathogenesis in lesions of chronical apical periodontitis. MG63 was treated with different concentrations of P.e-LPS(0-50 microg/mL) for different hours(0-24h). The expression of IL-1 beta mRNA and IL-6 mRNA was detected by reverse transcription polymerase chain reaction (RT-PCR).Statistical analysis was performed using one- way ANOVA and Dunnett t test with SPSS11.0 software package. The level of IL-1 beta mRNA and IL-6 mRNA increased significantly after treatment with P.e-LPS at more than 5 microg/mL (P<0.01)and for more than 1 hour (P<0.01), which indicated that P.e-LPS induced osteoblasts to express IL-1 beta mRNA and IL-6 mRNA in dose and time dependent manners. P.e-LPS may promote bone resorption in lesions of chronical apical periodontitis by inducing IL-1 beta mRNA and IL-6 mRNA expression in osteoblasts.

EARLINET Single Calculus Chain - technical - Part 1: Pre-processing of raw lidar data

Science.gov (United States)

D'Amico, Giuseppe; Amodeo, Aldo; Mattis, Ina; Freudenthaler, Volker; Pappalardo, Gelsomina

2016-02-01

In this paper we describe an automatic tool for the pre-processing of aerosol lidar data called ELPP (EARLINET Lidar Pre-Processor). It is one of two calculus modules of the EARLINET Single Calculus Chain (SCC), the automatic tool for the analysis of EARLINET data. ELPP is an open source module that executes instrumental corrections and data handling of the raw lidar signals, making the lidar data ready to be processed by the optical retrieval algorithms. According to the specific lidar configuration, ELPP automatically performs dead-time correction, atmospheric and electronic background subtraction, gluing of lidar signals, and trigger-delay correction. Moreover, the signal-to-noise ratio of the pre-processed signals can be improved by means of configurable time integration of the raw signals and/or spatial smoothing. ELPP delivers the statistical uncertainties of the final products by means of error propagation or Monte Carlo simulations. During the development of ELPP, particular attention has been payed to make the tool flexible enough to handle all lidar configurations currently used within the EARLINET community. Moreover, it has been designed in a modular way to allow an easy extension to lidar configurations not yet implemented. The primary goal of ELPP is to enable the application of quality-assured procedures in the lidar data analysis starting from the raw lidar data. This provides the added value of full traceability of each delivered lidar product. Several tests have been performed to check the proper functioning of ELPP. The whole SCC has been tested with the same synthetic data sets, which were used for the EARLINET algorithm inter-comparison exercise. ELPP has been successfully employed for the automatic near-real-time pre-processing of the raw lidar data measured during several EARLINET inter-comparison campaigns as well as during intense field campaigns.

Translation initiation in bacterial polysomes through ribosome loading on a standby site on a highly translated mRNA

Science.gov (United States)

Andreeva, Irena

2018-01-01

During translation, consecutive ribosomes load on an mRNA and form a polysome. The first ribosome binds to a single-stranded mRNA region and moves toward the start codon, unwinding potential mRNA structures on the way. In contrast, the following ribosomes can dock at the start codon only when the first ribosome has vacated the initiation site. Here we show that loading of the second ribosome on a natural 38-nt-long 5′ untranslated region of lpp mRNA, which codes for the outer membrane lipoprotein from Escherichia coli, takes place before the leading ribosome has moved away from the start codon. The rapid formation of this standby complex depends on the presence of ribosomal proteins S1/S2 in the leading ribosome. The early recruitment of the second ribosome to the standby site before translation by the leading ribosome and the tight coupling between translation elongation by the first ribosome and the accommodation of the second ribosome can contribute to high translational efficiency of the lpp mRNA. PMID:29632209

CYP3A5 mRNA degradation by nonsense-mediated mRNA decay.

Science.gov (United States)

Busi, Florent; Cresteil, Thierry

2005-09-01

The total CYP3A5 mRNA level is significantly greater in carriers of the CYP3A5*1 allele than in CYP3A5*3 homozygotes. Most of the CYP3A5*3 mRNA includes an intronic sequence (exon 3B) containing premature termination codons (PTCs) between exons 3 and 4. Two models were used to investigate the degradation of CYP3A5 mRNA: a CYP3A5 minigene consisting of CYP3A5 exons and introns 3 to 6 transfected into MCF7 cells, and the endogenous CYP3A5 gene expressed in HepG2 cells. The 3'-untranslated region g.31611C>T mutation has no effect on CYP3A5 mRNA decay. Splice variants containing exon 3B were more unstable than wild-type (wt) CYP3A5 mRNA. Cycloheximide prevents the recognition of PTCs by ribosomes: in transfected MCF7 and HepG2 cells, cycloheximide slowed down the degradation of exon 3B-containing splice variants, suggesting the participation of nonsense-mediated decay (NMD). When PTCs were removed from pseudoexon 3B or when UPF1 small interfering RNA was used to impair the NMD mechanism, the decay of the splice variant was reduced, confirming the involvement of NMD in the degradation of CYP3A5 splice variants. Induction could represent a source of variability for CYP3A5 expression and could modify the proportion of splice variants. The extent of CYP3A5 induction was investigated after exposure to barbiturates or steroids: CYP3A4 was markedly induced in a pediatric population compared with untreated neonates. However, no effect could be detected in either the total CYP3A5 RNA, the proportion of splice variant RNA, or the protein level. Therefore, in these carriers, induction is unlikely to switch on the phenotypic CYP3A5 expression in carriers of CYP3A5*3/*3.

Processivity and coupling in messenger RNA transcription.

Directory of Open Access Journals (Sweden)

Stuart Aitken

2010-01-01

Full Text Available The complexity of messenger RNA processing is now being uncovered by experimental techniques that are capable of detecting individual copies of mRNA in cells, and by quantitative real-time observations that reveal the kinetics. This processing is commonly modelled by permitting mRNA to be transcribed only when the promoter is in the on state. In this simple on/off model, the many processes involved in active transcription are represented by a single reaction. These processes include elongation, which has a minimum time for completion and processing that is not captured in the model.In this paper, we explore the impact on the mRNA distribution of representing the elongation process in more detail. Consideration of the mechanisms of elongation leads to two alternative models of the coupling between the elongating polymerase and the state of the promoter: Processivity allows polymerases to complete elongation irrespective of the promoter state, whereas coupling requires the promoter to be active to produce a full-length transcript. We demonstrate that these alternatives have a significant impact on the predicted distributions. Models are simulated by the Gillespie algorithm, and the third and fourth moments of the resulting distribution are computed in order to characterise the length of the tail, and sharpness of the peak. By this methodology, we show that the moments provide a concise summary of the distribution, showing statistically-significant differences across much of the feasible parameter range.We conclude that processivity is not fully consistent with the on/off model unless the probability of successfully completing elongation is low--as has been observed. The results also suggest that some form of coupling between the promoter and a rate-limiting step in transcription may explain the cell's inability to maintain high mRNA levels at low noise--a prediction of the on/off model that has no supporting evidence.

The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma.

Science.gov (United States)

Tao, T; Sondalle, S B; Shi, H; Zhu, S; Perez-Atayde, A R; Peng, J; Baserga, S J; Look, A T

2017-07-06

The nucleolar factor, digestive organ expansion factor (DEF), has a key role in ribosome biogenesis, functioning in pre-ribosomal RNA (pre-rRNA) processing as a component of the small ribosomal subunit (SSU) processome. Here we show that the peripheral sympathetic nervous system (PSNS) is very underdeveloped in def-deficient zebrafish, and that def haploinsufficiency significantly decreases disease penetrance and tumor growth rate in a MYCN-driven transgenic zebrafish model of neuroblastoma that arises in the PSNS. Consistent with these findings, DEF is highly expressed in human neuroblastoma, and its depletion in human neuroblastoma cell lines induces apoptosis. Interestingly, overexpression of MYCN in zebrafish and in human neuroblastoma cells results in the appearance of intermediate pre-rRNAs species that reflect the processing of pre-rRNAs through Pathway 2, a pathway that processes pre-rRNAs in a different temporal order than the more often used Pathway 1. Our results indicate that DEF and possibly other components of the SSU processome provide a novel site of vulnerability in neuroblastoma cells that could be exploited for targeted therapy.

Contour extraction of echocardiographic images based on pre-processing

Energy Technology Data Exchange (ETDEWEB)

Hussein, Zinah Rajab; Rahmat, Rahmita Wirza; Abdullah, Lili Nurliyana [Department of Multimedia, Faculty of Computer Science and Information Technology, Department of Computer and Communication Systems Engineering, Faculty of Engineering University Putra Malaysia 43400 Serdang, Selangor (Malaysia); Zamrin, D M [Department of Surgery, Faculty of Medicine, National University of Malaysia, 56000 Cheras, Kuala Lumpur (Malaysia); Saripan, M Iqbal

2011-02-15

In this work we present a technique to extract the heart contours from noisy echocardiograph images. Our technique is based on improving the image before applying contours detection to reduce heavy noise and get better image quality. To perform that, we combine many pre-processing techniques (filtering, morphological operations, and contrast adjustment) to avoid unclear edges and enhance low contrast of echocardiograph images, after implementing these techniques we can get legible detection for heart boundaries and valves movement by traditional edge detection methods.

Contour extraction of echocardiographic images based on pre-processing

International Nuclear Information System (INIS)

Hussein, Zinah Rajab; Rahmat, Rahmita Wirza; Abdullah, Lili Nurliyana; Zamrin, D M; Saripan, M Iqbal

2011-01-01

In this work we present a technique to extract the heart contours from noisy echocardiograph images. Our technique is based on improving the image before applying contours detection to reduce heavy noise and get better image quality. To perform that, we combine many pre-processing techniques (filtering, morphological operations, and contrast adjustment) to avoid unclear edges and enhance low contrast of echocardiograph images, after implementing these techniques we can get legible detection for heart boundaries and valves movement by traditional edge detection methods.

Validation of DWI pre-processing procedures for reliable differentiation between human brain gliomas.

Science.gov (United States)

Vellmer, Sebastian; Tonoyan, Aram S; Suter, Dieter; Pronin, Igor N; Maximov, Ivan I

2018-02-01

Diffusion magnetic resonance imaging (dMRI) is a powerful tool in clinical applications, in particular, in oncology screening. dMRI demonstrated its benefit and efficiency in the localisation and detection of different types of human brain tumours. Clinical dMRI data suffer from multiple artefacts such as motion and eddy-current distortions, contamination by noise, outliers etc. In order to increase the image quality of the derived diffusion scalar metrics and the accuracy of the subsequent data analysis, various pre-processing approaches are actively developed and used. In the present work we assess the effect of different pre-processing procedures such as a noise correction, different smoothing algorithms and spatial interpolation of raw diffusion data, with respect to the accuracy of brain glioma differentiation. As a set of sensitive biomarkers of the glioma malignancy grades we chose the derived scalar metrics from diffusion and kurtosis tensor imaging as well as the neurite orientation dispersion and density imaging (NODDI) biophysical model. Our results show that the application of noise correction, anisotropic diffusion filtering, and cubic-order spline interpolation resulted in the highest sensitivity and specificity for glioma malignancy grading. Thus, these pre-processing steps are recommended for the statistical analysis in brain tumour studies. Copyright © 2017. Published by Elsevier GmbH.

Supervised pre-processing approaches in multiple class variables classification for fish recruitment forecasting

KAUST Repository

Fernandes, José Antonio

2013-02-01

A multi-species approach to fisheries management requires taking into account the interactions between species in order to improve recruitment forecasting of the fish species. Recent advances in Bayesian networks direct the learning of models with several interrelated variables to be forecasted simultaneously. These models are known as multi-dimensional Bayesian network classifiers (MDBNs). Pre-processing steps are critical for the posterior learning of the model in these kinds of domains. Therefore, in the present study, a set of \\'state-of-the-art\\' uni-dimensional pre-processing methods, within the categories of missing data imputation, feature discretization and feature subset selection, are adapted to be used with MDBNs. A framework that includes the proposed multi-dimensional supervised pre-processing methods, coupled with a MDBN classifier, is tested with synthetic datasets and the real domain of fish recruitment forecasting. The correctly forecasting of three fish species (anchovy, sardine and hake) simultaneously is doubled (from 17.3% to 29.5%) using the multi-dimensional approach in comparison to mono-species models. The probability assessments also show high improvement reducing the average error (estimated by means of Brier score) from 0.35 to 0.27. Finally, these differences are superior to the forecasting of species by pairs. © 2012 Elsevier Ltd.

Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation.

Science.gov (United States)

Tao, Wenjing; Sun, Lina; Shi, Hongjuan; Cheng, Yunying; Jiang, Dongneng; Fu, Beide; Conte, Matthew A; Gammerdinger, William J; Kocher, Thomas D; Wang, Deshou

2016-05-04

MicroRNAs (miRNAs) represent a second regulatory network that has important effects on gene expression and protein translation during biological process. However, the possible role of miRNAs in the early stages of fish sex differentiation is not well understood. In this study, we carried an integrated analysis of miRNA and mRNA expression profiles to explore their possibly regulatory patterns at the critical stage of sex differentiation in tilapia. We identified 279 pre-miRNA genes in tilapia genome, which were highly conserved in other fish species. Based on small RNA library sequencing, we identified 635 mature miRNAs in tilapia gonads, in which 62 and 49 miRNAs showed higher expression in XX and XY gonads, respectively. The predicted targets of these sex-biased miRNAs (e.g., miR-9, miR-21, miR-30a, miR-96, miR-200b, miR-212 and miR-7977) included genes encoding key enzymes in steroidogenic pathways (Cyp11a1, Hsd3b, Cyp19a1a, Hsd11b) and key molecules involved in vertebrate sex differentiation (Foxl2, Amh, Star1, Sf1, Dmrt1, and Gsdf). These genes also showed sex-biased expression in tilapia gonads at 5 dah. Some miRNAs (e.g., miR-96 and miR-737) targeted multiple genes involved in steroid synthesis, suggesting a complex miRNA regulatory network during early sex differentiation in this fish. The sequence and expression patterns of most miRNAs in tilapia are conserved in fishes, indicating the basic functions of vertebrate miRNAs might share a common evolutionary origin. This comprehensive analysis of miRNA and mRNA at the early stage of molecular sex differentiation in tilapia XX and XY gonads lead to the discovery of differentially expressed miRNAs and their putative targets, which will facilitate studies of the regulatory network of molecular sex determination and differentiation in fishes.

The Modification of siRNA with 3′ Cholesterol to Increase Nuclease Protection and Suppression of Native mRNA by Select siRNA Polyplexes

Science.gov (United States)

Ambardekar, Vishakha V.; Han, Huai-Yun; Varney, Michelle L.; Vinogradov, Serguei V.; Singh, Rakesh K.; Vetro, Joseph A.

2010-01-01

Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3′ cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. PMID:21047680

Growth inhibition of head and neck squamous cell carcinoma cells by sgRNA targeting the cyclin D1 mRNA based on TRUE gene silencing.

Directory of Open Access Journals (Sweden)

Satoshi Iizuka

Full Text Available Head and neck squamous cell carcinoma (HNSCC exhibits increased expression of cyclin D1 (CCND1. Previous studies have shown a correlation between poor prognosis of HNSCC and cyclin D1 overexpression. tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing is one of the RNA-mediated gene expression control technologies that have therapeutic potential. This technology is based on a unique enzymatic property of mammalian tRNase ZL, which is that it can cleave any target RNA at any desired site by recognizing a pre-tRNA-like complex formed between the target RNA and an artificial small guide RNA (sgRNA. In this study, we designed several sgRNAs targeting human cyclin D1 mRNA to examine growth inhibition of HNSCC cells. Transfection of certain sgRNAs decreased levels of cyclin D1 mRNA and protein in HSC-2 and HSC-3 cells, and also inhibited their proliferation. The combination of these sgRNAs and cisplatin showed more than additive inhibition of cancer cell growth. These findings demonstrate that TRUE gene silencing of cyclin D1 leads to inhibition of the growth of HNSCC cells and suggest that these sgRNAs alone or combined with cisplatin may be a useful new therapy for HNSCCs.

International Best Practices for Pre-Processing and Co-Processing Municipal Solid Waste and Sewage Sludge in the Cement Industry

Energy Technology Data Exchange (ETDEWEB)

Hasanbeigi, Ali [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lu, Hongyou [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Williams, Christopher [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Price, Lynn [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2012-07-01

The purpose of this report is to describe international best practices for pre-processing and coprocessing of MSW and sewage sludge in cement plants, for the benefit of countries that wish to develop co-processing capacity. The report is divided into three main sections. Section 2 describes the fundamentals of co-processing, Section 3 describes exemplary international regulatory and institutional frameworks for co-processing, and Section 4 describes international best practices related to the technological aspects of co-processing.

Investigating the Representational Fluency of Pre-Service Mathematics Teachers in a Modelling Process

Science.gov (United States)

Delice, Ali; Kertil, Mahmut

2015-01-01

This article reports the results of a study that investigated pre-service mathematics teachers' modelling processes in terms of representational fluency in a modelling activity related to a cassette player. A qualitative approach was used in the data collection process. Students' individual and group written responses to the mathematical modelling…

Inclusive Education as Complex Process and Challenge for School System

Directory of Open Access Journals (Sweden)

Al-Khamisy Danuta

2015-08-01

Full Text Available Education may be considered as a number of processes, actions and effects affecting human being, as the state or level of the results of these processes or as the modification of the functions, institutions and social practices roles, which in the result of inclusion become new, integrated system. Thus this is very complex process. Nowadays the complexity appears to be one of very significant terms both in science and in philosophy. It appears that despite searching for simple rules, strategies, solutions everything is still more complex. The environment is complex, the organism living in it and exploring it, and just the exploration itself is a complex phenomenon, much more than this could initially seem to be.

Recruitment of Staufen2 Enhances Dendritic Localization of an Intron-Containing CaMKIIα mRNA

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Raúl Ortiz

2017-07-01

Full Text Available Regulation of mRNA localization is a conserved cellular process observed in many types of cells and organisms. Asymmetrical mRNA distribution plays a particularly important role in the nervous system, where local translation of localized mRNA represents a key mechanism in synaptic plasticity. CaMKIIα is a very abundant mRNA detected in neurites, consistent with its crucial role at glutamatergic synapses. Here, we report the presence of CaMKIIα mRNA isoforms that contain intron i16 in dendrites, RNA granules, and synaptoneurosomes from primary neurons and brain. This subpopulation of unspliced mRNA preferentially localizes to distal dendrites in a synaptic-activity-dependent manner. Staufen2, a well-established marker of RNA transport in dendrites, interacts with intron i16 sequences and enhances its distal dendritic localization, pointing to the existence of intron-mediated mechanisms in the molecular pathways that modulate dendritic transport and localization of synaptic mRNAs.

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism.

Science.gov (United States)

Backlund, Michael; Paukku, Kirsi; Kontula, Kimmo K; Lehtonen, Jukka Y A

2016-04-20

As the formation of ribonucleoprotein complexes is a major mechanism of angiotensin II type 1 receptor (AT1R) regulation, we sought to identify novel AT1R mRNA binding proteins. By affinity purification and mass spectroscopy, we identified TIA-1. This interaction was confirmed by colocalization of AT1R mRNA and TIA-1 by FISH and immunofluorescence microscopy. In immunoprecipitates of endogenous TIA- 1, reverse transcription-PCR amplified AT1R mRNA. TIA-1 has two binding sites within AT1R 3'-UTR. The binding site proximal to the coding region is glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-dependent whereas the distal binding site is not. TIA-1 functions as a part of endoplasmic reticulum (ER) stress response leading to stress granule (SG) formation and translational silencing. We and others have shown that AT1R expression is increased by ER stress-inducing factors. In unstressed cells, TIA-1 binds to AT1R mRNA and decreases AT1R protein expression. Fluorescence microscopy shows that ER stress induced by thapsigargin leads to the transfer of TIA-1 to SGs. In FISH analysis AT1R mRNA remains in the cytoplasm and no longer colocalizes with TIA-1. Thus, release of TIA-1-mediated suppression by ER stress increases AT1R protein expression. In conclusion, AT1R mRNA is regulated by TIA-1 in a ER stress-dependent manner. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Impact of virtual chemistry laboratory instruction on pre-service science teachers’ scientific process skills

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Mutlu Ayfer

2016-01-01

Full Text Available This study aimed to investigate the impact of virtual chemistry laboratory instruction on pre-service science teachers’ scientific process skills. For this purpose, eight laboratory activities related to chemical kinetic, chemical equilibrium, thermochemistry, acids-bases, and electrochemistry were developed. Those activities were performed in virtual laboratory environment by the pre-service teachers in the experimental group and in the real laboratory environment by c the preservice teachers in the control group during eight weeks. Scientific process skills test developed by Burns, Okey and Wise [3], and translated into Turkish by Ateş and Bahar [2] was used before and after the instructions for data collection. According to results, while there was no significant difference between pre-test mean scores (U=133.500, p>0.05, significant difference between post-test mean scores was found in favour of experimental group (U=76.000, p<0.05. In addition, while no significant difference between pre-test mean scores for each sub-dimension was found, significant difference between post-test mean scores for designing investigation and formulating hypothesis skills was found in favour of experimental group.

SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function.

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Xiao-Peng Xiong

2015-08-01

Full Text Available microRNAs (miRNAs are a class of endogenous regulatory RNAs that play a key role in myriad biological processes. Upon transcription, primary miRNA transcripts are sequentially processed by Drosha and Dicer ribonucleases into ~22-24 nt miRNAs. Subsequently, miRNAs are incorporated into the RNA-induced silencing complexes (RISCs that contain Argonaute (AGO family proteins and guide RISC to target RNAs via complementary base pairing, leading to post-transcriptional gene silencing by a combination of translation inhibition and mRNA destabilization. Select pre-mRNA splicing factors have been implicated in small RNA-mediated gene silencing pathways in fission yeast, worms, flies and mammals, but the underlying molecular mechanisms are not well understood. Here, we show that SmD1, a core component of the Drosophila small nuclear ribonucleoprotein particle (snRNP implicated in splicing, is required for miRNA biogenesis and function. SmD1 interacts with both the microprocessor component Pasha and pri-miRNAs, and is indispensable for optimal miRNA biogenesis. Depletion of SmD1 impairs the assembly and function of the miRISC without significantly affecting the expression of major canonical miRNA pathway components. Moreover, SmD1 physically and functionally associates with components of the miRISC, including AGO1 and GW182. Notably, miRNA defects resulting from SmD1 silencing can be uncoupled from defects in pre-mRNA splicing, and the miRNA and splicing machineries are physically and functionally distinct entities. Finally, photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP analysis identifies numerous SmD1-binding events across the transcriptome and reveals direct SmD1-miRNA interactions. Our study suggests that SmD1 plays a direct role in miRNA-mediated gene silencing independently of its pre-mRNA splicing activity and indicates that the dual roles of splicing factors in post-transcriptional gene regulation may be

Extending Practical Pre-Aggregation in On-Line Analytical Processing

DEFF Research Database (Denmark)

Pedersen, Torben Bach; Jensen, Christian Søndergaard; Dyreson, Curtis E.

On-Line Analytical Processing (OLAP) based on a dimensional view of data is being used increasingly in traditional business applications as well as in applications such as health care for the purpose of analyzing very large amounts of data. Pre-aggregation, the prior materialization of aggregate...... select combinations of aggregates and then re-use these for efficiently computing other aggregates. However, this re-use of aggregates is contingent on the dimension hierarchies and the relationships between facts and dimensions satisfying stringent constraints. This severely limits the scope...

Binding of DEAD-box helicase Dhh1 to the 5'-untranslated region of ASH1 mRNA represses localized translation of ASH1 in yeast cells.

Science.gov (United States)

Zhang, Qianjun; Meng, Xiuhua; Li, Delin; Chen, Shaoyin; Luo, Jianmin; Zhu, Linjie; Singer, Robert H; Gu, Wei

2017-06-09

Local translation of specific mRNAs is regulated by dynamic changes in their subcellular localization, and these changes are due to complex mechanisms controlling cytoplasmic mRNA transport. The budding yeast Saccharomyces cerevisiae is well suited to studying these mechanisms because many of its transcripts are transported from the mother cell to the budding daughter cell. Here, we investigated the translational control of ASH1 mRNA after transport and localization. We show that although ASH1 transcripts were translated after they reached the bud tip, some mRNAs were bound by the RNA-binding protein Puf6 and were non-polysomal. We also found that the DEAD-box helicase Dhh1 complexed with the untranslated ASH1 mRNA and Puf6. Loss of Dhh1 affected local translation of ASH1 mRNA and resulted in delocalization of ASH1 transcript in the bud. Forcibly shifting the non-polysomal ASH1 mRNA into polysomes was associated with Dhh1 dissociation. We further demonstrated that Dhh1 is not recruited to ASH1 mRNA co-transcriptionally, suggesting that it could bind to ASH1 mRNA within the cytoplasm. Of note, Dhh1 bound to the 5'-UTR of ASH1 mRNA and inhibited its translation in vitro These results suggest that after localization to the bud tip, a portion of the localized ASH1 mRNA becomes translationally inactive because of binding of Dhh1 and Puf6 to the 5'- and 3'-UTRs of ASH1 mRNA. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Differences in metabolite profiles caused by pre-analytical blood processing procedures.

Science.gov (United States)

Nishiumi, Shin; Suzuki, Makoto; Kobayashi, Takashi; Yoshida, Masaru

2018-05-01

Recently, the use of metabolomic analysis of human serum and plasma for biomarker discovery and disease diagnosis in clinical studies has been increasing. The feasibility of using a metabolite biomarker for disease diagnosis is strongly dependent on the metabolite's stability during pre-analytical blood processing procedures, such as serum or plasma sampling and sample storage prior to centrifugation. However, the influence of blood processing procedures on the stability of metabolites has not been fully characterized. In the present study, we compared the levels of metabolites in matched human serum and plasma samples using gas chromatography coupled with mass spectrometry and liquid chromatography coupled with mass spectrometry. In addition, we evaluated the changes in plasma metabolite levels induced by storage at room temperature or at a cold temperature prior to centrifugation. As a result, it was found that 76 metabolites exhibited significant differences between their serum and plasma levels. Furthermore, the pre-centrifugation storage conditions significantly affected the plasma levels of 45 metabolites. These results highlight the importance of blood processing procedures during metabolome analysis, which should be considered during biomarker discovery and the subsequent use of biomarkers for disease diagnosis. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Effects of chemical-physical pre-treatment processes on hemp fibres for reinforcement of composites and textiles

DEFF Research Database (Denmark)

Thomsen, Anne Belinda; Thygesen, Anders; Bohn, Vibeke

2006-01-01

Retted hemp fibres were treated using chemical-physical pre-treatments and the material was characterised chemically in order to evaluate the effect of the pre-treatments, respectively, wet oxidation (WO), hydrothermal treatment (HT) and steam explosion (STEX). Process variables were addition...

Messenger RNA 3' end formation in plants.

Science.gov (United States)

Hunt, A G

2008-01-01

Messenger RNA 3' end formation is an integral step in the process that gives rise to mature, translated messenger RNAs in eukaryotes. With this step, a pre-messenger RNA is processed and polyadenylated, giving rise to a mature mRNA bearing the characteristic poly(A) tract. The poly(A) tract is a fundamental feature of mRNAs, participating in the process of translation initiation and being the focus of control mechanisms that define the lifetime of mRNAs. Thus messenger RNA 3' end formation impacts two steps in mRNA biogenesis and function. Moreover, mRNA 3' end formation is something of a bridge that integrates numerous other steps in mRNA biogenesis and function. While the process is essential for the expression of most genes, it is also one that is subject to various forms of regulation, such that both quantitative and qualitative aspects of gene expression may be modulated via the polyadenylation complex. In this review, the current status of understanding of mRNA 3' end formation in plants is discussed. In particular, the nature of mRNA 3' ends in plants is reviewed, as are recent studies that are beginning to yield insight into the functioning and regulation of plant polyadenylation factor subunits.

The Effect of an Instructional Intervention on Enhancement Pre-Service Science Teachers' Science Processes Skills

Science.gov (United States)

Durmaz, Hüsnüye

2016-01-01

The aim of this study is to investigate the effects of an instructional intervention on enhancement the pre-service science teachers' (PSTs) science process skills (SPSs) and to identify problems in using SPSs through Laboratory Applications in Science Education-I course (LASE-I). One group pretest-posttest pre-experimental design was employed. An…

Bioinspired nanocomplex for spatiotemporal imaging of sequential mRNA expression in differentiating neural stem cells.

Science.gov (United States)

Wang, Zhe; Zhang, Ruili; Wang, Zhongliang; Wang, He-Fang; Wang, Yu; Zhao, Jun; Wang, Fu; Li, Weitao; Niu, Gang; Kiesewetter, Dale O; Chen, Xiaoyuan

2014-12-23

Messenger RNA plays a pivotal role in regulating cellular activities. The expression dynamics of specific mRNA contains substantial information on the intracellular milieu. Unlike the imaging of stationary mRNAs, real-time intracellular imaging of the dynamics of mRNA expression is of great value for investigating mRNA biology and exploring specific cellular cascades. In addition to advanced imaging methods, timely extracellular stimulation is another key factor in regulating the mRNA expression repertoire. The integration of effective stimulation and imaging into a single robust system would significantly improve stimulation efficiency and imaging accuracy, producing fewer unwanted artifacts. In this study, we developed a multifunctional nanocomplex to enable self-activating and spatiotemporal imaging of the dynamics of mRNA sequential expression during the neural stem cell differentiation process. This nanocomplex showed improved enzymatic stability, fast recognition kinetics, and high specificity. With a mechanism regulated by endogenous cell machinery, this nanocomplex realized the successive stimulating motif release and the dynamic imaging of chronological mRNA expression during neural stem cell differentiation without the use of transgenetic manipulation. The dynamic imaging montage of mRNA expression ultimately facilitated genetic heterogeneity analysis. In vivo lateral ventricle injection of this nanocomplex enabled endogenous neural stem cell activation and labeling at their specific differentiation stages. This nanocomplex is highly amenable as an alternative tool to explore the dynamics of intricate mRNA activities in various physiological and pathological conditions.

The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing.

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Luis G Morello

Full Text Available NIP7 is one of the many trans-acting factors required for eukaryotic ribosome biogenesis, which interacts with nascent pre-ribosomal particles and dissociates as they complete maturation and are exported to the cytoplasm. By using conditional knockdown, we have shown previously that yeast Nip7p is required primarily for 60S subunit synthesis while human NIP7 is involved in the biogenesis of 40S subunit. This raised the possibility that human NIP7 interacts with a different set of proteins as compared to the yeast protein. By using the yeast two-hybrid system we identified FTSJ3, a putative ortholog of yeast Spb1p, as a human NIP7-interacting protein. A functional association between NIP7 and FTSJ3 is further supported by colocalization and coimmunoprecipitation analyses. Conditional knockdown revealed that depletion of FTSJ3 affects cell proliferation and causes pre-rRNA processing defects. The major pre-rRNA processing defect involves accumulation of the 34S pre-rRNA encompassing from site A' to site 2b. Accumulation of this pre-rRNA indicates that processing of sites A0, 1 and 2 are slower in cells depleted of FTSJ3 and implicates FTSJ3 in the pathway leading to 18S rRNA maturation as observed previously for NIP7. The results presented in this work indicate a close functional interaction between NIP7 and FTSJ3 during pre-rRNA processing and show that FTSJ3 participates in ribosome synthesis in human cells.

Zebrafish usp39 mutation leads to rb1 mRNA splicing defect and pituitary lineage expansion.

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Yesenia Ríos

2011-01-01

Full Text Available Loss of retinoblastoma (Rb tumor suppressor function is associated with human malignancies. Molecular and genetic mechanisms responsible for tumorigenic Rb downregulation are not fully defined. Through a forward genetic screen and positional cloning, we identified and characterized a zebrafish ubiquitin specific peptidase 39 (usp39 mutation, the yeast and human homolog of which encodes a component of RNA splicing machinery. Zebrafish usp39 mutants exhibit microcephaly and adenohypophyseal cell lineage expansion without apparent changes in major hypothalamic hormonal and regulatory signals. Gene expression profiling of usp39 mutants revealed decreased rb1 and increased e2f4, rbl2 (p130, and cdkn1a (p21 expression. Rb1 mRNA overexpression, or antisense morpholino knockdown of e2f4, partially reversed embryonic pituitary expansion in usp39 mutants. Analysis of pre-mRNA splicing status of critical cell cycle regulators showed misspliced Rb1 pre-mRNA resulting in a premature stop codon. These studies unravel a novel mechanism for rb1 regulation by a neuronal mRNA splicing factor, usp39. Zebrafish usp39 regulates embryonic pituitary homeostasis by targeting rb1 and e2f4 expression, respectively, contributing to increased adenohypophyseal sensitivity to these altered cell cycle regulators. These results provide a mechanism for dysregulated rb1 and e2f4 pathways that may result in pituitary tumorigenesis.

Pre-authorization processes have no effect on patients undergoing knee MRI in a pediatric setting when evaluated by specialists

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Pierce, Drew; Kan, J.H.; Bisset, George S. [Texas Children' s Hospital, Department of Radiology, Houston, TX (United States); May, Megan [Texas Children' s Hospital, Department of Sports Medicine, Houston, TX (United States)

2017-02-15

Pre-authorization processes are often used by medical insurance companies to reduce costs by managing the utilization of advanced diagnostic imaging, and their impact on patient care is unclear. The purpose of our study is to determine if a pre-authorization process increases the rate of surgically significant abnormal knee MRI and surgical referrals compared with patients referred from pediatric orthopedic specialists who do not undergo a pre-authorization process. A retrospective study was performed; 124 patients were identified who were referred for knee MRI by a pediatric orthopedist. The study population included patients who underwent an insurance pre-authorization process and the control group consisted of those who did not. The results of the MRI and whether they were deemed surgically significant, in addition to surgical referral, were recorded and compared. The study and control groups showed no statistically significant difference in outcome with regard to surgically significant findings on MRI (p = 0.92) or whether the patient required surgery (p = 0.6). In this population, there is no difference in the likelihood of an abnormal knee MRI demonstrating surgically significant findings or referral to surgery in patients who did and those who did not undergo an insurance pre-authorization process when patients are referred from a pediatric orthopedic specialist. The insurance pre-authorization process does not appear to have an impact on patient diagnosis and treatment and may unnecessarily add bureaucracy and costs. (orig.)

Single-cell analysis reveals early manifestation of cancerous phenotype in pre-malignant esophageal cells.

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Jiangxin Wang

Full Text Available Cellular heterogeneity plays a pivotal role in a variety of functional processes in vivo including carcinogenesis. However, our knowledge about cell-to-cell diversity and how differences in individual cells manifest in alterations at the population level remains very limited mainly due to the lack of appropriate tools enabling studies at the single-cell level. We present a study on changes in cellular heterogeneity in the context of pre-malignant progression in response to hypoxic stress. Utilizing pre-malignant progression of Barrett's esophagus (BE as a disease model system we studied molecular mechanisms underlying the progression from metaplastic to dysplastic (pre-cancerous stage. We used newly developed methods enabling measurements of cell-to-cell differences in copy numbers of mitochondrial DNA, expression levels of a set of mitochondrial and nuclear genes involved in hypoxia response pathways, and mitochondrial membrane potential. In contrast to bulk cell studies reported earlier, our study shows significant differences between metaplastic and dysplastic BE cells in both average values and single-cell parameter distributions of mtDNA copy numbers, mitochondrial function, and mRNA expression levels of studied genes. Based on single-cell data analysis, we propose that mitochondria may be one of the key factors in pre-malignant progression in BE.

H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication.

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Wu, Rentian; Wang, Zhiquan; Zhang, Honglian; Gan, Haiyun; Zhang, Zhiguo

2017-01-09

DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase δ, but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Textural Analysis of Fatique Crack Surfaces: Image Pre-processing

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H. Lauschmann

2000-01-01

Full Text Available For the fatique crack history reconstitution, new methods of quantitative microfractography are beeing developed based on the image processing and textural analysis. SEM magnifications between micro- and macrofractography are used. Two image pre-processing operatins were suggested and proved to prepare the crack surface images for analytical treatment: 1. Normalization is used to transform the image to a stationary form. Compared to the generally used equalization, it conserves the shape of brightness distribution and saves the character of the texture. 2. Binarization is used to transform the grayscale image to a system of thick fibres. An objective criterion for the threshold brightness value was found as that resulting into the maximum number of objects. Both methods were succesfully applied together with the following textural analysis.

The alkaline pre-filming process of the RWCU piping surface

Energy Technology Data Exchange (ETDEWEB)

Kao, D-Y.; Wen, T-J., E-mail: dahyukao@iner.gov.tw [Atomic Energy Council, Inst. of Nuclear Energy Research, Lungtan Taoyuan, Taiwan (China); Fong, C., E-mail: clinton@itri.org.tw [Industrial Technology Research Inst., Chutung, Hsinchu (China); Lu, J-H., E-mail: u879864@taipower.com.tw [Taiwan Power Co., Lungmen Nuclear Power Plant, Gongliao Township, Taipei County (China)

2010-07-01

The radiation dose rate on a BWR can cause great damage to operators and their maintenances working quality, so it is very important to lower it. The RWCU of a BWR primary system has the highest radiation dose rate and deposition of an active corrosion product because of: continually cleaning the reactor water and the repeated, acute change of temperature. The Lungmen NPP was built as an advanced BWR (ABWR) system. All new ABWRs in Japan, such as Kashiwazaki-Kariwa NPP units K6 and K7, Hamaoka NPP unit H5, and Shika NPP unit2, were given in passivation treatment in the stage of nuclear heating or flow-induced vibration (FIV) testing before each plant's initial start up. The conditions of alkaline pre-filming process include: pH, dissolve oxygen (DO) and temperature. This project had been decided by the results of earlier water loop testing. Three kinds of specimens including stainless steel AISI SS316L and carbon steel SA106 GrB, SA333 Gr6 were put into the autoclave located at a bypass system during the process of passivation treatment. The materials of these specimens have been used in RWCU piping, and during the alkaline pre-filming process they were monitored by AC impedances and electrochemical corrosion potential (ECP). Their surface analyses including SEM, EDS, ESCA and SIMS data were obtained from the initial test, and obtained every six months thereafter. From the SEM plot of first issue it was found that the specimens' surface of all three different materials presented excellent levels of oxidized pellets. They are almost completely packed, for both large and small granules, and the porosity is less than 40%. The deposition tests of cobalt ion were also completed. The material of stainless steel was nearly not affected through the passive process. However, carbon steel could reduce about 30% to 50% of deposited cobalt ion. This result follows the conclusion of Hatch Company. Based on the nominal cost of radiation protection, i.e. 10000 USD

Atmospheric processes over complex terrain

Science.gov (United States)

Banta, Robert M.; Berri, G.; Blumen, William; Carruthers, David J.; Dalu, G. A.; Durran, Dale R.; Egger, Joseph; Garratt, J. R.; Hanna, Steven R.; Hunt, J. C. R.

1990-06-01

A workshop on atmospheric processes over complex terrain, sponsored by the American Meteorological Society, was convened in Park City, Utah from 24 vto 28 October 1988. The overall objective of the workshop was one of interaction and synthesis--interaction among atmospheric scientists carrying out research on a variety of orographic flow problems, and a synthesis of their results and points of view into an assessment of the current status of topical research problems. The final day of the workshop was devoted to an open discussion on the research directions that could be anticipated in the next decade because of new and planned instrumentation and observational networks, the recent emphasis on development of mesoscale numerical models, and continual theoretical investigations of thermally forced flows, orographic waves, and stratified turbulence. This monograph represents an outgrowth of the Park City Workshop. The authors have contributed chapters based on their lecture material. Workshop discussions indicated interest in both the remote sensing and predictability of orographic flows. These chapters were solicited following the workshop in order to provide a more balanced view of current progress and future directions in research on atmospheric processes over complex terrain.

Complexity in Evolutionary Processes

International Nuclear Information System (INIS)

Schuster, P.

2010-01-01

Darwin's principle of evolution by natural selection is readily casted into a mathematical formalism. Molecular biology revealed the mechanism of mutation and provides the basis for a kinetic theory of evolution that models correct reproduction and mutation as parallel chemical reaction channels. A result of the kinetic theory is the existence of a phase transition in evolution occurring at a critical mutation rate, which represents a localization threshold for the population in sequence space. Occurrence and nature of such phase transitions depend critically on fitness landscapes. The fitness landscape being tantamount to a mapping from sequence or genotype space into phenotype space is identified as the true source of complexity in evolution. Modeling evolution as a stochastic process is discussed and neutrality with respect to selection is shown to provide a major challenge for understanding evolutionary processes (author)

Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP

Science.gov (United States)

Wickramasinghe, Vihandha O.; Andrews, Robert; Ellis, Peter; Langford, Cordelia; Gurdon, John B.; Stewart, Murray; Venkitaraman, Ashok R.; Laskey, Ronald A.

2014-01-01

The nuclear phase of the gene expression pathway culminates in the export of mature messenger RNAs (mRNAs) to the cytoplasm through nuclear pore complexes. GANP (germinal- centre associated nuclear protein) promotes the transfer of mRNAs bound to the transport factor NXF1 to nuclear pore complexes. Here, we demonstrate that GANP, subunit of the TRanscription-EXport-2 (TREX-2) mRNA export complex, promotes selective nuclear export of a specific subset of mRNAs whose transport depends on NXF1. Genome-wide gene expression profiling showed that half of the transcripts whose nuclear export was impaired following NXF1 depletion also showed reduced export when GANP was depleted. GANP-dependent transcripts were highly expressed, yet short-lived, and were highly enriched in those encoding central components of the gene expression machinery such as RNA synthesis and processing factors. After injection into Xenopus oocyte nuclei, representative GANP-dependent transcripts showed faster nuclear export kinetics than representative transcripts that were not influenced by GANP depletion. We propose that GANP promotes the nuclear export of specific classes of mRNAs that may facilitate rapid changes in gene expression. PMID:24510098

Increased FXYD1 and PGC-1α mRNA after blood flow-restricted running is related to fibre type-specific AMPK signalling and oxidative stress in human muscle

DEFF Research Database (Denmark)

Christiansen, Danny; Murphy, Robyn M; Bangsbo, Jens

2018-01-01

). A muscle sample was collected before (Pre) and after exercise (+0h, +3h) to quantify mRNA, indicators of oxidative stress (HSP27 protein in type I and II fibres, and catalase and HSP70 mRNA), metabolites, and α-AMPK Thr172 /α-AMPK, ACC Ser221 /ACC, CaMKII Thr287 /CaMKII, and PLBSer16 /PLB ratios in type I...

Status of pre-processing of waste electrical and electronic equipment in Germany and its influence on the recovery of gold.

Science.gov (United States)

Chancerel, Perrine; Bolland, Til; Rotter, Vera Susanne

2011-03-01

Waste electrical and electronic equipment (WEEE) contains gold in low but from an environmental and economic point of view relevant concentration. After collection, WEEE is pre-processed in order to generate appropriate material fractions that are sent to the subsequent end-processing stages (recovery, reuse or disposal). The goal of this research is to quantify the overall recovery rates of pre-processing technologies used in Germany for the reference year 2007. To achieve this goal, facilities operating in Germany were listed and classified according to the technology they apply. Information on their processing capacity was gathered by evaluating statistical databases. Based on a literature review of experimental results for gold recovery rates of different pre-processing technologies, the German overall recovery rate of gold at the pre-processing level was quantified depending on the characteristics of the treated WEEE. The results reveal that - depending on the equipment groups - pre-processing recovery rates of gold of 29 to 61% are achieved in Germany. Some practical recommendations to reduce the losses during pre-processing could be formulated. Defining mass-based recovery targets in the legislation does not set incentives to recover trace elements. Instead, the priorities for recycling could be defined based on other parameters like the environmental impacts of the materials. The implementation of measures to reduce the gold losses would also improve the recovery of several other non-ferrous metals like tin, nickel, and palladium.

Investigation of the Nature of Metaconceptual Processes of Pre-Service Biology Teachers

Science.gov (United States)

Yuruk, Nejla; Selvi, Meryem; Yakisan, Mehmet

2017-01-01

Purpose of Study: The aim of this study is to investigate the nature of pre-service biology teachers' metaconceptual processes that were active as they participated in metaconceptual teaching activities. Methods: Several instructional activities, including poster drawing, concept mapping, group and class discussions, and journal writing, were…

Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

NARCIS (Netherlands)

Bosse, T.; Jonker, C.M.; Treur, J.

2005-01-01

This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics

Specificity in endoplasmic reticulum-stress signaling in yeast entails a step-wise engagement of HAC1 mRNA to clusters of the stress sensor Ire1.

Science.gov (United States)

van Anken, Eelco; Pincus, David; Coyle, Scott; Aragón, Tomás; Osman, Christof; Lari, Federica; Gómez Puerta, Silvia; Korennykh, Alexei V; Walter, Peter

2014-12-30

Insufficient protein-folding capacity in the endoplasmic reticulum (ER) induces the unfolded protein response (UPR). In the ER lumen, accumulation of unfolded proteins activates the transmembrane ER-stress sensor Ire1 and drives its oligomerization. In the cytosol, Ire1 recruits HAC1 mRNA, mediating its non-conventional splicing. The spliced mRNA is translated into Hac1, the key transcription activator of UPR target genes that mitigate ER-stress. In this study, we report that oligomeric assembly of the ER-lumenal domain is sufficient to drive Ire1 clustering. Clustering facilitates Ire1's cytosolic oligomeric assembly and HAC1 mRNA docking onto a positively charged motif in Ire1's cytosolic linker domain that tethers the kinase/RNase to the transmembrane domain. By the use of a synthetic bypass, we demonstrate that mRNA docking per se is a pre-requisite for initiating Ire1's RNase activity and, hence, splicing. We posit that such step-wise engagement between Ire1 and its mRNA substrate contributes to selectivity and efficiency in UPR signaling.

Complex p63 mRNA isoform expression patterns in squamous cell carcinoma of the head and neck

DEFF Research Database (Denmark)

Thurfjell, N.; Coates, P.J.; Uusitalo, T.

2004-01-01

on the role of p63 expression in human tumours, we used quantitative real-time RT-PCR to study individual p63 isoforms in squamous cell carcinomas of the head and neck (SCCHN). In keeping with previous reports, expression of the deltaN- and p63alpha-isoforms predominated and deltaNp63 mRNA was expressed...

mRNA localization mechanisms in Trypanosoma cruzi.

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Lysangela R Alves

Full Text Available Asymmetric mRNA localization is a sophisticated tool for regulating and optimizing protein synthesis and maintaining cell polarity. Molecular mechanisms involved in the regulated localization of transcripts are widespread in higher eukaryotes and fungi, but not in protozoa. Trypanosomes are ancient eukaryotes that branched off early in eukaryote evolution. We hypothesized that these organisms would have basic mechanisms of mRNA localization. FISH assays with probes against transcripts coding for proteins with restricted distributions showed a discrete localization of the mRNAs in the cytoplasm. Moreover, cruzipain mRNA was found inside reservosomes suggesting new unexpected functions for this vacuolar organelle. Individual mRNAs were also mobilized to RNA granules in response to nutritional stress. The cytoplasmic distribution of these transcripts changed with cell differentiation, suggesting that localization mechanisms might be involved in the regulation of stage-specific protein expression. Transfection assays with reporter genes showed that, as in higher eukaryotes, 3'UTRs were responsible for guiding mRNAs to their final location. Our results strongly suggest that Trypanosoma cruzi have a core, basic mechanism of mRNA localization. This kind of controlled mRNA transport is ancient, dating back to early eukaryote evolution.

A pilot trial assessing urinary gene expression profiling with an mRNA array for diabetic nephropathy.

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Min Zheng

Full Text Available BACKGROUND: The initiation and progression of diabetic nephropathy (DN is complex. Quantification of mRNA expression in urinary sediment has emerged as a novel strategy for studying renal diseases. Considering the numerous molecules involved in DN development, a high-throughput platform with parallel detection of multiple mRNAs is needed. In this study, we constructed a self-assembling mRNA array to analyze urinary mRNAs in DN patients with aims to reveal its potential in searching novel biomarkers. METHODS: mRNA array containing 88 genes were fabricated and its performance was evaluated. A pilot study with 9 subjects including 6 DN patients and 3 normal controls were studied with the array. DN patients were assigned into two groups according to their estimate glomerular rate (eGFR: DNI group (eGFR>60 ml/min/1.73 m(2, n = 3 and DNII group (eGFR<60 ml/min/1.73 m(2, n = 3. Urinary cell pellet was collected from each study participant. Relative abundance of these target mRNAs from urinary pellet was quantified with the array. RESULTS: The array we fabricated displayed high sensitivity and specificity. Moreover, the Cts of Positive PCR Controls in our experiments were 24±0.5 which indicated high repeatability of the array. A total of 29 mRNAs were significantly increased in DN patients compared with controls (p<0.05. Among these genes, α-actinin4, CDH2, ACE, FAT1, synaptopodin, COL4α, twist, NOTCH3 mRNA expression were 15-fold higher than those in normal controls. In contrast, urinary TIMP-1 mRNA was significantly decreased in DN patients (p<0.05. It was shown that CTGF, MCP-1, PAI-1, ACE, CDH1, CDH2 mRNA varied significantly among the 3 study groups, and their mRNA levels increased with DN progression (p<0.05. CONCLUSION: Our pilot study demonstrated that mRNA array might serve as a high-throughput and sensitive tool for detecting mRNA expression in urinary sediment. Thus, this primary study indicated that mRNA array probably could be a

HITS-CLIP analysis uncovers a link between the Kaposi's sarcoma-associated herpesvirus ORF57 protein and host pre-mRNA metabolism.

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Emi Sei

2015-02-01

Full Text Available The Kaposi's sarcoma associated herpesvirus (KSHV is an oncogenic virus that causes Kaposi's sarcoma, primary effusion lymphoma (PEL, and some forms of multicentric Castleman's disease. The KSHV ORF57 protein is a conserved posttranscriptional regulator of gene expression that is essential for virus replication. ORF57 is multifunctional, but most of its activities are directly linked to its ability to bind RNA. We globally identified virus and host RNAs bound by ORF57 during lytic reactivation in PEL cells using high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP. As expected, ORF57-bound RNA fragments mapped throughout the KSHV genome, including the known ORF57 ligand PAN RNA. In agreement with previously published ChIP results, we observed that ORF57 bound RNAs near the oriLyt regions of the genome. Examination of the host RNA fragments revealed that a subset of the ORF57-bound RNAs was derived from transcript 5' ends. The position of these 5'-bound fragments correlated closely with the 5'-most exon-intron junction of the pre-mRNA. We selected four candidates (BTG1, EGR1, ZFP36, and TNFSF9 and analyzed their pre-mRNA and mRNA levels during lytic phase. Analysis of both steady-state and newly made RNAs revealed that these candidate ORF57-bound pre-mRNAs persisted for longer periods of time throughout infection than control RNAs, consistent with a role for ORF57 in pre-mRNA metabolism. In addition, exogenous expression of ORF57 was sufficient to increase the pre-mRNA levels and, in one case, the mRNA levels of the putative ORF57 targets. These results demonstrate that ORF57 interacts with specific host pre-mRNAs during lytic reactivation and alters their processing, likely by stabilizing pre-mRNAs. These data suggest that ORF57 is involved in modulating host gene expression in addition to KSHV gene expression during lytic reactivation.

IGF-1R mRNA expression is increased in obese children.

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Ricco, Rafaela Cristina; Ricco, Rubens Garcia; Queluz, Mariangela Carletti; de Paula, Mariana Teresa Sarti; Atique, Patricia Volpon; Custódio, Rodrigo José; Tourinho Filho, Hugo; Del Roio Liberatori, Raphael; Martinelli, Carlos Eduardo

2018-04-01

Obese children are often taller than age-matched subjects. Reports on GH and IGF-I levels in obese individuals are controversial, with normal and reduced GH-IGF-I levels having been reported in this group of patients. Thus, the aim of this study was to analyse insulin-like growth factor type 1 receptor (IGF-IR) mRNA expression in obese children. Forty-seven pre-pubertal children were included in this study: 29 were obese and taller than their target height, and 18 were normal eutrophic controls. Fasting blood samples were collected for IGF-IR mRNA expression in isolated lymphocytes and serum IGF-I, ALS, IGFBP-3, and IGFBP-1 concentration analysis. Relative IGF-IR gene expression (2 -ΔΔCT ) was significantly (P=0.025) higher in obese children (median 1.87) than in controls (1.15). Fourteen of the 29 obese subjects showed 2 -ΔΔCT values greater than or equal to 2, while only 2 individuals in the control group showed values above 2 (P=0.01). Obese children showed significantly (P=0.01) higher IGF-I concentrations than the control group (237ng/ml and 144ng/ml, respectively). Among obese patients, 65.5% had IGF-I values above the 75 percentile of the control group (P=0.02). ALS concentration was significantly (P=0.04) higher in the obese group, while IGFBP-3 levels were similar in obese and control children. IGFBP-1 concentration was lower in obese children, while insulin levels and HOMA-IR index were higher than in controls. The higher IGF-IR mRNA expression observed in obese children, associated with the higher IGF-I and ALS and the lower IGFBP-1 levels, suggest that the higher stature observed in these children may be due to increased IGF-I bioactivity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exploiting Pre-rRNA Processing in Diamond Blackfan Anemia Gene Discovery and Diagnosis

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Farrar, Jason E.; Quarello, Paola; Fisher, Ross; O’Brien, Kelly A.; Aspesi, Anna; Parrella, Sara; Henson, Adrianna L.; Seidel, Nancy E.; Atsidaftos, Eva; Prakash, Supraja; Bari, Shahla; Garelli, Emanuela; Arceci, Robert J.; Dianzani, Irma; Ramenghi, Ugo; Vlachos, Adrianna; Lipton, Jeffrey M.; Bodine, David M.; Ellis, Steven R.

2014-01-01

Diamond Blackfan anemia (DBA), a syndrome primarily characterized by anemia and physical abnormalities, is one among a group of related inherited bone marrow failure syndromes (IBMFS) which share overlapping clinical features. Heterozygous mutations or single-copy deletions have been identified in 12 ribosomal protein genes in approximately 60% of DBA cases, with the genetic etiology unexplained in most remaining patients. Unlike many IBMFS, for which functional screening assays complement clinical and genetic findings, suspected DBA in the absence of typical alterations of the known genes must frequently be diagnosed after exclusion of other IBMFS. We report here a novel deletion in a child that presented such a diagnostic challenge and prompted development of a novel functional assay that can assist in the diagnosis of a significant fraction of patients with DBA. The ribosomal proteins affected in DBA are required for pre-rRNA processing, a process which can be interrogated to monitor steps in the maturation of 40S and 60S ribosomal subunits. In contrast to prior methods used to assess pre-rRNA processing, the assay reported here, based on capillary electrophoresis measurement of the maturation of rRNA in pre-60S ribosomal subunits, would be readily amenable to use in diagnostic laboratories. In addition to utility as a diagnostic tool, we applied this technique to gene discovery in DBA, resulting in the identification of RPL31 as a novel DBA gene. PMID:25042156

Tissue-specific mRNA expression profiling in grape berry tissues

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Grimplet, Jerome; Deluc, Laurent G; Tillett, Richard L; Wheatley, Matthew D; Schlauch, Karen A; Cramer, Grant R; Cushman, John C

2007-01-01

transport processes. Seeds, which supply essential resources for embryo development, showed higher mRNA abundance of genes encoding phenylpropanoid biosynthetic enzymes, seed storage proteins, and late embryogenesis abundant proteins. Water-deficit stress affected the mRNA abundance of 13% of the genes with differential expression patterns occurring mainly in the pulp and skin. In pulp and seed tissues transcript abundance in most functional categories declined in water-deficit stressed vines relative to well-watered vines with transcripts for storage proteins and novel (no-hit) functional assignments being over represented. In the skin of berries from water-deficit stressed vines, however, transcripts from several functional categories including general phenypropanoid and ethylene metabolism, pathogenesis-related responses, energy, and interaction with the environment were significantly over-represented. Conclusion These results revealed novel insights into the tissue-specific expression mRNA expression patterns of an extensive repertoire of genes expressed in berry tissues. This work also establishes an extensive catalogue of gene expression patterns for future investigations aimed at the dissection of the transcriptional regulatory hierarchies that govern tissue-specific expression patterns associated with tissue differentiation within berries. These results also confirmed that water-deficit stress has a profound effect on mRNA expression patterns particularly associated with the biosynthesis of aroma and color metabolites within skin and pulp tissues that ultimately impact wine quality. PMID:17584945

Tissue-specific mRNA expression profiling in grape berry tissues

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Cramer Grant R

2007-06-01

wall function and transport processes. Seeds, which supply essential resources for embryo development, showed higher mRNA abundance of genes encoding phenylpropanoid biosynthetic enzymes, seed storage proteins, and late embryogenesis abundant proteins. Water-deficit stress affected the mRNA abundance of 13% of the genes with differential expression patterns occurring mainly in the pulp and skin. In pulp and seed tissues transcript abundance in most functional categories declined in water-deficit stressed vines relative to well-watered vines with transcripts for storage proteins and novel (no-hit functional assignments being over represented. In the skin of berries from water-deficit stressed vines, however, transcripts from several functional categories including general phenypropanoid and ethylene metabolism, pathogenesis-related responses, energy, and interaction with the environment were significantly over-represented. Conclusion These results revealed novel insights into the tissue-specific expression mRNA expression patterns of an extensive repertoire of genes expressed in berry tissues. This work also establishes an extensive catalogue of gene expression patterns for future investigations aimed at the dissection of the transcriptional regulatory hierarchies that govern tissue-specific expression patterns associated with tissue differentiation within berries. These results also confirmed that water-deficit stress has a profound effect on mRNA expression patterns particularly associated with the biosynthesis of aroma and color metabolites within skin and pulp tissues that ultimately impact wine quality.

Maternal separation induces hippocampal changes in cadherin-1 (CDH-1) mRNA and recognition memory impairment in adolescent mice.

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de Azeredo, Lucas Araújo; Wearick-Silva, Luis Eduardo; Viola, Thiago Wendt; Tractenberg, Saulo Gantes; Centeno-Silva, Anderson; Orso, Rodrigo; Schröder, Nadja; Bredy, Timothy William; Grassi-Oliveira, Rodrigo

2017-05-01

In rodents, disruption of mother-infant attachment induced by maternal separation (MS) is associated with recognition memory impairment and long-term neurobiological consequences. Particularly stress-induced modifications have been associated to disruption of cadherin (CDH) adhesion function, which plays an important role in remodeling of neuronal connection and synaptic plasticity. This study investigated the sex-dependent effect of MS on recognition memory and mRNA levels of classical type I and type II CDH and the related β -catenin (β -Cat) in the hippocampus and prefrontal cortex of late adolescent mice. We provided evidence that the BALB/c mice exposed to MS present deficit in recognition memory, especially females. Postnatal MS induced higher hippocampal CDH-2 and CDH-8 mRNA levels, as well as an upregulation of CDH-1 in the prefrontal cortex in both males and females. MS-reared female mice presented lower CDH-1 mRNA levels in the hippocampus. In addition, hippocampal CDH-1 mRNA levels were positively correlated with recognition memory performance in females. MS-reared male mice exhibited higher β -Cat mRNA levels in the hippocampus. Considering sex-specific effects on CDH mRNA levels, it has been demonstrated mRNA changes in CDH-1, β -Cat, and CDH-6 in the hippocampus, as well as CDH-1, CDH-8 and CDH-11 in the prefrontal cortex. Overall, these findings suggest a complex interplay among MS, CDH mRNA expression, and sex differences in the PFC and hippocampus of adolescent mice. Copyright © 2017 Elsevier Inc. All rights reserved.

Pre- and post-processing of hydro-meteorological ensembles for the Norwegian flood forecasting system in 145 basins.

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Jahr Hegdahl, Trine; Steinsland, Ingelin; Merete Tallaksen, Lena; Engeland, Kolbjørn

2016-04-01

Probabilistic flood forecasting has an added value for decision making. The Norwegian flood forecasting service is based on a flood forecasting model that run for 145 basins. Covering all of Norway the basins differ in both size and hydrological regime. Currently the flood forecasting is based on deterministic meteorological forecasts, and an auto-regressive procedure is used to achieve probabilistic forecasts. An alternative approach is to use meteorological and hydrological ensemble forecasts to quantify the uncertainty in forecasted streamflow. The hydrological ensembles are based on forcing a hydrological model with meteorological ensemble forecasts of precipitation and temperature. However, the ensembles of precipitation are often biased and the spread is too small, especially for the shortest lead times, i.e. they are not calibrated. These properties will, to some extent, propagate to hydrological ensembles, that most likely will be uncalibrated as well. Pre- and post-processing methods are commonly used to obtain calibrated meteorological and hydrological ensembles respectively. Quantitative studies showing the effect of the combined processing of the meteorological (pre-processing) and the hydrological (post-processing) ensembles are however few. The aim of this study is to evaluate the influence of pre- and post-processing on the skill of streamflow predictions, and we will especially investigate if the forecasting skill depends on lead-time, basin size and hydrological regime. This aim is achieved by applying the 51 medium-range ensemble forecast of precipitation and temperature provided by the European Center of Medium-Range Weather Forecast (ECMWF). These ensembles are used as input to the operational Norwegian flood forecasting model, both raw and pre-processed. Precipitation ensembles are calibrated using a zero-adjusted gamma distribution. Temperature ensembles are calibrated using a Gaussian distribution and altitude corrected by a constant gradient

The effects of pre-processing strategies in sentiment analysis of online movie reviews

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Zin, Harnani Mat; Mustapha, Norwati; Murad, Masrah Azrifah Azmi; Sharef, Nurfadhlina Mohd

2017-10-01

With the ever increasing of internet applications and social networking sites, people nowadays can easily express their feelings towards any products and services. These online reviews act as an important source for further analysis and improved decision making. These reviews are mostly unstructured by nature and thus, need processing like sentiment analysis and classification to provide a meaningful information for future uses. In text analysis tasks, the appropriate selection of words/features will have a huge impact on the effectiveness of the classifier. Thus, this paper explores the effect of the pre-processing strategies in the sentiment analysis of online movie reviews. In this paper, supervised machine learning method was used to classify the reviews. The support vector machine (SVM) with linear and non-linear kernel has been considered as classifier for the classification of the reviews. The performance of the classifier is critically examined based on the results of precision, recall, f-measure, and accuracy. Two different features representations were used which are term frequency and term frequency-inverse document frequency. Results show that the pre-processing strategies give a significant impact on the classification process.

Selection of mRNA 5'-untranslated region sequence with high translation efficiency through ribosome display

International Nuclear Information System (INIS)

Mie, Masayasu; Shimizu, Shun; Takahashi, Fumio; Kobatake, Eiry

2008-01-01

The 5'-untranslated region (5'-UTR) of mRNAs functions as a translation enhancer, promoting translation efficiency. Many in vitro translation systems exhibit a reduced efficiency in protein translation due to decreased translation initiation. The use of a 5'-UTR sequence with high translation efficiency greatly enhances protein production in these systems. In this study, we have developed an in vitro selection system that favors 5'-UTRs with high translation efficiency using a ribosome display technique. A 5'-UTR random library, comprised of 5'-UTRs tagged with a His-tag and Renilla luciferase (R-luc) fusion, were in vitro translated in rabbit reticulocytes. By limiting the translation period, only mRNAs with high translation efficiency were translated. During translation, mRNA, ribosome and translated R-luc with His-tag formed ternary complexes. They were collected with translated His-tag using Ni-particles. Extracted mRNA from ternary complex was amplified using RT-PCR and sequenced. Finally, 5'-UTR with high translation efficiency was obtained from random 5'-UTR library

An Intelligent Complex Event Processing with D Numbers under Fuzzy Environment

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Fuyuan Xiao

2016-01-01

Full Text Available Efficient matching of incoming mass events to persistent queries is fundamental to complex event processing systems. Event matching based on pattern rule is an important feature of complex event processing engine. However, the intrinsic uncertainty in pattern rules which are predecided by experts increases the difficulties of effective complex event processing. It inevitably involves various types of the intrinsic uncertainty, such as imprecision, fuzziness, and incompleteness, due to the inability of human beings subjective judgment. Nevertheless, D numbers is a new mathematic tool to model uncertainty, since it ignores the condition that elements on the frame must be mutually exclusive. To address the above issues, an intelligent complex event processing method with D numbers under fuzzy environment is proposed based on the Technique for Order Preferences by Similarity to an Ideal Solution (TOPSIS method. The novel method can fully support decision making in complex event processing systems. Finally, a numerical example is provided to evaluate the efficiency of the proposed method.

Integrating complex business processes for knowledge-driven clinical decision support systems.

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Kamaleswaran, Rishikesan; McGregor, Carolyn

2012-01-01

This paper presents in detail the component of the Complex Business Process for Stream Processing framework that is responsible for integrating complex business processes to enable knowledge-driven Clinical Decision Support System (CDSS) recommendations. CDSSs aid the clinician in supporting the care of patients by providing accurate data analysis and evidence-based recommendations. However, the incorporation of a dynamic knowledge-management system that supports the definition and enactment of complex business processes and real-time data streams has not been researched. In this paper we discuss the process web service as an innovative method of providing contextual information to a real-time data stream processing CDSS.

Influence of pre-cure freezing of Iberian ham on proteolytic changes throughout the ripening process.

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Pérez-Palacios, Trinidad; Ruiz, Jorge; Barat, Jose Manuel; Aristoy, María Concepción; Antequera, Teresa

2010-05-01

This work aimed to investigate the effect of pre-cure freezing Iberian hams on proteolysis phenomena throughout the ripening process. Non-protein nitrogen (NPN), peptide nitrogen (PN) and amino acid nitrogen (AN) as well as amino acid and dipeptide evolution followed the same trend in both refrigerated (R) and pre-cure frozen (F) Iberian hams during processing. At the different stages of ripening, there were no differences in the content of NPN and AN while F dry-cured hams had higher levels of PN than R hams at the final step. This seemed to be more related to the salt content (lower in F than in R hams) than to the pre-cure freezing treatment. Most amino acids and dipeptides detected showed higher concentrations in F than in R Iberian hams at the green stage, being rather similar at the intermediate phases. At the final stage, the effects of pre-cure freezing of Iberian hams were not well defined, higher levels of some amino acids and dipeptides were found in R than in F Iberian hams whereas other amino acids were lower in R than in F hams. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

The role of mRNA translation in the adaptation to hypoxia

International Nuclear Information System (INIS)

Koritzinsky, M.; Wouters, B.G.; Koumenis, C.

2003-01-01

Hypoxia commonly occurs in human tumours and is associated with a poor prognosis. We and others have shown that global mRNA translation is rapidly inhibited during hypoxia. However, some mRNAs, such as those coding for HIF-1 α and VEGF, remain efficiently translated. We therefore hypothesize that the inhibition of mRNA translation serves to promote hypoxia tolerance in two ways: i) through conservation of energy and ii) through differential gene expression involved in hypoxia adaptation. We are investigating the mechanisms responsible for the down regulation of protein synthesis during hypoxia, and how specific mRNAs maintain their ability to be translated under such conditions. Our goal is to understand the significance of these regulatory mechanisms for hypoxia tolerance in vitro and tumor growth in vivo. We have previously shown that one mechanism responsible for inhibiting protein synthesis during hypoxia is the activation of PERK, which inhibits the essential translation factor eIF2 α . Here we show that PERK-/- MEFs are not able to inhibit protein synthesis efficiently during hypoxia and are significantly less tolerant to hypoxia than wt cells. We also show that other mechanisms are important for sustained low protein synthesis during chronic hypoxia. We demonstrate that the eIF4F complex is disrupted during prolonged hypoxia, and that this is mediated by 4E-BP1 and 4E-T. eIF4F is essential for translation which is dependent upon the 5'mRNA cap-structure. These studies therefore indicate a switch from the inhibition of all translation through eIF2 α during acute hypoxia, to the inhibition of only cap-dependent translation during chronic hypoxia. This model predicts the differential induction of genes that can be translated cap-independently during chronic hypoxia, which is consistent with the observed differential translation of HIF-1 α and VEGF. The functional significance of the disruption of the eIF4F complex during hypoxia is currently being addressed

Understanding Student Cognition about Complex Earth System Processes Related to Climate Change

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McNeal, K. S.; Libarkin, J.; Ledley, T. S.; Dutta, S.; Templeton, M. C.; Geroux, J.; Blakeney, G. A.

2011-12-01

The Earth's climate system includes complex behavior and interconnections with other Earth spheres that present challenges to student learning. To better understand these unique challenges, we have conducted experiments with high-school and introductory level college students to determine how information pertaining to the connections between the Earth's atmospheric system and the other Earth spheres (e.g., hydrosphere and cryosphere) are processed. Specifically, we include psychomotor tests (e.g., eye-tracking) and open-ended questionnaires in this research study, where participants were provided scientific images of the Earth (e.g., global precipitation and ocean and atmospheric currents), eye-tracked, and asked to provide causal or relational explanations about the viewed images. In addition, the students engaged in on-line modules (http://serc.carleton.edu/eslabs/climate/index.html) focused on Earth system science as training activities to address potential cognitive barriers. The developed modules included interactive media, hands-on lessons, links to outside resources, and formative assessment questions to promote a supportive and data-rich learning environment. Student eye movements were tracked during engagement with the materials to determine the role of perception and attention on understanding. Students also completed a conceptual questionnaire pre-post to determine if these on-line curriculum materials assisted in their development of connections between Earth's atmospheric system and the other Earth systems. The pre-post results of students' thinking about climate change concepts, as well as eye-tracking results, will be presented.

Learning Processes of Students in Pre-Vocational Secondary Education: Relations between Goal Orientations, Information Processing Strategies and Development of Conceptual Knowledge

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Koopman, Maaike; Den Brok, Perry; Beijaard, Douwe; Teune, Peter

2011-01-01

The purpose of this study was to investigate relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education students (n = 719; 14 schools). Students' preferences for certain types of goals and information processing strategies were examined using questionnaires.…

Constructing squares as a mathematical problem solving process in pre-school

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MARIA ANGELA SHIAKALLI

2014-06-01

Full Text Available Could problem solving be the object of teaching in early education? Could children’s engagement in problem solving processes lead to skills and conceptual understanding development? Could appropriate teaching interventions scaffold children’s efforts? The sample consisted of 25 children attending public pre-school in Cyprus. The children were asked to construct different sized squares. Findings show that children responded positively to the problem and were successful in solving it. During the problem solving process children demonstrated development of skills and conceptual understanding. Teacher-children and children-children interactions played an important role in the positive outcome of the activity.

Economical analysis of the spray drying process by pre-dehumidification of the inlet air

Energy Technology Data Exchange (ETDEWEB)

Madeira, A.N.; Camargo, J.R. [University of Taubate (UNITAU), SP (Brazil). Mechanical Engineering Dept.

2009-07-01

Spray drying is a dehumidification process by atomization in a closed chamber that aims to remove moisture of a product by heat and mass transfer from the product's contained water to the air that, in this process is previously heated. This paper presents a case study for an industry that produces food ingredients. The current process applied in the product to heat the air can uses one of these two systems: a direct heating process that burns liquid petroleum gas in contact with the inlet air or indirect heating that uses a heat exchanger which heat the air. This heating system consumes 90% of the total process energy. However, this inlet air can reach the dehumidifier with high moisture from the atmosphere condition requesting, in this case, more energy consumption according to the year's seasons. This paper promotes a utilization study of the current process through the installation of a pre-dehumidification device of the inlet air and shows a study to three different dehumidification systems that means by refrigeration, adsorption and actual comparing their performance in an energetic and economical point of view. The goals of this study are to analyze the capacity of moisture removing of each removing device, the influence of moisture variation of the inlet air in the process as well as the economic impact of each device in the global system. It concludes that the utilization of dehumidification devices can eliminate the heating system reducing this way the energy consumption. Moreover it promotes the increasing of moisture gradient between the inlet air and the product optimizing the drying process and increasing the global energy efficiency in the global system. Choosing the most appropriate system for the pre-dehumidification device depends on the desired initial and final moisture content of the product, but applying pre-dehumidifiers at the inlet air promotes an energetic optimization in the spray drying process. (author)

The Process of Solving Complex Problems

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Fischer, Andreas; Greiff, Samuel; Funke, Joachim

2012-01-01

This article is about Complex Problem Solving (CPS), its history in a variety of research domains (e.g., human problem solving, expertise, decision making, and intelligence), a formal definition and a process theory of CPS applicable to the interdisciplinary field. CPS is portrayed as (a) knowledge acquisition and (b) knowledge application…

T-lymphocyte cytokine mRNA expression in cystic echinococcosis.

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Fauser, S; Kern, P

1997-04-01

In the present study we investigated cytokine mRNA expression by peripheral blood mononuclear cells (PBMC) from patients with cystic echinococcosis (CE) after stimulation with different antigens. By using reverse transcriptase polymerase chain reaction (RT-PCR) we could demonstrate that restimulation with crude Echinococcus granulosus antigen (Eg-Ag) induced or enhanced Th2 cytokine mRNA expression, especially IL-5 (by using antigen from sheep cyst fluid) in 23 out of 26 investigated CE patients and IL-10 (by using antigen from camel cyst fluid) in 10 out of 10 investigated CE patients. In contrast, IL-5 mRNA expression was absent in PBMC of healthy controls after Eg-Ag stimulation. To determine the specificity of this reaction we stimulated PBMC from 11 CE patients with crude Echinococcus multilocularis antigen (Em-Ag) and PBMC from 8 CE patients with Toxocara canis antigen (Tc-Ag). We found that the PBMC of patients showed a similar mRNA cytokine pattern on stimulation with Em-Ag when compared with Eg-Ag stimulation. The cytokine mRNA pattern on stimulation with Tc-Ag, however, resembled the cytokine mRNA pattern of unstimulated PBMC. Furthermore, the stimulation of PBMC with crude Mycobacterium tuberculosis antigen (H37Ra) and purified protein derivative (PPD) of M. tuberculosis revealed distinct IL-5 mRNA expression in all investigated CE patients, whereas in healthy controls IL-5 mRNA expression was very weak or totally absent. Thus, our results indicate an induction of Th2 cytokine mRNA expression in CE patients, which is frequently observed in parasite infections. Interestingly, this response persists after stimulation with tuberculosis antigens, which normally induce Th1 response.

Correlation of mRNA Profiles, miRNA Profiles, and Functional Immune Response in Rainbow Trout (Oncorrhynkus Mykiss) Infected With Viral Hemorrhagic Septicemia Virus (VHSV) and in Fish Vaccinated With a DNA Vaccine Against VHSV

DEFF Research Database (Denmark)

Bela-Ong, Dennis; Schyth, Brian Dall; Jørgensen, Hanne

2011-01-01

and are incorporated into the RNA-Induced Silencing Complex (RISC), which target specific mRNA sequences, causing either mRNA degradation or translation repression. This results in altered mRNA and protein profiles characteristic of a particular cellular phenotype or physiological state. By targeting immune relevant m...

Sensitivity, Specificity, and Clinical Value of Human Papillomavirus (HPV) E6/E7 mRNA Assay as a Triage Test for Cervical Cytology and HPV DNA Test ▿

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Benevolo, Maria; Vocaturo, Amina; Caraceni, Donatella; French, Deborah; Rosini, Sandra; Zappacosta, Roberta; Terrenato, Irene; Ciccocioppo, Lucia; Frega, Antonio; Rossi, Paolo Giorgi

2011-01-01

There is evidence that testing for human papillomavirus (HPV) E6/E7 mRNA is more specific than testing for HPV DNA. A retrospective study was carried out to evaluate the performance of the PreTect HPV-Proofer E6/E7 mRNA assay (Norchip) as a triage test for cytology and HPV DNA testing. This study analyzed 1,201 women, 688 of whom had a colposcopy follow-up and 195 of whom had histology-confirmed high-grade intraepithelial neoplasia or worse (CIN2+). The proportion of positive results and the sensitivity and specificity for CIN2+ were determined for HPV mRNA in comparison to HPV DNA and cytology. All data were adjusted for follow-up completeness. Stratified by cytological grades, the HPV mRNA sensitivity was 83% (95% confidence interval [CI] = 63 to 94%) in ASC-US (atypical squamous cells of undetermined significance), 62% (95% CI = 47 to 75%) in L-SIL (low-grade squamous intraepithelial lesion), and 67% (95% CI = 57 to 76%) in H-SIL (high-grade squamous intraepithelial lesion). The corresponding figures were 99, 91, and 96%, respectively, for HPV DNA. The specificities were 82, 76, and 45%, respectively, for HPV mRNA and 29, 13, and 4%, respectively, for HPV DNA. Used as a triage test for ASC-US and L-SIL, mRNA reduced colposcopies by 79% (95% CI = 74 to 83%) and 69% (95% CI = 65 to 74%), respectively, while HPV DNA reduced colposcopies by 38% (95% CI = 32 to 44%) and by 15% (95% CI = 12 to 19%), respectively. As a HPV DNA positivity triage test, mRNA reduced colposcopies by 63% (95% CI = 60 to 66%), having 68% sensitivity (95% CI = 61 to 75%), whereas cytology at the ASC-US+ threshold reduced colposcopies by 23% (95% CI = 20 to 26%), showing 92% sensitivity (95% CI = 87 to 95%). In conclusion, PreTect HPV-Proofer mRNA can serve as a better triage test than HPV DNA to reduce colposcopy referral in both ASC-US and L-SIL. It is also more efficient than cytology for the triage of HPV DNA-positive women. Nevertheless, its low sensitivity demands a strict follow-up of

The effect of pre-mutation of X chromosome CGG trinucleotide repeats on brain anatomy.

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Moore, Caroline J; Daly, Eileen M; Tassone, Flora; Tysoe, Carolyn; Schmitz, Nicole; Ng, Virginia; Chitnis, Xavier; McGuire, Philip; Suckling, John; Davies, Kay E; Hagerman, Randi J; Hagerman, Paul J; Murphy, Kieran C; Murphy, Declan G M

2004-12-01

Expanded trinucleotide repeats are associated with several neuropsychiatric disorders, including fragile X syndrome (FraX) which is the most common inherited form of mental retardation. It is currently thought that FraX results from having >200 CGG trinucleotide repeats, with consequent methylation of the fragile X mental retardation gene (FMR1) and loss of FMR1 protein (FMRP). Pre-mutation carriers of FraX (with 55-200 CGG trinucleotide repeats) were originally considered unaffected, although recent studies challenge this view. However, there are few studies on the effect of pre-mutation trinucleotide repeat expansion on the male human brain using quantitative MRI. Also the results of prior investigations may be confounded because people were selected on the basis of clinical and neurological features, and not genetic phenotype. We compared the brain anatomy of 20 adult male pre-mutation members of known FraX families with 20 healthy male controls. The two groups did not differ significantly in age, intelligence quotient (IQ) or handedness. We also investigated whether any observed effects were associated with: (i) ageing; (ii) expansion of pre-mutation CGG trinucleotide repeats; (iii) reduction in the percentage of lymphocytes staining with anti-FMRP antibodies [%FMRP(+) lymphocytes]; and (iv) elevation of FMR1 mRNA levels. Male pre-mutation carriers of FraX, compared with matched controls, had significantly less voxel density in several brain regions, including the cerebellum, amygdalo-hippocampal complex and thalamus. Within pre-mutation carriers of FraX, ageing, increases in the number of CGG trinucleotide repeats and decreases in %FMRP(+) lymphocytes were associated with decreasing voxel density of regions previously identified as decreased relative to controls. Regional grey and white matter density is significantly affected in male pre-mutation carriers of FraX recruited on the basis of genetic, not clinical, phenotype. The association of voxel density

Theoretical analysis of the distribution of isolated particles in totally asymmetric exclusion processes: Application to mRNA translation rate estimation

Science.gov (United States)

Dao Duc, Khanh; Saleem, Zain H.; Song, Yun S.

2018-01-01

The Totally Asymmetric Exclusion Process (TASEP) is a classical stochastic model for describing the transport of interacting particles, such as ribosomes moving along the messenger ribonucleic acid (mRNA) during translation. Although this model has been widely studied in the past, the extent of collision between particles and the average distance between a particle to its nearest neighbor have not been quantified explicitly. We provide here a theoretical analysis of such quantities via the distribution of isolated particles. In the classical form of the model in which each particle occupies only a single site, we obtain an exact analytic solution using the matrix ansatz. We then employ a refined mean-field approach to extend the analysis to a generalized TASEP with particles of an arbitrary size. Our theoretical study has direct applications in mRNA translation and the interpretation of experimental ribosome profiling data. In particular, our analysis of data from Saccharomyces cerevisiae suggests a potential bias against the detection of nearby ribosomes with a gap distance of less than approximately three codons, which leads to some ambiguity in estimating the initiation rate and protein production flux for a substantial fraction of genes. Despite such ambiguity, however, we demonstrate theoretically that the interference rate associated with collisions can be robustly estimated and show that approximately 1% of the translating ribosomes get obstructed.

Infrared pre-drying and dry-dehulling of walnuts for improved processing efficiency and product quality

Science.gov (United States)

The walnut industry is faced with an urgent need to improve post-harvest processing efficiency, particularly drying and dehulling operations. This research investigated the feasibility of dry-dehulling and infrared (IR) pre-drying of walnuts for improved processing efficiency and dried product quali...

Removal of inhibitors from pre-hydrolysis liquor of kraft-based dissolving pulp production process using adsorption and flocculation processes.

Science.gov (United States)

Liu, Xin; Fatehi, Pedram; Ni, Yonghao

2012-07-01

A process for removing inhibitors from pre-hydrolysis liquor (PHL) of a kraft-based dissolving pulp production process by adsorption and flocculation, and the characteristics of this process were studied. In this process, industrially produced PHL was treated with unmodified and oxidized activated carbon as an absorbent and polydiallyldimethylammonium chloride (PDADMAC) as a flocculant. The overall removal of lignin and furfural in the developed process was 83.3% and 100%, respectively, while that of hemicelluloses was 32.7%. These results confirmed that the developed process can remove inhibitors from PHL prior to producing value-added products, e.g. ethanol and xylitol via fermentation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Excitatory Modulation of the preBötzinger Complex Inspiratory Rhythm Generating Network by Endogenous Hydrogen Sulfide

Directory of Open Access Journals (Sweden)

Glauber S. F. da Silva

2017-06-01

Full Text Available Hydrogen Sulfide (H2S is one of three gasotransmitters that modulate excitability in the CNS. Global application of H2S donors or inhibitors of H2S synthesis to the respiratory network has suggested that inspiratory rhythm is modulated by exogenous and endogenous H2S. However, effects have been variable, which may reflect that the RTN/pFRG (retrotrapezoid nucleus, parafacial respiratory group and the preBötzinger Complex (preBötC, critical for inspiratory rhythm generation are differentially modulated by exogenous H2S. Importantly, site-specific modulation of respiratory nuclei by H2S means that targeted, rather than global, manipulation of respiratory nuclei is required to understand the role of H2S signaling in respiratory control. Thus, our aim was to test whether endogenous H2S, which is produced by cystathionine-β-synthase (CBS in the CNS, acts specifically within the preBötC to modulate inspiratory activity under basal (in vitro/in vivo and hypoxic conditions (in vivo. Inhibition of endogenous H2S production by bath application of the CBS inhibitor, aminooxyacetic acid (AOAA, 0.1–1.0 mM to rhythmic brainstem spinal cord (BSSC and medullary slice preparations from newborn rats, or local application of AOAA into the preBötC (slices only caused a dose-dependent decrease in burst frequency. Unilateral injection of AOAA into the preBötC of anesthetized, paralyzed adult rats decreased basal inspiratory burst frequency, amplitude and ventilatory output. AOAA in vivo did not affect the initial hypoxia-induced (10% O2, 5 min increase in ventilatory output, but enhanced the secondary hypoxic respiratory depression. These data suggest that the preBötC inspiratory network receives tonic excitatory modulation from the CBS-H2S system, and that endogenous H2S attenuates the secondary hypoxic respiratory depression.

Identification of a functionally distinct truncated BDNF mRNA splice variant and protein in Trachemys scripta elegans.

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Ganesh Ambigapathy

Full Text Available Brain-derived neurotrophic factor (BDNF has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform. Nine different mRNA transcripts from the BDNF gene of the pond turtle Trachemys scripta elegans (tBDNF are selectively regulated during classical conditioning: exon I mRNA transcripts show no change, exon II transcripts are downregulated, while exon III transcripts are upregulated. One unique transcript that codes from exon II, tBDNF2a, contains a 40 base pair deletion in the protein coding exon that generates a truncated tBDNF protein. The truncated transcript and protein are expressed in the naïve untrained state and are fully repressed during conditioning when full-length mature tBDNF is expressed, thereby having an alternate pattern of expression in conditioning. Truncated BDNF is not restricted to turtles as a truncated mRNA splice variant has been described for the human BDNF gene. Further studies are required to determine the ubiquity of truncated BDNF alternative splice variants across species and the mechanisms of regulation and function of this newly recognized BDNF protein.

Identification of a functionally distinct truncated BDNF mRNA splice variant and protein in Trachemys scripta elegans.

Science.gov (United States)

Ambigapathy, Ganesh; Zheng, Zhaoqing; Li, Wei; Keifer, Joyce

2013-01-01

Brain-derived neurotrophic factor (BDNF) has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform. Nine different mRNA transcripts from the BDNF gene of the pond turtle Trachemys scripta elegans (tBDNF) are selectively regulated during classical conditioning: exon I mRNA transcripts show no change, exon II transcripts are downregulated, while exon III transcripts are upregulated. One unique transcript that codes from exon II, tBDNF2a, contains a 40 base pair deletion in the protein coding exon that generates a truncated tBDNF protein. The truncated transcript and protein are expressed in the naïve untrained state and are fully repressed during conditioning when full-length mature tBDNF is expressed, thereby having an alternate pattern of expression in conditioning. Truncated BDNF is not restricted to turtles as a truncated mRNA splice variant has been described for the human BDNF gene. Further studies are required to determine the ubiquity of truncated BDNF alternative splice variants across species and the mechanisms of regulation and function of this newly recognized BDNF protein.

Porphyromonas gingivalis Differentially Modulates Cell Death Profile in Ox-LDL and TNF-α Pre-Treated Endothelial Cells.

Directory of Open Access Journals (Sweden)

Isaac Maximiliano Bugueno

Full Text Available Clinical studies demonstrated a potential link between atherosclerosis and periodontitis. Porphyromonas gingivalis (Pg, one of the main periodontal pathogen, has been associated to atheromatous plaque worsening. However, synergism between infection and other endothelial stressors such as oxidized-LDL or TNF-α especially on endothelial cell (EC death has not been investigated. This study aims to assess the role of Pg on EC death in an inflammatory context and to determine potential molecular pathways involved.Human umbilical vein ECs (HUVECs were infected with Pg (MOI 100 or stimulated by its lipopolysaccharide (Pg-LPS (1μg/ml for 24 to 48 hours. Cell viability was measured with AlamarBlue test, type of cell death induced was assessed using Annexin V/propidium iodide staining. mRNA expression regarding caspase-1, -3, -9, Bcl-2, Bax-1 and Apaf-1 has been evaluated with RT-qPCR. Caspases enzymatic activity and concentration of APAF-1 protein were evaluated to confirm mRNA results.Pg infection and Pg-LPS stimulation induced EC death. A cumulative effect has been observed in Ox-LDL pre-treated ECs infected or stimulated. This effect was not observed in TNF-α pre-treated cells. Pg infection promotes EC necrosis, however, in infected Ox-LDL pre-treated ECs, apoptosis was promoted. This effect was not observed in TNF-α pre-treated cells highlighting specificity of molecular pathways activated. Regarding mRNA expression, Pg increased expression of pro-apoptotic genes including caspases-1,-3,-9, Bax-1 and decreased expression of anti-apoptotic Bcl-2. In Ox-LDL pre-treated ECs, Pg increased significantly the expression of Apaf-1. These results were confirmed at the protein level.This study contributes to demonstrate that Pg and its Pg-LPS could exacerbate Ox-LDL and TNF-α induced endothelial injury through increase of EC death. Interestingly, molecular pathways are differentially modulated by the infection in function of the pre-stimulation.

Extrinsic and intrinsic complexities of the Los Alamos plutonium processing facility

International Nuclear Information System (INIS)

Bearse, R.C.; Roberts, N.J.; Longmire, V.L.

1985-01-01

Analysis of the data obtained in one year of plutonium accounting at Los Alamos reveals significant complexity. Much of this complexity arises from the complexity of the processes themselves. Additional complexity is induced by errors in the data entry process. It is important to note that there is no evidence that this complexity is adversely affecting the accounting in the plant. The authors have been analyzing transaction data from fiscal year 1983 processing. This study involved 62,595 transactions. The data have been analyzed using the relational database program INGRES on a VAX 11/780 computer. This software allows easy manipulation of the original data and subsets drawn from it. The authors have been attempting for several years to understand the global features of the TA-55 accounting data. This project has underscored several of the system's complexities

mRNA expression of genes regulating lipid metabolism in ringed seals (Pusa hispida) from differently polluted areas

International Nuclear Information System (INIS)

Castelli, Martina Galatea; Rusten, Marte; Goksøyr, Anders; Routti, Heli

2014-01-01

encoding hepatic PPARγ, adipose FABP4, adipose ADIPOQ and ΣPOP concentrations was observed. These findings suggest that lipid metabolism may be affected by contaminant exposure in the Baltic population. mRNA expression of genes encoding PPARβ, PPARγ, FABP4 and ADIPOQ were similar between the mid and inner adipose layer. Hepatic mRNA expression of genes encoding PPARα and PPARγ was higher in the pre-molting individuals compared to the molting ones highlighting differential regulation of these metabolic sensors through the molting period

mRNA expression of genes regulating lipid metabolism in ringed seals (Pusa hispida) from differently polluted areas

Energy Technology Data Exchange (ETDEWEB)

Castelli, Martina Galatea [Norwegian Polar Institute, Fram Centre, 9296 Tromsø (Norway); University of Bergen, Department of Biology, 5020 Bergen (Norway); Rusten, Marte; Goksøyr, Anders [University of Bergen, Department of Biology, 5020 Bergen (Norway); Routti, Heli, E-mail: heli.routti@npolar.no [Norwegian Polar Institute, Fram Centre, 9296 Tromsø (Norway)

2014-01-15

encoding hepatic PPARγ, adipose FABP4, adipose ADIPOQ and ΣPOP concentrations was observed. These findings suggest that lipid metabolism may be affected by contaminant exposure in the Baltic population. mRNA expression of genes encoding PPARβ, PPARγ, FABP4 and ADIPOQ were similar between the mid and inner adipose layer. Hepatic mRNA expression of genes encoding PPARα and PPARγ was higher in the pre-molting individuals compared to the molting ones highlighting differential regulation of these metabolic sensors through the molting period.

Ire1 mediated mRNA splicing in a C-terminus deletion mutant of Drosophila Xbp1.

Directory of Open Access Journals (Sweden)

Dina S Coelho

Full Text Available The Unfolded Protein Response is a homeostatic mechanism that permits eukaryotic cells to cope with Endoplasmic Reticulum (ER stress caused by excessive accumulation of misfolded proteins in the ER lumen. The more conserved branch of the UPR relies on an ER transmembrane enzyme, Ire1, which, upon ER stress, promotes the unconventional splicing of a small intron from the mRNA encoding the transcription factor Xbp1. In mammals, two specific regions (the hydrophobic region 2--HR2--and the C-terminal translational pausing site present in the Xbp1unspliced protein mediate the recruitment of the Xbp1 mRNA-ribosome-nascent chain complex to the ER membrane, so that Xbp1 mRNA can be spliced by Ire1. Here, we generated a Drosophila Xbp1 deletion mutant (Excision101 lacking both HR2 and C-terminal region, but not the Ire1 splicing site. We show that Ire1-dependent splicing of Xbp1 mRNA is reduced, but not abolished in Excision101. Our results suggest the existence of additional mechanisms for ER membrane targeting of Xbp1 mRNA that are independent of the C-terminal domain of Drosophila Xbp1unspliced.

Efficiency of Dinucleosides as the Backbone to Pre-Organize Multi-Porphyrins and Enhance Their Stability as Sandwich Type Complexes with DABCO

Directory of Open Access Journals (Sweden)

Sonja Merkaš

2017-07-01

Full Text Available Flexible linkers such as uridine or 2′-deoxyuridine pre-organize bis-porphyrins in a face-to-face conformation, thus forming stable sandwich complexes with a bidentate base such as 1,4-diazabicyclo[2.2.2]octane (DABCO. Increased stability can be even greater when a dinucleotide linker is used. Such pre-organization increases the association constant by one to two orders of magnitude when compared to the association constant of DABCO with a reference porphyrin. Comparison with rigid tweezers shows a better efficiency of nucleosidic dimers. Thus, the choice of rigid spacers is not the only way to pre-organize bis-porphyrins, and well-chosen nucleosidic linkers offer an interesting option for the synthesis of such devices.

Pre design processing of waste of ex-resin without materials matrix from nuclear power plant type PWR 1000 MW

International Nuclear Information System (INIS)

Cerdas Tarigan

2010-01-01

Have been done pre design processing of waste ex-resin without capacities matrix materials from nuclear power plant type PWR 1000 MW During the time radioactive waste of ex-resin processed to use process of immobilization use matrix materials like mixture cement and epoxy resin and then conditioning. This process is not effective and efficient because end result volume of end product bigger than volume early operation system and maintenance of its installation more difficult. To overcome this created a design of technology processing of waste of ex- resin without matrix materials through process of strainer, drying and conditioning represent technological innovation newly processing of radioactive waste of ex-resin. Besides this process more effective and efficient, volume of end product waste much more small from volume early and operation system and maintenance of its easier installation. Pre design is expected to be used as a basis to make conceptual of pre design installation of strainer, drying and conditioning for the processing of waste of ex-resin from nuclear power plant type PWR 1000 MW. (author)

Muscle individual phospholipid classes throughout the processing of dry-cured ham: influence of pre-cure freezing.

Science.gov (United States)

Pérez-Palacios, Trinidad; Ruiz, Jorge; Dewettinck, Koen; Le, Thien Trung; Antequera, Teresa

2010-03-01

This paper aims to study the profile of phospholipid (PL) classes of Iberian ham throughout its processing and the changes it underwent due to the influence of the pre-cure freezing treatment. The general profile of each PL class did not vary during the ripening stage. Phosphatidylcholine (PC) showed the highest proportion, followed by phosphatidyletanolamine (PE) and phosphatidylserine (PS) and phosphatidylinositol (PI) being the minor PL. The four PL classes were highly hydrolysed during the salting stage and their degradation continued during the rest of the processing. Pre-cure freezing of Iberian ham influenced the levels of the four PL classes at the initial stage, all of them being higher in refrigerated (R) than in pre-cure frozen (F) hams. Moreover, the pattern of hydrolysis was not the same in these two groups. Copyright 2009 Elsevier Ltd. All rights reserved.

Extrinsic and intrinsic complexities of the Los Alamos Plutonium Processing Facility

International Nuclear Information System (INIS)

Bearse, R.C.; Longmire, V.L.; Roberts, N.J.

1985-01-01

Analysis of the data obtained in one year of plutonium accounting at Los Alamos reveals significant complexity. Much of this complexity arises from the complexity of the processes themselves. Additional complexity is induced by errors in the data entry process. It is important to note that there is no evidence that this complexity is adversely affecting the accounting in the plant. We have been analyzing transaction data from fiscal year 1983 processing. This study involved 62,595 transactions. The data have been analyzed using the relational database program INGRES on a VAX 11/780 computer. This software allows easy manipulation of the original data and subsets drawn from it. We have been attempting for several years to understand the global features of the TA-55 accounting data. This project has underscored several of the system's complexities. Examples that will be reported here include audit trails, lot-name multiplicity, etc

The Cognitive, Social and Emotional Processes of Teacher Identity Construction in a Pre-Service Teacher Education Programme

Science.gov (United States)

Yuan, Rui; Lee, Icy

2015-01-01

This research investigates how three Government-funded Normal Students constructed and reconstructed their identities in a pre-service teacher education programme in China. Drawing upon data from interviews, field observation and the pre-service teachers' written reflections, the study explores the cognitive, social and emotional processes of…

Applying Enhancement Filters in the Pre-processing of Images of Lymphoma

International Nuclear Information System (INIS)

Silva, Sérgio Henrique; Do Nascimento, Marcelo Zanchetta; Neves, Leandro Alves; Batista, Valério Ramos

2015-01-01

Lymphoma is a type of cancer that affects the immune system, and is classified as Hodgkin or non-Hodgkin. It is one of the ten types of cancer that are the most common on earth. Among all malignant neoplasms diagnosed in the world, lymphoma ranges from three to four percent of them. Our work presents a study of some filters devoted to enhancing images of lymphoma at the pre-processing step. Here the enhancement is useful for removing noise from the digital images. We have analysed the noise caused by different sources like room vibration, scraps and defocusing, and in the following classes of lymphoma: follicular, mantle cell and B-cell chronic lymphocytic leukemia. The filters Gaussian, Median and Mean-Shift were applied to different colour models (RGB, Lab and HSV). Afterwards, we performed a quantitative analysis of the images by means of the Structural Similarity Index. This was done in order to evaluate the similarity between the images. In all cases we have obtained a certainty of at least 75%, which rises to 99% if one considers only HSV. Namely, we have concluded that HSV is an important choice of colour model at pre-processing histological images of lymphoma, because in this case the resulting image will get the best enhancement

Pre-engineering assessment of Enersolve Demonstration Project. Dairy processing plant. Final report

Energy Technology Data Exchange (ETDEWEB)

1985-07-15

This study involved evaluation of a dairy processing plant to demonstrate energy conservation potential and developing a strategy to realize energy savings through retrofitting and revamping. The cheese and whey making plant of Agropur Cooperative Agro-Alimentaire located in Quebec was selected as a representative Canadian dairy processing plant. The pre-engineering assessment included a review of existing facility at the plant and plant operation, identification of plant equipment or process steps where substantial economic benefits would result from retrofitting and revamping, and estimation of budgetary cost for the subsequent engineering, procurement, construction management and monitoring of the retrofitted equipment. 3 figs., 2 tabs.

Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

LENUS (Irish Health Repository)

Moreau, Isabelle

2012-02-03

Pre-treatment HCV quasispecies complexity and diversity may predict response to interferon based anti-viral therapy. The objective of this study was to retrospectively (1) examine temporal changes in quasispecies prior to the start of therapy and (2) investigate extensively quasispecies evolution in a group of 10 chronically infected patients with genotype 3a, treated with pegylated alpha2a-Interferon and ribavirin. The degree of sequence heterogeneity within the hypervariable region 1 was assessed by analyzing 20-30 individual clones in serial serum samples. Genetic parameters, including amino acid Shannon entropy, Hamming distance and genetic distance were calculated for each sample. Treatment outcome was divided into (1) sustained virological responders (SVR) and (2) treatment failure (TF). Our results indicate, (1) quasispecies complexity and diversity are lower in the SVR group, (2) quasispecies vary temporally and (3) genetic heterogeneity at baseline can be use to predict treatment outcome. We discuss the results from the perspective of replicative homeostasis.

β-glucuronidase use as a single internal control gene may confound analysis in FMR1 mRNA toxicity studies.

Science.gov (United States)

Kraan, Claudine M; Cornish, Kim M; Bui, Quang M; Li, Xin; Slater, Howard R; Godler, David E

2018-01-01

Relationships between Fragile X Mental Retardation 1 (FMR1) mRNA levels in blood and intragenic FMR1 CGG triplet expansions support the pathogenic role of RNA gain of function toxicity in premutation (PM: 55-199 CGGs) related disorders. Real-time PCR (RT-PCR) studies reporting these findings normalised FMR1 mRNA level to a single internal control gene called β-glucuronidase (GUS). This study evaluated FMR1 mRNA-CGG correlations in 33 PM and 33 age- and IQ-matched control females using three normalisation strategies in peripheral blood mononuclear cells (PBMCs): (i) GUS as a single internal control; (ii) the mean of GUS, Eukaryotic Translation Initiation Factor 4A2 (EIF4A2) and succinate dehydrogenase complex flavoprotein subunit A (SDHA); and (iii) the mean of EIF4A2 and SDHA (with no contribution from GUS). GUS mRNA levels normalised to the mean of EIF4A2 and SDHA mRNA levels and EIF4A2/SDHA ratio were also evaluated. FMR1mRNA level normalised to the mean of EIF4A2 and SDHA mRNA levels, with no contribution from GUS, showed the most significant correlation with CGG size and the greatest difference between PM and control groups (p = 10-11). Only 15% of FMR1 mRNA PM results exceeded the maximum control value when normalised to GUS, compared with over 42% when normalised to the mean of EIF4A2 and SDHA mRNA levels. Neither GUS mRNA level normalised to the mean RNA levels of EIF4A2 and SDHA, nor to the EIF4A2/SDHA ratio were correlated with CGG size. However, greater variability in GUS mRNA levels were observed for both PM and control females across the full range of CGG repeat as compared to the EIF4A2/SDHA ratio. In conclusion, normalisation with multiple control genes, excluding GUS, can improve assessment of the biological significance of FMR1 mRNA-CGG size relationships.

Learning processes of students pre-vocational secondary education: relations between goal orientations, information processing strategies and development of conceptual knowledge

NARCIS (Netherlands)

Koopman, M.; Brok, den P.J.; Beijaard, D.; Teune, P.J.

2011-01-01

The purpose of this study was to investigate relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education students (n = 719; 14 schools). Students' preferences for certain types of goals and information

[Complex automatic data processing in multi-profile hospitals].

Science.gov (United States)

Dovzhenko, Iu M; Panov, G D

1990-01-01

The computerization of data processing in multi-disciplinary hospitals is the key factor in raising the quality of medical care provided to the population, intensifying the work of the personnel, improving the curative and diagnostic process and the use of resources. Even a small experience in complex computerization at the Botkin Hospital indicates that due to the use of the automated system the quality of data processing in being improved, a high level of patients' examination is being provided, a speedy training of young specialists is being achieved, conditions are being created for continuing education of physicians through the analysis of their own activity. At big hospitals a complex solution of administrative and curative diagnostic tasks on the basis of general hospital network of display connection and general hospital data bank is the most prospective form of computerization.

Improving Robustness of Hydrologic Ensemble Predictions Through Probabilistic Pre- and Post-Processing in Sequential Data Assimilation

Science.gov (United States)

Wang, S.; Ancell, B. C.; Huang, G. H.; Baetz, B. W.

2018-03-01

Data assimilation using the ensemble Kalman filter (EnKF) has been increasingly recognized as a promising tool for probabilistic hydrologic predictions. However, little effort has been made to conduct the pre- and post-processing of assimilation experiments, posing a significant challenge in achieving the best performance of hydrologic predictions. This paper presents a unified data assimilation framework for improving the robustness of hydrologic ensemble predictions. Statistical pre-processing of assimilation experiments is conducted through the factorial design and analysis to identify the best EnKF settings with maximized performance. After the data assimilation operation, statistical post-processing analysis is also performed through the factorial polynomial chaos expansion to efficiently address uncertainties in hydrologic predictions, as well as to explicitly reveal potential interactions among model parameters and their contributions to the predictive accuracy. In addition, the Gaussian anamorphosis is used to establish a seamless bridge between data assimilation and uncertainty quantification of hydrologic predictions. Both synthetic and real data assimilation experiments are carried out to demonstrate feasibility and applicability of the proposed methodology in the Guadalupe River basin, Texas. Results suggest that statistical pre- and post-processing of data assimilation experiments provide meaningful insights into the dynamic behavior of hydrologic systems and enhance robustness of hydrologic ensemble predictions.

A Case Study on Pre-Service Secondary School Mathematics Teachers' Cognitive-Metacognitive Behaviours in Mathematical Modelling Process

Science.gov (United States)

Sagirli, Meryem Özturan

2016-01-01

The aim of the present study is to investigate pre-service secondary mathematics teachers' cognitive-metacognitive behaviours during the mathematical problem-solving process considering class level. The study, in which the case study methodology was employed, was carried out with eight pre-service mathematics teachers, enrolled at a university in…

A stability comparison of redox-active layers produced by chemical coupling of an osmium redox complex to pre-functionalized gold and carbon electrodes

International Nuclear Information System (INIS)

Boland, Susan; Foster, Kevin; Leech, Donal

2009-01-01

The production of stable redox active layers on electrode surfaces is a key factor for the development of practical electronic and electrochemical devices. Here, we report on a comparison of the stability of redox layers formed by covalently coupling an osmium redox complex to pre-functionalized gold and graphite electrode surfaces. Pre-treatment of gold and graphite electrodes to provide surface carboxylic acid groups is achieved via classical thiolate self-assembled monolayer formation on gold surfaces and the electro-reduction of an in situ generated aryldiazonium salt from 4-aminobenzoic acid on gold, glassy carbon and graphite surfaces. These surfaces have been characterized by AFM and electrochemical blocking studies. The surface carboxylate is then used to tether an osmium complex, [Os(2,2'-bipyridyl) 2 (4-aminomethylpyridine)Cl]PF 6 , to provide a covalently bound redox active layer, E 0 '' of 0.29 V (vs. Ag/AgCl in phosphate buffer, pH 7.4), on the pre-treated electrodes. The aryldiazonium salt-treated carbon-based surfaces showed the greatest stability, represented by a decrease of <5% in the peak current for the Os(II/III) redox transition of the immobilized complex over a 3-day period, compared to a decrease of 19% and 14% for the aryldiazonium salt treated and thiolate treated gold surfaces, respectively, over the same period

Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression.

Science.gov (United States)

Stinchcombe, Adam R; Peskin, Charles S; Tranchina, Daniel

2012-06-01

We present a generalization of a population density approach for modeling and analysis of stochastic gene expression. In the model, the gene of interest fluctuates stochastically between an inactive state, in which transcription cannot occur, and an active state, in which discrete transcription events occur; and the individual mRNA molecules are degraded stochastically in an independent manner. This sort of model in simplest form with exponential dwell times has been used to explain experimental estimates of the discrete distribution of random mRNA copy number. In our generalization, the random dwell times in the inactive and active states, T_{0} and T_{1}, respectively, are independent random variables drawn from any specified distributions. Consequently, the probability per unit time of switching out of a state depends on the time since entering that state. Our method exploits a connection between the fully discrete random process and a related continuous process. We present numerical methods for computing steady-state mRNA distributions and an analytical derivation of the mRNA autocovariance function. We find that empirical estimates of the steady-state mRNA probability mass function from Monte Carlo simulations of laboratory data do not allow one to distinguish between underlying models with exponential and nonexponential dwell times in some relevant parameter regimes. However, in these parameter regimes and where the autocovariance function has negative lobes, the autocovariance function disambiguates the two types of models. Our results strongly suggest that temporal data beyond the autocovariance function is required in general to characterize gene switching.

ENDF/B Pre-Processing Codes: Implementing and testing on a Personal Computer

International Nuclear Information System (INIS)

McLaughlin, P.K.

1987-05-01

This document describes the contents of the diskettes containing the ENDF/B Pre-Processing codes by D.E. Cullen, and example data for use in implementing and testing these codes on a Personal Computer of the type IBM-PC/AT. Upon request the codes are available from the IAEA Nuclear Data Section, free of charge, on a series of 7 diskettes. (author)

Learning processes of students in competence-based pre-vocational secondary education: relations between goal orientations, information processing strategies and development of conceptual knowledge

NARCIS (Netherlands)

Dr. M. Koopman; prof dr Douwe Beijaard; Dr P.J. Teune; P. den Brok

2011-01-01

The purpose of this study was to investigate relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education students (n=719; 14 schools). Students' preferences for certain types of goals and information processing

Cloudy Solar Software - Enhanced Capabilities for Finding, Pre-processing, and Visualizing Solar Data

Science.gov (United States)

Istvan Etesi, Laszlo; Tolbert, K.; Schwartz, R.; Zarro, D.; Dennis, B.; Csillaghy, A.

2010-05-01

In our project "Extending the Virtual Solar Observatory (VSO)” we have combined some of the features available in Solar Software (SSW) to produce an integrated environment for data analysis, supporting the complete workflow from data location, retrieval, preparation, and analysis to creating publication-quality figures. Our goal is an integrated analysis experience in IDL, easy-to-use but flexible enough to allow more sophisticated procedures such as multi-instrument analysis. To that end, we have made the transition from a locally oriented setting where all the analysis is done on the user's computer, to an extended analysis environment where IDL has access to services available on the Internet. We have implemented a form of Cloud Computing that uses the VSO search and a new data retrieval and pre-processing server (PrepServer) that provides remote execution of instrument-specific data preparation. We have incorporated the interfaces to the VSO search and the PrepServer into an IDL widget (SHOW_SYNOP) that provides user-friendly searching and downloading of raw solar data and optionally sends search results for pre-processing to the PrepServer prior to downloading the data. The raw and pre-processed data can be displayed with our plotting suite, PLOTMAN, which can handle different data types (light curves, images, and spectra) and perform basic data operations such as zooming, image overlays, solar rotation, etc. PLOTMAN is highly configurable and suited for visual data analysis and for creating publishable figures. PLOTMAN and SHOW_SYNOP work hand-in-hand for a convenient working environment. Our environment supports a growing number of solar instruments that currently includes RHESSI, SOHO/EIT, TRACE, SECCHI/EUVI, HINODE/XRT, and HINODE/EIS.

Changes in cognitive control in pre-manifest Huntington's disease examined using pre-saccadic EEG potentials - a longitudinal study.

Science.gov (United States)

Ness, Vanessa; Bestgen, Anne-Kathrin; Saft, Carsten; Beste, Christian

2014-01-01

It is well-known that Huntington's disease (HD) affects saccadic processing. However, saccadic dysfunctions in HD may be seen as a result of dysfunctional processes occurring at the oculomotor level prior to the execution of saccades, i.e., at a pre-saccadic level. Virtually nothing is known about possible changes in pre-saccadic processes in HD. This study examines pre-saccadic processing in pre-manifest HD gene mutation carriers (pre-HDs) by using clinically available EEG measures. Error rates, pre-saccadic EEG potentials and saccade onset EEG potentials were measured in 14 pre-HDs and case-matched controls performing prosaccades and antisaccades in a longitudinal study over a 15-month period. The results show that pre-saccadic potentials were changed in pre-HDs, relative to controls and also revealed changes across the 15-month longitudinal period. In particular, pre-saccadic ERP in pre-HDs were characterized by lower amplitudes and longer latencies, which revealed longitudinal changes. These changes were observed for anti-saccades, but not for pro-saccades. Overt saccadic trajectories (potentials) were not different to those in controls, showing that pre-saccadic processes are sensitive to subtle changes in fronto-striatal networks in pre-HDs. Deficits in pre-saccadic processes prior the execution of an erroneous anti-saccade can be seen as an effect of dysfunctional cognitive control in HD. This may underlie saccadic abnormalities and hence a major phenotype of HD. Pre-saccadic EEG potentials preceding erroneous anti-saccades are sensitive to pre-manifest disease progression in HD.

Quality Measures in Pre-Analytical Phase of Tissue Processing: Understanding Its Value in Histopathology.

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Rao, Shalinee; Masilamani, Suresh; Sundaram, Sandhya; Duvuru, Prathiba; Swaminathan, Rajendiran

2016-01-01

Quality monitoring in histopathology unit is categorized into three phases, pre-analytical, analytical and post-analytical, to cover various steps in the entire test cycle. Review of literature on quality evaluation studies pertaining to histopathology revealed that earlier reports were mainly focused on analytical aspects with limited studies on assessment of pre-analytical phase. Pre-analytical phase encompasses several processing steps and handling of specimen/sample by multiple individuals, thus allowing enough scope for errors. Due to its critical nature and limited studies in the past to assess quality in pre-analytical phase, it deserves more attention. This study was undertaken to analyse and assess the quality parameters in pre-analytical phase in a histopathology laboratory. This was a retrospective study done on pre-analytical parameters in histopathology laboratory of a tertiary care centre on 18,626 tissue specimens received in 34 months. Registers and records were checked for efficiency and errors for pre-analytical quality variables: specimen identification, specimen in appropriate fixatives, lost specimens, daily internal quality control performance on staining, performance in inter-laboratory quality assessment program {External quality assurance program (EQAS)} and evaluation of internal non-conformities (NC) for other errors. The study revealed incorrect specimen labelling in 0.04%, 0.01% and 0.01% in 2007, 2008 and 2009 respectively. About 0.04%, 0.07% and 0.18% specimens were not sent in fixatives in 2007, 2008 and 2009 respectively. There was no incidence of specimen lost. A total of 113 non-conformities were identified out of which 92.9% belonged to the pre-analytical phase. The predominant NC (any deviation from normal standard which may generate an error and result in compromising with quality standards) identified was wrong labelling of slides. Performance in EQAS for pre-analytical phase was satisfactory in 6 of 9 cycles. A low incidence

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

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Tachibana Taro

2011-10-01

Full Text Available Abstract Background Cellular function is regulated by the balance of stringently regulated amounts of mRNA. Previous reports revealed that RNA polymerase II (RNAPII, which transcribes mRNA, can be classified into the pausing state and the active transcription state according to the phosphorylation state of RPB1, the catalytic subunit of RNAPII. However, genome-wide association between mRNA expression level and the phosphorylation state of RNAPII is unclear. While the functional importance of pausing genes is clear, such as in mouse Embryonic Stem cells for differentiation, understanding this association is critical for distinguishing pausing genes from active transcribing genes in expression profiling data, such as microarrays and RNAseq. Therefore, we examined the correlation between the phosphorylation of RNAPII and mRNA expression levels using a combined analysis by ChIPseq and RNAseq. Results We first performed a precise quantitative measurement of mRNA by performing an optimized calculation in RNAseq. We then visualized the recruitment of various phosphorylated RNAPIIs, such as Ser2P and Ser5P. A combined analysis using optimized RNAseq and ChIPseq for phosphorylated RNAPII revealed that mRNA levels correlate with the various phosphorylation states of RNAPII. Conclusions We demonstrated that the amount of mRNA is precisely reflected by the phased phosphorylation of Ser2 and Ser5. In particular, even the most "pausing" genes, for which only Ser5 is phosphorylated, were detectable at a certain level of mRNA. Our analysis indicated that the complexity of quantitative regulation of mRNA levels could be classified into three categories according to the phosphorylation state of RNAPII.

Data pre-processing for web log mining: Case study of commercial bank website usage analysis

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Jozef Kapusta

2013-01-01

Full Text Available We use data cleaning, integration, reduction and data conversion methods in the pre-processing level of data analysis. Data processing techniques improve the overall quality of the patterns mined. The paper describes using of standard pre-processing methods for preparing data of the commercial bank website in the form of the log file obtained from the web server. Data cleaning, as the simplest step of data pre-processing, is non–trivial as the analysed content is highly specific. We had to deal with the problem of frequent changes of the content and even frequent changes of the structure. Regular changes in the structure make use of the sitemap impossible. We presented approaches how to deal with this problem. We were able to create the sitemap dynamically just based on the content of the log file. In this case study, we also examined just the one part of the website over the standard analysis of an entire website, as we did not have access to all log files for the security reason. As the result, the traditional practices had to be adapted for this special case. Analysing just the small fraction of the website resulted in the short session time of regular visitors. We were not able to use recommended methods to determine the optimal value of session time. Therefore, we proposed new methods based on outliers identification for raising the accuracy of the session length in this paper.

Students' goal orientations, information processing strategies and knowledge development in competence-based pre-vocational secondary education

NARCIS (Netherlands)

Koopman, M.

2010-01-01

In this study, learning processes of students in competence-based Pre-Vocational Secondary Education (PVSE; in Dutch vmbo) were investigated. The study aimed at describing the relation between goal orientations, information processing strategies and the development of knowledge of these students.

Lariat capping as a tool to manipulate the 5' end of individual yeast mRNA species in vivo

DEFF Research Database (Denmark)

Krogh, Nicolai; Pietschmann, Max; Schmid, Manfred

2017-01-01

The 5' cap structure of eukaryotic mRNA is critical for its processing, transport, translation, and stability. The many functions of the cap and the fact that most, if not all, mRNA carries the same type of cap makes it difficult to analyze cap function in vivo at individual steps of gene...... in the budding yeast Saccharomyces cerevisiae presumably without cofactors and that lariat capping occurs cotranscriptionally. The lariat-capped reporter mRNA is efficiently exported to the cytoplasm where it is found to be oligoadenylated and evenly distributed. Both the oligoadenylated form and a lariat......-capped mRNA with a templated poly(A) tail translates poorly, underlining the critical importance of the m(7)G cap in translation. Finally, the lariat-capped RNA exhibits a threefold longer half-life compared to its m(7)G-capped counterpart, consistent with a key role for the m(7)G cap in mRNA turnover. Our...

[Impacts of the formula of Suoquanwan(SQW) on expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney of rat polyuria model of Yang-deficiency].

Science.gov (United States)

Cao, Hong-Ying; Wu, Qing-He; Huang, Ping; He, Jin-Yang

2009-06-01

To observe the impacts of the formula of Suoquanwan (SQW) on the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney of rat polyuria model of Yang-deficiency. The model rats were induced by adenine (250 mg/kg) for 4 weeks, then treated respectively with SQW or dDAVP. The expression of AQP-2 mRNA and AVPR-V2 mRNA in kidney of Yang-deficiency model by realtime fluorescence quantitative PCR method were investigated. In model rats, the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney decreased, dDAVP and SQW high dose could increased the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney. The others had no influence on the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney. SQW can increase the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney of rat polyuria model of Yang-deficiency.

Anticancer Activity of Metal Complexes: Involvement of Redox Processes

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Jungwirth, Ute; Kowol, Christian R.; Keppler, Bernhard K.; Hartinger, Christian G.; Berger, Walter; Heffeter, Petra

2012-01-01

Cells require tight regulation of the intracellular redox balance and consequently of reactive oxygen species for proper redox signaling and maintenance of metal (e.g., of iron and copper) homeostasis. In several diseases, including cancer, this balance is disturbed. Therefore, anticancer drugs targeting the redox systems, for example, glutathione and thioredoxin, have entered focus of interest. Anticancer metal complexes (platinum, gold, arsenic, ruthenium, rhodium, copper, vanadium, cobalt, manganese, gadolinium, and molybdenum) have been shown to strongly interact with or even disturb cellular redox homeostasis. In this context, especially the hypothesis of “activation by reduction” as well as the “hard and soft acids and bases” theory with respect to coordination of metal ions to cellular ligands represent important concepts to understand the molecular modes of action of anticancer metal drugs. The aim of this review is to highlight specific interactions of metal-based anticancer drugs with the cellular redox homeostasis and to explain this behavior by considering chemical properties of the respective anticancer metal complexes currently either in (pre)clinical development or in daily clinical routine in oncology. PMID:21275772

Performance Comparison of Several Pre-Processing Methods in a Hand Gesture Recognition System based on Nearest Neighbor for Different Background Conditions

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Iwan Setyawan

2012-12-01

Full Text Available This paper presents a performance analysis and comparison of several pre-processing methods used in a hand gesture recognition system. The pre-processing methods are based on the combinations of several image processing operations, namely edge detection, low pass filtering, histogram equalization, thresholding and desaturation. The hand gesture recognition system is designed to classify an input image into one of six possible classes. The input images are taken with various background conditions. Our experiments showed that the best result is achieved when the pre-processing method consists of only a desaturation operation, achieving a classification accuracy of up to 83.15%.

A Polypyrimidine Tract Binding Protein, Pumpkin RBP50, Forms the Basis of a Phloem-Mobile Ribonucleoprotein Complex[W

Science.gov (United States)

Ham, Byung-Kook; Brandom, Jeri L.; Xoconostle-Cázares, Beatriz; Ringgold, Vanessa; Lough, Tony J.; Lucas, William J.

2009-01-01

RNA binding proteins (RBPs) are integral components of ribonucleoprotein (RNP) complexes and play a central role in RNA processing. In plants, some RBPs function in a non-cell-autonomous manner. The angiosperm phloem translocation stream contains a unique population of RBPs, but little is known regarding the nature of the proteins and mRNA species that constitute phloem-mobile RNP complexes. Here, we identified and characterized a 50-kD pumpkin (Cucurbita maxima cv Big Max) phloem RNA binding protein (RBP50) that is evolutionarily related to animal polypyrimidine tract binding proteins. In situ hybridization studies indicated a high level of RBP50 transcripts in companion cells, while immunolocalization experiments detected RBP50 in both companion cells and sieve elements. A comparison of the levels of RBP50 present in vascular bundles and phloem sap indicated that this protein is highly enriched in the phloem sap. Heterografting experiments confirmed that RBP50 is translocated from source to sink tissues. Collectively, these findings established that RBP50 functions as a non-cell-autonomous RBP. Protein overlay, coimmunoprecipitation, and cross-linking experiments identified the phloem proteins and mRNA species that constitute RBP50-based RNP complexes. Gel mobility-shift assays demonstrated that specificity, with respect to the bound mRNA, is established by the polypyrimidine tract binding motifs within such transcripts. We present a model for RBP50-based RNP complexes within the pumpkin phloem translocation stream. PMID:19122103

Secondary Mathematics Pre-Service Teachers' Processes of Selection and Integration of Technology

Science.gov (United States)

Uzan, Erol

2017-01-01

This study investigated secondary mathematics pre-service teachers' (PSTs) knowledge of resources in terms of digital technologies, and explored the processes of both selection and integration of technology into their lesson plans. This study employed a case study design. Participants were six secondary mathematics PSTs who enrolled in a methods…

Elevating serotonin pre-partum alters the Holstein dairy cow hepatic adaptation to lactation

Science.gov (United States)

Weaver, Samantha R.; Prichard, Allan S.; Maerz, Noah L.; Prichard, Austin P.; Endres, Elizabeth L.; Hernández-Castellano, Lorenzo E.; Akins, Matthew S.; Bruckmaier, Rupert M.

2017-01-01

Serotonin is known to regulate energy and calcium homeostasis in several mammalian species. The objective of this study was to determine if pre-partum infusions of 5-hydroxytryptophan (5-HTP), the immediate precursor to serotonin synthesis, could modulate energy homeostasis at the level of the hepatocyte in post-partum Holstein and Jersey dairy cows. Twelve multiparous Holstein cows and twelve multiparous Jersey cows were intravenously infused daily for approximately 7 d pre-partum with either saline or 1 mg/kg bodyweight of 5-HTP. Blood was collected for 14 d post-partum and on d30 post-partum. Liver biopsies were taken on d1 and d7 post-partum. There were no changes in the circulating concentrations of glucose, insulin, glucagon, non-esterified fatty acids, or urea nitrogen in response to treatment, although there were decreased beta-hydroxybutyrate concentrations with 5-HTP treatment around d6 to d10 post-partum, particularly in Jersey cows. Cows infused with 5-HTP had increased hepatic serotonin content and increased mRNA expression of the serotonin 2B receptor on d1 and d7 post-partum. Minimal changes were seen in the hepatic mRNA expression of various gluconeogenic enzymes. There were no changes in the mRNA expression profile of cell-cycle progression marker cyclin-dependent kinase 4 or apoptotic marker caspase 3, although proliferating cell nuclear antigen expression tended to be increased in Holstein cows infused with 5-HTP on d1 post-partum. Immunofluorescence assays showed an increased number of CASP3- and Ki67-positive cells in Holstein cows infused with 5-HTP on d1 post-partum. Given the elevated hepatic serotonin content and increased mRNA abundance of 5HTR2B, 5-HTP infusions may be stimulating an autocrine-paracrine adaptation to lactation in the Holstein cow liver. PMID:28922379

Elevating serotonin pre-partum alters the Holstein dairy cow hepatic adaptation to lactation.

Directory of Open Access Journals (Sweden)

Samantha R Weaver

Full Text Available Serotonin is known to regulate energy and calcium homeostasis in several mammalian species. The objective of this study was to determine if pre-partum infusions of 5-hydroxytryptophan (5-HTP, the immediate precursor to serotonin synthesis, could modulate energy homeostasis at the level of the hepatocyte in post-partum Holstein and Jersey dairy cows. Twelve multiparous Holstein cows and twelve multiparous Jersey cows were intravenously infused daily for approximately 7 d pre-partum with either saline or 1 mg/kg bodyweight of 5-HTP. Blood was collected for 14 d post-partum and on d30 post-partum. Liver biopsies were taken on d1 and d7 post-partum. There were no changes in the circulating concentrations of glucose, insulin, glucagon, non-esterified fatty acids, or urea nitrogen in response to treatment, although there were decreased beta-hydroxybutyrate concentrations with 5-HTP treatment around d6 to d10 post-partum, particularly in Jersey cows. Cows infused with 5-HTP had increased hepatic serotonin content and increased mRNA expression of the serotonin 2B receptor on d1 and d7 post-partum. Minimal changes were seen in the hepatic mRNA expression of various gluconeogenic enzymes. There were no changes in the mRNA expression profile of cell-cycle progression marker cyclin-dependent kinase 4 or apoptotic marker caspase 3, although proliferating cell nuclear antigen expression tended to be increased in Holstein cows infused with 5-HTP on d1 post-partum. Immunofluorescence assays showed an increased number of CASP3- and Ki67-positive cells in Holstein cows infused with 5-HTP on d1 post-partum. Given the elevated hepatic serotonin content and increased mRNA abundance of 5HTR2B, 5-HTP infusions may be stimulating an autocrine-paracrine adaptation to lactation in the Holstein cow liver.

3-D image pre-processing algorithms for improved automated tracing of neuronal arbors.

Science.gov (United States)

Narayanaswamy, Arunachalam; Wang, Yu; Roysam, Badrinath

2011-09-01

The accuracy and reliability of automated neurite tracing systems is ultimately limited by image quality as reflected in the signal-to-noise ratio, contrast, and image variability. This paper describes a novel combination of image processing methods that operate on images of neurites captured by confocal and widefield microscopy, and produce synthetic images that are better suited to automated tracing. The algorithms are based on the curvelet transform (for denoising curvilinear structures and local orientation estimation), perceptual grouping by scalar voting (for elimination of non-tubular structures and improvement of neurite continuity while preserving branch points), adaptive focus detection, and depth estimation (for handling widefield images without deconvolution). The proposed methods are fast, and capable of handling large images. Their ability to handle images of unlimited size derives from automated tiling of large images along the lateral dimension, and processing of 3-D images one optical slice at a time. Their speed derives in part from the fact that the core computations are formulated in terms of the Fast Fourier Transform (FFT), and in part from parallel computation on multi-core computers. The methods are simple to apply to new images since they require very few adjustable parameters, all of which are intuitive. Examples of pre-processing DIADEM Challenge images are used to illustrate improved automated tracing resulting from our pre-processing methods.

Possibility of content change in bioethanol gasoline during pre-treatment process for using accelerator mass spectroscopy

International Nuclear Information System (INIS)

Saito, Masaaki; Yunoki, Shunji; Suzuki, Takashi

2010-01-01

We attempted to determine the bioethanol content of E3 gasoline by applying ASTM D6866 method B. In the pre-treatment process using accelerator mass spectroscopy(AMS), the graphite samples were prepared from E3 gasoline. Three portions of the same graphite sample were measured, and the contents agreed within the measurement error of AMS. The graphite samples prepared from eight portions of the same E3 gasoline sample were measured, but the accuracy was insufficient. There are many kinds of hydrocarbon compounds in the gasoline and their boiling points are different. The content of bioethanol was found to decrease with vaporization when E3 gasoline was placed in open air. A very small amount of E3 gasoline is pre-treated for AMS and the volatile loss cannot be ignored. It seems that the content change of bioethanol was caused by vaporization of E3 gasoline during the pre-treatment process. (author)

Automated Pre-processing for NMR Assignments with Reduced Tedium

Energy Technology Data Exchange (ETDEWEB)

2004-05-11

An important rate-limiting step in the reasonance asignment process is accurate identification of resonance peaks in MNR spectra. NMR spectra are noisy. Hence, automatic peak-picking programs must navigate between the Scylla of reliable but incomplete picking, and the Charybdis of noisy but complete picking. Each of these extremes complicates the assignment process: incomplete peak-picking results in the loss of essential connectivities, while noisy picking conceals the true connectivities under a combinatiorial explosion of false positives. Intermediate processing can simplify the assignment process by preferentially removing false peaks from noisy peak lists. This is accomplished by requiring consensus between multiple NMR experiments, exploiting a priori information about NMR spectra, and drawing on empirical statistical distributions of chemical shift extracted from the BioMagResBank. Experienced NMR practitioners currently apply many of these techniques "by hand", which is tedious, and may appear arbitrary to the novice. To increase efficiency, we have created a systematic and automated approach to this process, known as APART. Automated pre-processing has three main advantages: reduced tedium, standardization, and pedagogy. In the hands of experienced spectroscopists, the main advantage is reduced tedium (a rapid increase in the ratio of true peaks to false peaks with minimal effort). When a project is passed from hand to hand, the main advantage is standardization. APART automatically documents the peak filtering process by archiving its original recommendations, the accompanying justifications, and whether a user accepted or overrode a given filtering recommendation. In the hands of a novice, this tool can reduce the stumbling block of learning to differentiate between real peaks and noise, by providing real-time examples of how such decisions are made.

Increase of CTGF mRNA expression by respiratory syncytial virus infection is abrogated by caffeine in lung epithelial cells.

Science.gov (United States)

Kunzmann, Steffen; Krempl, Christine; Seidenspinner, Silvia; Glaser, Kirsten; Speer, Christian P; Fehrholz, Markus

2018-04-16

Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract infection in early childhood. Underlying pathomechanisms of elevated pulmonary morbidity in later infancy are largely unknown. We found that RSV-infected H441 cells showed increased mRNA expression of connective tissue growth factor (CTGF), a key factor in airway remodeling. Additional dexamethasone treatment led to further elevated mRNA levels, indicating additive effects. Caffeine treatment prevented RSV-mediated increase of CTGF mRNA. RSV may be involved in airway remodeling processes by increasing CTGF mRNA expression. Caffeine might abrogate these negative effects and thereby help to restore lung homeostasis. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Understanding the implementation of complex interventions in health care: the normalization process model

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Rogers Anne

2007-09-01

Full Text Available Abstract Background The Normalization Process Model is a theoretical model that assists in explaining the processes by which complex interventions become routinely embedded in health care practice. It offers a framework for process evaluation and also for comparative studies of complex interventions. It focuses on the factors that promote or inhibit the routine embedding of complex interventions in health care practice. Methods A formal theory structure is used to define the model, and its internal causal relations and mechanisms. The model is broken down to show that it is consistent and adequate in generating accurate description, systematic explanation, and the production of rational knowledge claims about the workability and integration of complex interventions. Results The model explains the normalization of complex interventions by reference to four factors demonstrated to promote or inhibit the operationalization and embedding of complex interventions (interactional workability, relational integration, skill-set workability, and contextual integration. Conclusion The model is consistent and adequate. Repeated calls for theoretically sound process evaluations in randomized controlled trials of complex interventions, and policy-makers who call for a proper understanding of implementation processes, emphasize the value of conceptual tools like the Normalization Process Model.

Procurement of complex performance in public infrastructure: a process perspective

OpenAIRE

Hartmann, Andreas; Roehrich, Jens; Davies, Andrew; Frederiksen, Lars; Davies, J.; Harrington, T.; Kirkwood, D.; Holweg, M.

2011-01-01

The paper analyzes the process of transitioning from procuring single products and services to procuring complex performance in public infrastructure. The aim is to examine the change in the interactions between buyer and supplier, the emergence of value co-creation and the capability development during the transition process. Based on a multiple, longitudinal case study the paper proposes three generic transition stages towards increased performance and infrastructural complexity. These stag...

Dynamic Proteomics Emphasizes the Importance of Selective mRNA Translation and Protein Turnover during Arabidopsis Seed Germination*

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Galland, Marc; Huguet, Romain; Arc, Erwann; Cueff, Gwendal; Job, Dominique; Rajjou, Loïc

2014-01-01

During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [35S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment. PMID:24198433

Cytoplasmic protein binding to highly conserved sequences in the 3' untranslated region of mouse protamine 2 mRNA, a translationally regulated transcript of male germ cells

International Nuclear Information System (INIS)

Kwon, Y.K.; Hecht, N.B.

1991-01-01

The expression of the protamines, the predominant nuclear proteins of mammalian spermatozoa, is regulated translationally during male germ-cell development. The 3' untranslated region (UTR) of protamine 1 mRNA has been reported to control its time of translation. To understand the mechanisms controlling translation of the protamine mRNAs, we have sought to identify cis elements of the 3' UTR of protamine 2 mRNA that are recognized by cytoplasmic factors. From gel retardation assays, two sequence elements are shown to form specific RNA-protein complexes. Protein binding sites of the two complexes were determined by RNase T1 mapping, by blocking the putative binding sites with antisense oligonucleotides, and by competition assays. The sequences of these elements, located between nucleotides + 537 and + 572 in protamine 2 mRNA, are highly conserved among postmeiotic translationally regulated nuclear proteins of the mammalian testis. Two closely linked protein binding sites were detected. UV-crosslinking studies revealed that a protein of about 18 kDa binds to one of the conserved sequences. These data demonstrate specific protein binding to a highly conserved 3' UTR of translationally regulated testicular mRNA

Habitat Complexity in Aquatic Microcosms Affects Processes Driven by Detritivores.

Directory of Open Access Journals (Sweden)

Lorea Flores

Full Text Available Habitat complexity can influence predation rates (e.g. by providing refuge but other ecosystem processes and species interactions might also be modulated by the properties of habitat structure. Here, we focussed on how complexity of artificial habitat (plastic plants, in microcosms, influenced short-term processes driven by three aquatic detritivores. The effects of habitat complexity on leaf decomposition, production of fine organic matter and pH levels were explored by measuring complexity in three ways: 1. as the presence vs. absence of habitat structure; 2. as the amount of structure (3 or 4.5 g of plastic plants; and 3. as the spatial configuration of structures (measured as fractal dimension. The experiment also addressed potential interactions among the consumers by running all possible species combinations. In the experimental microcosms, habitat complexity influenced how species performed, especially when comparing structure present vs. structure absent. Treatments with structure showed higher fine particulate matter production and lower pH compared to treatments without structures and this was probably due to higher digestion and respiration when structures were present. When we explored the effects of the different complexity levels, we found that the amount of structure added explained more than the fractal dimension of the structures. We give a detailed overview of the experimental design, statistical models and R codes, because our statistical analysis can be applied to other study systems (and disciplines such as restoration ecology. We further make suggestions of how to optimise statistical power when artificially assembling, and analysing, 'habitat complexity' by not confounding complexity with the amount of structure added. In summary, this study highlights the importance of habitat complexity for energy flow and the maintenance of ecosystem processes in aquatic ecosystems.

Role of cytochrome B in the processing of the subunits of complex III in the yeast mitochondria

International Nuclear Information System (INIS)

Sen, K.G.

1986-01-01

The work described in this dissertation deals with the effect of cytochrome b on the biogenesis and assembly of the subunits of complex III in the mitochondrial membrane of the yeast Saccharomyces cerevisiae. The cytochrome b-mutants (Box mutants of S. cerevisiae form an excellent system to study such a role of cytochome B. The amounts of cytochrome c 1 in the mitochrondria, as determined both spectroscopically and immunologically, were not affected by the absence of cytochrome b. Pulse labelling of the cells with ( 35 S) methionine in the presence of CCCP showed the accumulation of the precursors to the core protein I and the iron-sulfur protein in similar amounts in the mutant Box 6-2 and the wild type cells. Synthesis of the iron sulfur protein and the cytochrome c 1 by in vitro translation of mRNA isolated from wild type and mutant Box 6-2 in a rabbit reticulocyte lysate system, also confirmed that the synthesis of the nuclear encoded subunits was not affected in the mutants. Pulse labeling of the cells in the absence of CCCP and subsequent chase with cold methionine, however, showed much less of the mature subunits of core protein I and the iron-sulfur protein in the mitochrondria of the mutant cells relative to the wild type. These results indicate that cytochrome b is necessary for the proper processing of certain subunits of complex III

The effect of leptin receptor deficiency and fasting on cannabinoid receptor 1 mRNA expression in the rat hypothalamus, brainstem and nodose ganglion.

Science.gov (United States)

Jelsing, Jacob; Larsen, Philip Just; Vrang, Niels

2009-10-02

Despite ample evidence for the involvement of the endocannabinoid system in the control of appetite, food intake and energy balance, relatively little is known about the regulation of cannabinoid receptor 1 (CB(1)R) expression in respect to leptin signalling and fasting. In the present study, we examined CB(1)R mRNA levels in lean (Fa/?) and obese (fa/fa) male Zucker rats under basal and food-restricted conditions. Using stereological sampling principles coupled with semi-quantitative radioactive in situ hybridization we provide semi-quantitative estimates of CB(1)R mRNA expression in key appetite regulatory hypothalamic and brainstem areas, as well as in the nodose ganglia. Whereas no effect of fasting were determined on CB(1)R mRNA levels in the paraventricular (PVN) and ventromedial hypothalamic (VMH) nucleus, in the brainstem dorsal vagal complex or nodose ganglion of lean Zucker rats, CB(1)R mRNA levels were consistently elevated in obese Zucker rats pointing to a direct influence of disrupted leptin signalling on CB(1)R mRNA regulation.

Skeletal muscle myostatin mRNA expression is fiber-type specific and increases during hindlimb unloading

Science.gov (United States)

Carlson, C. J.; Booth, F. W.; Gordon, S. E.

1999-01-01

Transgenic mice lacking a functional myostatin (MSTN) gene demonstrate greater skeletal muscle mass resulting from muscle fiber hypertrophy and hyperplasia (McPherron, A. C., A. M. Lawler, and S. -J. Lee. Nature 387: 83-90, 1997). Therefore, we hypothesized that, in normal mice, MSTN may act as a negative regulator of muscle mass. Specifically, we hypothesized that the predominately slow (type I) soleus muscle, which demonstrates greater atrophy than the fast (type II) gastrocnemius-plantaris complex (Gast/PLT), would show more elevation in MSTN mRNA abundance during hindlimb unloading (HU). Surprisingly, MSTN mRNA was not detectable in weight-bearing or HU soleus muscle, which atrophied 42% by the 7th day of HU in female ICR mice. In contrast, MSTN mRNA was present in weight-bearing Gast/PLT muscle and was significantly elevated (67%) at 1 day but not at 3 or 7 days of HU. However, the Gast/PLT muscle had only atrophied 17% by the 7th day of HU. Because the soleus is composed only of type I and IIa fibers, whereas the Gast/PLT expresses type IId/x and IIb in addition to type I and IIa, it was necessary to perform a more careful analysis of the relationship between MSTN mRNA levels and myosin heavy-chain (MHC) isoform expression (as a marker of fiber type). A significant correlation (r = 0.725, P < 0. 0005) was noted between the percentage of MHC isoform IIb expression and MSTN mRNA abundance in several muscles of the mouse hindlimb. These results indicate that MSTN expression is not strongly associated with muscle atrophy induced by HU; however, it is strongly associated with MHC isoform IIb expression in normal muscle.

Permissive effect of dexamethasone on the increase of proenkephalin mRNA induced by depolarization of chromaffin cells

International Nuclear Information System (INIS)

Naranjo, J.R.; Mocchetti, I.; Schwartz, J.P.; Costa, E.

1986-01-01

In cultured bovine chromaffin cells, changes in the dynamic state of enkephalin stores elicited experimentally were studied by measuring cellular proenkephalin mRNA, as well as enkephalin precursors and authentic enkephalin content of cells and culture media. In parallel, tyrosine hydroxylase mRNA and catecholamine cell content were also determined. Low concentrations (0.5-100 pM) of dexamethasone increased the cell contents of proenkephalin mRNA and enkephalin-containing peptides. High concentrations of the hormone(1 μM) were required to increase the cell contents of tyrosine hydroxylase mRNA and catecholamines. Depolarization of the cells with 10 μM veratridine resulted in a depletion of enkephalin and catecholamine stores after 24 hr. The enkephalin, but not the catecholamine, content was restored by 48 hr. An increase in proenkephalin mRNA content might account for the recovery; this increase was curtailed by tetrodotoxin and enhanced by 10 pM dexamethasone. Tyrosine hydroxylase mRNA content was not significantly modified by depolarization, even in the presence of 1 μM dexamethasone. Aldosterone, progesterone, testosterone, or estradiol (1 μM) failed to change proenkephalin mRNA. Hence, dexamethasone appears to exert a specific permissive action on the stimulation of the proenkephalin gene elicited by depolarization. Though the catecholamines and enkephalins are localized in the same chromaffin granules and are coreleased by depolarization, the genes coding for the processes that are rate limiting in the production of these neuromodulators can be differentially regulated

Overcoming the Recalcitrance for the Conversion of Kenaf Pulp to Glucose via Microwave-Assisted Pre-Treatment Processes

Directory of Open Access Journals (Sweden)

Miguel A. Hurtado

2011-02-01

Full Text Available This study evaluates the pre-treatment of cellulose from kenaf plant to yield sugar precursors for the production of ethanol or butanol for use as biofuel additives. In order to convert the crystalline cellulosic form to the amorphous form that can undergo enzymatic hydrolysis of the glycosidic bond to yield sugars, kenaf pulp samples were subjected to two different pre-treatment processes. In the acid pre-treatment, the pulp samples were treated with 37.5% hydrochloric acid in the presence of FeCl3 at 50 °C or 90 °C whereas in the alkaline method, the pulp samples were treated with 25% sodium hydroxide at room temperature and with 2% or 5% sodium hydroxide at 50 °C. Microwave-assisted NaOH-treatment of the cellulose was also investigated and demonstrated to be capable of producing high glucose yield without adverse environmental impact by circumventing the use of large amounts of concentrated acids i.e., 83–85% phosphoric acid employed in most digestion processes. The treated samples were digested with the cellulase enzyme from Trichoderma reesei. The amount of glucose produced was quantified using the QuantichromTM glucose bioassay for assessing the efficiency of glucose production for each of the treatment processes. The microwave-assisted alkaline pre-treatment processes conducted at 50 °C were found to be the most effective in the conversion of the crystalline cellulose to the amorphous form based on the significantly higher yields of sugar produced by enzymatic hydrolysis compared to the untreated sample.

Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

KAUST Repository

Ding, Feng

2014-06-04

Background: Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress.Results: To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS.Conclusions: Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress. 2014 Ding et al.; licensee BioMed Central Ltd.

An Interaction between KSHV ORF57 and UIF Provides mRNA-Adaptor Redundancy in Herpesvirus Intronless mRNA Export

Science.gov (United States)

Jackson, Brian R.; Boyne, James R.; Noerenberg, Marko; Taylor, Adam; Hautbergue, Guillaume M.; Walsh, Matthew J.; Wheat, Rachel; Blackbourn, David J.; Wilson, Stuart A.; Whitehouse, Adrian

2011-01-01

The hTREX complex mediates cellular bulk mRNA nuclear export by recruiting the nuclear export factor, TAP, via a direct interaction with the export adaptor, Aly. Intriguingly however, depletion of Aly only leads to a modest reduction in cellular mRNA nuclear export, suggesting the existence of additional mRNA nuclear export adaptor proteins. In order to efficiently export Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs from the nucleus, the KSHV ORF57 protein recruits hTREX onto viral intronless mRNAs allowing access to the TAP-mediated export pathway. Similarly however, depletion of Aly only leads to a modest reduction in the nuclear export of KSHV intronless mRNAs. Herein, we identify a novel interaction between ORF57 and the cellular protein, UIF. We provide the first evidence that the ORF57-UIF interaction enables the recruitment of hTREX and TAP to KSHV intronless mRNAs in Aly-depleted cells. Strikingly, depletion of both Aly and UIF inhibits the formation of an ORF57-mediated nuclear export competent ribonucleoprotein particle and consequently prevents ORF57-mediated mRNA nuclear export and KSHV protein production. Importantly, these findings highlight that redundancy exists in the eukaryotic system for certain hTREX components involved in the mRNA nuclear export of intronless KSHV mRNAs. PMID:21814512

(Pre-) calibration of a Reduced Complexity Model of the Antarctic Contribution to Sea-level Changes

Science.gov (United States)

Ruckert, K. L.; Guan, Y.; Shaffer, G.; Forest, C. E.; Keller, K.

2015-12-01

(Pre-) calibration of a Reduced Complexity Model of the Antarctic Contribution to Sea-level ChangesKelsey L. Ruckert1*, Yawen Guan2, Chris E. Forest1,3,7, Gary Shaffer 4,5,6, and Klaus Keller1,7,81 Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, USA 2 Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania, USA 3 Department of Meteorology, The Pennsylvania State University, University Park, Pennsylvania, USA 4 GAIA_Antarctica, University of Magallanes, Punta Arenas, Chile 5 Center for Advanced Studies in Arid Zones, La Serena, Chile 6 Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark 7 Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, Pennsylvania, USA 8 Department of Engineering and Public Policy, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA * Corresponding author. E-mail klr324@psu.eduUnderstanding and projecting future sea-level changes poses nontrivial challenges. Sea-level changes are driven primarily by changes in the density of seawater as well as changes in the size of glaciers and ice sheets. Previous studies have demonstrated that a key source of uncertainties surrounding sea-level projections is the response of the Antarctic ice sheet to warming temperatures. Here we calibrate a previously published and relatively simple model of the Antarctic ice sheet over a hindcast period from the last interglacial period to the present. We apply and compare a range of (pre-) calibration methods, including a Bayesian approach that accounts for heteroskedasticity. We compare the model hindcasts and projections for different levels of model complexity and calibration methods. We compare the projections with the upper bounds from previous studies and find our projections have a narrower range in 2100. Furthermore we discuss the implications for the design of climate risk management strategies.

Control of PNG kinase, a key regulator of mRNA translation, is coupled to meiosis completion at egg activation.

Science.gov (United States)

Hara, Masatoshi; Petrova, Boryana; Orr-Weaver, Terry L

2017-05-30

The oocyte-to-embryo transition involves extensive changes in mRNA translation, regulated in Drosophila by the PNG kinase complex whose activity we show here to be under precise developmental control. Despite presence of the catalytic PNG subunit and the PLU and GNU activating subunits in the mature oocyte, GNU is phosphorylated at Cyclin B/CDK1sites and unable to bind PNG and PLU. In vitro phosphorylation of GNU by CyclinB/CDK1 blocks activation of PNG. Meiotic completion promotes GNU dephosphorylation and PNG kinase activation to regulate translation. The critical regulatory effect of phosphorylation is shown by replacement in the oocyte with a phosphorylation-resistant form of GNU, which promotes PNG-GNU complex formation, elevation of Cyclin B, and meiotic defects consistent with premature PNG activation. After PNG activation GNU is destabilized, thus inactivating PNG. This short-lived burst in kinase activity links development with maternal mRNA translation and ensures irreversibility of the oocyte-to-embryo transition.

An Integrated Monitoring System of Pre-earthquake Processes in Peloponnese, Greece

Science.gov (United States)

Karastathis, V. K.; Tsinganos, K.; Kafatos, M.; Eleftheriou, G.; Ouzounov, D.; Mouzakiotis, E.; Papadopoulos, G. A.; Voulgaris, N.; Bocchini, G. M.; Liakopoulos, S.; Aspiotis, T.; Gika, F.; Tselentis, A.; Moshou, A.; Psiloglou, B.

2017-12-01

One of the controversial issues in the contemporary seismology is the ability of radon accumulation monitoring to provide reliable earthquake forecasting. Although there are many examples in the literature showing radon increase before earthquakes, skepticism arises from instability of the measurements, false alarms, difficulties in interpretation caused by the weather influence (eg. rainfall) and difficulties on the consideration an irrefutable theoretical background of the phenomenon.We have developed and extensively tested a multi parameter network aimed for studying of the pre-earthquake processes and operating as a part of integrated monitoring system in the high seismicity area of the Western Hellenic Arc (SW Peloponnese, Greece). The prototype consists of four components: A real-time monitoring system of Radon accumulation. It consists of three gamma radiation detectors [NaI(Tl) scintillators] A nine-station seismic array to monitor the microseismicity in the offshore area of the Hellenic arc. The processing of the data is based on F-K and beam-forming techniques. Real-time weather monitoring systems for air temperature, relative humidity, precipitation and pressure. Thermal radiation emission from AVHRR/NOAA-18 polar orbit satellite observation. The project revolved around the idea of jointly studying the emission of Radon that has been proven in many cases as a reliable indicator of the possible time of an event, with the accurate location of the foreshock activity detected by the seismic array that can be a more reliable indicator of the possible position of an event. In parallel a satellite thermal anomaly detection technique has been used for monitoring of larger magnitude events (possible indicator for strong events M ≥5.0.). The first year of operations revealed a number of pre-seismic radon variation anomalies before several local earthquakes (M>3.6). The Radon increases systematically before the larger events.Details about the overall performance

[Polyadenylated RNA and mRNA export factors in extrachromosomal nuclear domains of vitellogenic oocytes of the insect Tenebrio molitor].

Science.gov (United States)

Bogoliubov, D S; Kiselev, A M; Shabel'nikov, S V; Parfenov, V N

2012-01-01

The nucleus ofvitellogenic oocytes of the yellow mealworm, Tenebrio molitor, contains a karyosphere that consists of the condensed chromatin embedded in an extrachromosomal fibrogranular material. Numerous nuclear bodies located freely in the nucleoplasm are also observed. Amongst these bodies, counterparts of nuclear speckles (= interchromatin granule clusters, IGCs) can be identified by the presence of the marker protein SC35. Microinjections of fluorescently tagged methyloligoribonucleotide probes 2'-O-Me(U)22, complementary to poly(A) tails of RNAs, revealed poly(A)+ RNA in the vast majority of IGCs. We found that all T. molitor oocyte IGCs contain heterogeneous ribonucleoprotein (hnRNP) core protein Al that localizes to IGCs in an RNA-dependent manner. The extrachromosomal material of the karyosphere and a part of nucleoplasmic IGCs also contain the adapter protein Aly that is known to provide a link between pre-mRNA splicing and mRNA export. The essential mRNA export factor/receptor NXF1 was observed to colocalize with Aly. In nucleoplasmic IGCs, NXF1 was found to localize in an RNA-dependent manner whereas it is RNA-independently located in the extrachromosomal material of the karyosphere. We believe our data suggest on a role of the nucleoplasmic IGCs in mRNA biogenesis and retention in a road to nuclear export.

Regulation of mRNA translation during mitosis.

Science.gov (United States)

Tanenbaum, Marvin E; Stern-Ginossar, Noam; Weissman, Jonathan S; Vale, Ronald D

2015-08-25

Passage through mitosis is driven by precisely-timed changes in transcriptional regulation and protein degradation. However, the importance of translational regulation during mitosis remains poorly understood. Here, using ribosome profiling, we find both a global translational repression and identified ~200 mRNAs that undergo specific translational regulation at mitotic entry. In contrast, few changes in mRNA abundance are observed, indicating that regulation of translation is the primary mechanism of modulating protein expression during mitosis. Interestingly, 91% of the mRNAs that undergo gene-specific regulation in mitosis are translationally repressed, rather than activated. One of the most pronounced translationally-repressed genes is Emi1, an inhibitor of the anaphase promoting complex (APC) which is degraded during mitosis. We show that full APC activation requires translational repression of Emi1 in addition to its degradation. These results identify gene-specific translational repression as a means of controlling the mitotic proteome, which may complement post-translational mechanisms for inactivating protein function.

Bim Automation: Advanced Modeling Generative Process for Complex Structures

Science.gov (United States)

Banfi, F.; Fai, S.; Brumana, R.

2017-08-01

The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

Simulating Complex, Cold-region Process Interactions Using a Multi-scale, Variable-complexity Hydrological Model

Science.gov (United States)

Marsh, C.; Pomeroy, J. W.; Wheater, H. S.

2017-12-01

Accurate management of water resources is necessary for social, economic, and environmental sustainability worldwide. In locations with seasonal snowcovers, the accurate prediction of these water resources is further complicated due to frozen soils, solid-phase precipitation, blowing snow transport, and snowcover-vegetation-atmosphere interactions. Complex process interactions and feedbacks are a key feature of hydrological systems and may result in emergent phenomena, i.e., the arising of novel and unexpected properties within a complex system. One example is the feedback associated with blowing snow redistribution, which can lead to drifts that cause locally-increased soil moisture, thus increasing plant growth that in turn subsequently impacts snow redistribution, creating larger drifts. Attempting to simulate these emergent behaviours is a significant challenge, however, and there is concern that process conceptualizations within current models are too incomplete to represent the needed interactions. An improved understanding of the role of emergence in hydrological systems often requires high resolution distributed numerical hydrological models that incorporate the relevant process dynamics. The Canadian Hydrological Model (CHM) provides a novel tool for examining cold region hydrological systems. Key features include efficient terrain representation, allowing simulations at various spatial scales, reduced computational overhead, and a modular process representation allowing for an alternative-hypothesis framework. Using both physics-based and conceptual process representations sourced from long term process studies and the current cold regions literature allows for comparison of process representations and importantly, their ability to produce emergent behaviours. Examining the system in a holistic, process-based manner can hopefully derive important insights and aid in development of improved process representations.

Increased FXYD1 and PGC-1α mRNA after blood flow-restricted running is related to fibre type-specific AMPK signalling and oxidative stress in human muscle

DEFF Research Database (Denmark)

Christiansen, Danny; Murphy, Robyn M; Bangsbo, Jens

2018-01-01

AIM: This study explored the effects of blood flow restriction (BFR) on mRNA responses of PGC-1α (total, 1α1, and 1α4) and Na+ ,K+ -ATPase isoforms (NKA; α1-3 , β1-3 , and FXYD1) to an interval running session, and determined if these effects were related to increased oxidative stress, hypoxia......). A muscle sample was collected before (Pre) and after exercise (+0h, +3h) to quantify mRNA, indicators of oxidative stress (HSP27 protein in type I and II fibres, and catalase and HSP70 mRNA), metabolites, and α-AMPK Thr172 /α-AMPK, ACC Ser221 /ACC, CaMKII Thr287 /CaMKII, and PLBSer16 /PLB ratios in type I...... of oxidative stress and type-I fibre ACC Ser221 /ACC ratio, but dissociated from muscle hypoxia, lactate, and CaMKII signalling. CONCLUSION: Blood flow restriction augmented exercise-induced increases in muscle FXYD1 and PGC-1α mRNA in men. This effect was related to increased oxidative stress and fibre type...

mRNA transfection of mouse and human neural stem cell cultures

OpenAIRE

McLenachan, Samuel; Zhang, D.; Palomo, A.B.; Edel, Michael John; Chen, F.K.

2013-01-01

The use of synthetic mRNA as an alternative gene delivery vector to traditional DNA-based constructs provides an effective method for inducing transient gene expression in cell cultures without genetic modification. Delivery of mRNA has been proposed as a safer alternative to viral vectors in the induction of pluripotent cells for regenerative therapies. Although mRNA transfection of fibroblasts, dendritic and embryonic stem cells has been described, mRNA delivery to neurosphere cultures has ...

Bayesian Optimization for Neuroimaging Pre-processing in Brain Age Classification and Prediction

Directory of Open Access Journals (Sweden)

Jenessa Lancaster

2018-02-01

Full Text Available Neuroimaging-based age prediction using machine learning is proposed as a biomarker of brain aging, relating to cognitive performance, health outcomes and progression of neurodegenerative disease. However, even leading age-prediction algorithms contain measurement error, motivating efforts to improve experimental pipelines. T1-weighted MRI is commonly used for age prediction, and the pre-processing of these scans involves normalization to a common template and resampling to a common voxel size, followed by spatial smoothing. Resampling parameters are often selected arbitrarily. Here, we sought to improve brain-age prediction accuracy by optimizing resampling parameters using Bayesian optimization. Using data on N = 2003 healthy individuals (aged 16–90 years we trained support vector machines to (i distinguish between young (<22 years and old (>50 years brains (classification and (ii predict chronological age (regression. We also evaluated generalisability of the age-regression model to an independent dataset (CamCAN, N = 648, aged 18–88 years. Bayesian optimization was used to identify optimal voxel size and smoothing kernel size for each task. This procedure adaptively samples the parameter space to evaluate accuracy across a range of possible parameters, using independent sub-samples to iteratively assess different parameter combinations to arrive at optimal values. When distinguishing between young and old brains a classification accuracy of 88.1% was achieved, (optimal voxel size = 11.5 mm3, smoothing kernel = 2.3 mm. For predicting chronological age, a mean absolute error (MAE of 5.08 years was achieved, (optimal voxel size = 3.73 mm3, smoothing kernel = 3.68 mm. This was compared to performance using default values of 1.5 mm3 and 4mm respectively, resulting in MAE = 5.48 years, though this 7.3% improvement was not statistically significant. When assessing generalisability, best performance was achieved when applying the entire Bayesian

Comparing Binaural Pre-processing Strategies II: Speech Intelligibility of Bilateral Cochlear Implant Users.

Science.gov (United States)

Baumgärtel, Regina M; Hu, Hongmei; Krawczyk-Becker, Martin; Marquardt, Daniel; Herzke, Tobias; Coleman, Graham; Adiloğlu, Kamil; Bomke, Katrin; Plotz, Karsten; Gerkmann, Timo; Doclo, Simon; Kollmeier, Birger; Hohmann, Volker; Dietz, Mathias

2015-12-30

Several binaural audio signal enhancement algorithms were evaluated with respect to their potential to improve speech intelligibility in noise for users of bilateral cochlear implants (CIs). 50% speech reception thresholds (SRT50) were assessed using an adaptive procedure in three distinct, realistic noise scenarios. All scenarios were highly nonstationary, complex, and included a significant amount of reverberation. Other aspects, such as the perfectly frontal target position, were idealized laboratory settings, allowing the algorithms to perform better than in corresponding real-world conditions. Eight bilaterally implanted CI users, wearing devices from three manufacturers, participated in the study. In all noise conditions, a substantial improvement in SRT50 compared to the unprocessed signal was observed for most of the algorithms tested, with the largest improvements generally provided by binaural minimum variance distortionless response (MVDR) beamforming algorithms. The largest overall improvement in speech intelligibility was achieved by an adaptive binaural MVDR in a spatially separated, single competing talker noise scenario. A no-pre-processing condition and adaptive differential microphones without a binaural link served as the two baseline conditions. SRT50 improvements provided by the binaural MVDR beamformers surpassed the performance of the adaptive differential microphones in most cases. Speech intelligibility improvements predicted by instrumental measures were shown to account for some but not all aspects of the perceptually obtained SRT50 improvements measured in bilaterally implanted CI users. © The Author(s) 2015.

Scene matching based on non-linear pre-processing on reference image and sensed image

Institute of Scientific and Technical Information of China (English)

Zhong Sheng; Zhang Tianxu; Sang Nong

2005-01-01

To solve the heterogeneous image scene matching problem, a non-linear pre-processing method for the original images before intensity-based correlation is proposed. The result shows that the proper matching probability is raised greatly. Especially for the low S/N image pairs, the effect is more remarkable.

Alterations in polyadenylation and its implications for endocrine disease

DEFF Research Database (Denmark)

Rehfeld, Anders Aagaard; Plass, Mireya; Krogh, Anders

2013-01-01

Introduction: Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms with dif......Introduction: Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms...... with different 3' untranslated regions (3' UTRs) and in some cases different coding regions. Two thirds of all human genes undergo APA. The efficiency of the polyadenylation process regulates gene expression and APA plays an important part in post-transcriptional regulation, as the 3' UTR contains various cis...

Increasing process understanding by analyzing complex interactions in experimental data

DEFF Research Database (Denmark)

Naelapaa, Kaisa; Allesø, Morten; Kristensen, Henning Gjelstrup

2009-01-01

understanding of a coating process. It was possible to model the response, that is, the amount of drug released, using both mentioned techniques. However, the ANOVAmodel was difficult to interpret as several interactions between process parameters existed. In contrast to ANOVA, GEMANOVA is especially suited...... for modeling complex interactions and making easily understandable models of these. GEMANOVA modeling allowed a simple visualization of the entire experimental space. Furthermore, information was obtained on how relative changes in the settings of process parameters influence the film quality and thereby drug......There is a recognized need for new approaches to understand unit operations with pharmaceutical relevance. A method for analyzing complex interactions in experimental data is introduced. Higher-order interactions do exist between process parameters, which complicate the interpretation...

Changes in Pre-service Science Teachers' Understandings After Being Involved in Explicit Nature of Science and Socioscientific Argumentation Processes

Science.gov (United States)

Kutluca, A. Y.; Aydın, A.

2017-08-01

The study explored the changes in pre-service science teachers' understanding of the nature of science and their opinions about the nature of science, science teaching and argumentation after their participation in explicit nature of science (NOS) and socioscientific argumentation processes. The participants were 56 third-grade pre-service science teachers studying in a state university in Turkey. The treatment group comprised 27 participants, and there were 29 participants in the comparison group. The comparison group participants were involved in a student-centred science-teaching process, and the participants of the treatment group were involved in explicit NOS and socioscientific argumentation processes. In the study, which lasted a total of 11 weeks, a NOS-as-argumentation questionnaire was administered to all the participants to determine their understanding of NOS at the beginning and end of the data collection process, and six random participants of the treatment group participated in semi-structured interview questions in order to further understand their views regarding NOS, science teaching and argumentation. Qualitative and quantitative data analysis revealed that the explicit NOS and socioscientific argumentation processes had a significant effect on pre-service science teachers' NOS understandings. Furthermore, NOS, argumentation and science teaching views of the participants in the treatment group showed a positive change. The results of this study are discussed in light of the related literature, and suggestions are made within the context of contribution to science-teaching literature, improvement of education quality and education of pre-service teachers.

Uncertainty Reduction for Stochastic Processes on Complex Networks

Science.gov (United States)

Radicchi, Filippo; Castellano, Claudio

2018-05-01

Many real-world systems are characterized by stochastic dynamical rules where a complex network of interactions among individual elements probabilistically determines their state. Even with full knowledge of the network structure and of the stochastic rules, the ability to predict system configurations is generally characterized by a large uncertainty. Selecting a fraction of the nodes and observing their state may help to reduce the uncertainty about the unobserved nodes. However, choosing these points of observation in an optimal way is a highly nontrivial task, depending on the nature of the stochastic process and on the structure of the underlying interaction pattern. In this paper, we introduce a computationally efficient algorithm to determine quasioptimal solutions to the problem. The method leverages network sparsity to reduce computational complexity from exponential to almost quadratic, thus allowing the straightforward application of the method to mid-to-large-size systems. Although the method is exact only for equilibrium stochastic processes defined on trees, it turns out to be effective also for out-of-equilibrium processes on sparse loopy networks.

Certain aspects of the reactivity of carotenoids. Redox processes and complexation

International Nuclear Information System (INIS)

Polyakov, Nikolay E; Leshina, Tatyana V

2006-01-01

The published data on the redox reactions of carotenoids, their supramolecular inclusion complexes and the composition, properties and practical application of these complexes are generalised. Special attention is given to the effect of complexation on radical processes involving carotenoids and on the antioxidant activity of carotenoids.