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Sample records for catalytic rna populations

Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube.

Science.gov (United States)

Díaz Arenas, Carolina; Lehman, Niles

2010-03-23

During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous. Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen with a catalytic RNA. Extensive genotypic sampling from two replicate lineages was gathered and phylogenetic networks were constructed to elucidate the structure of the evolving RNA populations. A common distribution was found in which a mutant sequence was present at high frequency, surrounded by a cloud of mutant with lower frequencies. This is a typical distribution of quasispecies. Most of the mutants in these clouds were connected by short Hamming distance values, indicating their close relatedness. The quasispecies nature of mutant RNA clouds facilitates the recovery of genotypes under pressure of being removed from the population by random drift. The empirical populations therefore evolved a genotypic resiliency despite a high mutation rate by adopting the characteristics of quasispecies, implying that primordial RNA pools could have used this strategy to avoid extinction.
Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube

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Lehman Niles

2010-03-01

Full Text Available Abstract Background During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous. Results Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen with a catalytic RNA. Extensive genotypic sampling from two replicate lineages was gathered and phylogenetic networks were constructed to elucidate the structure of the evolving RNA populations. A common distribution was found in which a mutant sequence was present at high frequency, surrounded by a cloud of mutant with lower frequencies. This is a typical distribution of quasispecies. Most of the mutants in these clouds were connected by short Hamming distance values, indicating their close relatedness. Conclusions The quasispecies nature of mutant RNA clouds facilitates the recovery of genotypes under pressure of being removed from the population by random drift. The empirical populations therefore evolved a genotypic resiliency despite a high mutation rate by adopting the characteristics of quasispecies, implying that primordial RNA pools could have used this strategy to avoid extinction.
DNA/RNA hybrid substrates modulate the catalytic activity of purified AID.

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Abdouni, Hala S; King, Justin J; Ghorbani, Atefeh; Fifield, Heather; Berghuis, Lesley; Larijani, Mani

2018-01-01

Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids. Here, we examined the binding and catalytic behavior of purified AID on DNA/RNA hybrid substrates bearing either random sequences or GC-rich sequences simulating Ig S regions. If substrates were made up of a random sequence, AID preferred substrates composed entirely of DNA over DNA/RNA hybrids. In contrast, if substrates were composed of S region sequences, AID preferred to mutate DNA/RNA hybrids over substrates composed entirely of DNA. Accordingly, AID exhibited a significantly higher affinity for binding DNA/RNA hybrid substrates composed specifically of S region sequences, than any other substrates composed of DNA. Thus, in the absence of any other cellular processes or factors, AID itself favors binding and mutating DNA/RNA hybrids composed of S region sequences. AID:DNA/RNA complex formation and supporting mutational analyses suggest that recognition of DNA/RNA hybrids is an inherent structural property of AID. Copyright © 2017 Elsevier Ltd. All rights reserved.
Effect of apolipoprotein B mRNA-editing catalytic polypeptide-like protein-3G in cervical cancer.

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Xu, Yanhua; Leng, Junhong; Xue, Fang; Dong, Ruiqian

2015-01-01

Cervical cancer is one of the most common gynecologic cancers. The role of apolipoprotein B mRNA-editing catalytic polypeptide-like protein-3G (APCBEC-3G) in cervical cancer has yet to be elucidated. This study intends to explore the effect of APCBEC-3G on cervical cancer cell proliferation and invasion. In vitro, the cervical cancer cell line Hela was transfected by APCBEC-3G plasmid. The mRNA and protein expression levels of APCBEC-3G were detected by Real-time PCR and Western blot, respectively. Cervical cancer cell proliferation was determined by MTT. Transwell assay was applied to measure the effect of APCBEC-3G on cell invasion. APCBEC-3G mRNA and protein increased significantly after transfection (P3G serves as a suppressor of cervical cancer cell proliferation and invasion. Our research provides theoretical basis for further investigation APOBEC-3G effect in cervical cancer occurrence and development.
The evolution of RNA viruses: A population genetics view

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Moya, Andrés; Elena, Santiago F.; Bracho, Alma; Miralles, Rosario; Barrio, Eladio

2000-01-01

RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses. PMID:10860958
Small catalytic RNA: Structure, function and application

Energy Technology Data Exchange (ETDEWEB)

Monforte, Joseph Albert [Univ. of California, Berkeley, CA (United States)

1991-04-01

We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the ``paperclip`` and ``hammerhead`` RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a ``hammerhead,`` to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 121±s are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus_minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.
Small catalytic RNA: Structure, function and application

Energy Technology Data Exchange (ETDEWEB)

Monforte, J.A.

1991-04-01

We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the paperclip'' and hammerhead'' RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a hammerhead,'' to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.
Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination.

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Marasco, Michelle; Li, Weiyi; Lynch, Michael; Pikaard, Craig S

2017-11-02

All eukaryotes have three essential nuclear multisubunit RNA polymerases, abbreviated as Pol I, Pol II and Pol III. Plants are remarkable in having two additional multisubunit RNA polymerases, Pol IV and Pol V, which synthesize noncoding RNAs that coordinate RNA-directed DNA methylation for silencing of transposons and a subset of genes. Based on their subunit compositions, Pols IV and V clearly evolved as specialized forms of Pol II, but their catalytic properties remain undefined. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is considerably more error-prone than Pols II or V, which may be tolerable in its synthesis of short RNAs that serve as precursors for siRNAs targeting non-identical members of transposon families. By contrast, Pol V exhibits high fidelity transcription, similar to Pol II, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci to which siRNA-Argonaute silencing complexes are recruited. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Prokaryotic Argonautes - variations on the RNA interference theme

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van der Oost, John; Swarts, Daan C.; Jore, Matthijs M.

2014-01-01

The discovery of RNA interference (RNAi) has been a major scientific breakthrough. This RNA-guided RNA interference system plays a crucial role in a wide range of regulatory and defense mechanisms in eukaryotes. The key enzyme of the RNAi system is Argonaute (Ago), an endo-ribonuclease that uses a small RNA guide molecule to specifically target a complementary RNA transcript. Two functional classes of eukaryotic Ago have been described: catalytically active Ago that cleaves RNA targets complementary to its guide, and inactive Ago that uses its guide to bind target RNA to down-regulate translation efficiency. A recent comparative genomics study has revealed that Argonaute-like proteins are also encoded by prokaryotic genomes. Interestingly, there is a lot of variation among these prokaryotic Argonaute (pAgo) proteins with respect to domain architecture: some resemble the eukaryotic Ago (long pAgo) containing a complete or disrupted catalytic site, while others are truncated versions (short pAgo) that generally contain an incomplete catalytic site. Prokaryotic Agos with an incomplete catalytic site often co-occur with (predicted) nucleases. Based on this diversity, and on the fact that homologs of other RNAi-related protein components (such as Dicer nucleases) have never been identified in prokaryotes, it has been predicted that variations on the eukaryotic RNAi theme may occur in prokaryotes. PMID:28357239
Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.

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Jiang, F; Kumar, R A; Jones, R A; Patel, D J

1996-07-11

The catalytic properties of RNA and its well known role in gene expression and regulation are the consequence of its unique solution structures. Identification of the structural determinants of ligand recognition by RNA molecules is of fundamental importance for understanding the biological functions of RNA, as well as for the rational design of RNA Sequences with specific catalytic activities. Towards this latter end, Szostak et al. used in vitro selection techniques to isolate RNA sequences ('aptamers') containing a high-affinity binding site for ATP, the universal currency of cellular energy, and then used this motif to engineer ribozymes with polynucleotide kinase activity. Here we present the solution structure, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations, of both uniformly and specifically 13C-, 15N-labelled 40-mer RNA containing the ATP-binding motif complexed with AMP. The aptamer adopts an L-shaped structure with two nearly orthogonal stems, each capped proximally by a G x G mismatch pair, binding the AMP ligand at their junction in a GNRA-like motif.
Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation.

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Wang, Peng; Yang, Lijiang; Gao, Yi Qin; Zhao, Xin Sheng

2015-09-03

H/ACA RNA-guided ribonucleoprotein particle (RNP), the most complicated RNA pseudouridylase so far known, uses H/ACA guide RNA for substrate capture and four proteins (Cbf5, Nop10, L7Ae and Gar1) for pseudouridylation. Although it was shown that Gar1 not only facilitates the product release, but also enhances the catalytic activity, the chemical role that Gar1 plays in this complicated machinery is largely unknown. Kinetics measurement on Pyrococcus furiosus RNPs at different temperatures making use of fluorescence anisotropy showed that Gar1 reduces the catalytic barrier through affecting the activation entropy instead of enthalpy. Site-directed mutagenesis combined with molecular dynamics simulations demonstrated that V149 in the thumb loop of Cbf5 is critical in placing the target uridine to the right position toward catalytic D85 of Cbf5. The enzyme elegantly aligns the position of uridine in the catalytic site with the help of Gar1. In addition, conversion of uridine to pseudouridine results in a rigid syn configuration of the target nucleotide in the active site and causes Gar1 to pull out the thumb. Both factors guarantee the efficient release of the product. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Chemical fidelity of an RNA polymerase ribozyme

DEFF Research Database (Denmark)

Attwater, J.; Tagami, S.; Kimoto, M.

2013-01-01

for function. Here we have explored the chemical fidelity, i.e. substrate selectivity and specificity for both single and multiple catalytic steps of the Z RNA polymerase ribozyme-a modern day analogue of the primordial RNA replicase. Using a wide range of nucleotide analogues and ionic conditions, we observe......The emergence of catalytically active RNA enzymes (ribozymes) is widely believed to have been an important transition in the origin of life. In the context of a likely heterogeneous chemical environment, substrate specificity and selectivity of these primordial enzymes would have been critical...
MicroRNA-triggered, cascaded and catalytic self-assembly of functional ``DNAzyme ferris wheel'' nanostructures for highly sensitive colorimetric detection of cancer cells

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Zhou, Wenjiao; Liang, Wenbin; Li, Xin; Chai, Yaqin; Yuan, Ruo; Xiang, Yun

2015-05-01

The construction of DNA nanostructures with various sizes and shapes has significantly advanced during the past three decades, yet the application of these DNA nanostructures for solving real problems is still in the early stage. On the basis of microRNA-triggered, catalytic self-assembly formation of the functional ``DNAzyme ferris wheel'' nanostructures, we show here a new signal amplification platform for highly sensitive, label-free and non-enzyme colorimetric detection of a small number of human prostate cancer cells. The microRNA (miR-141), which is catalytically recycled and reused, triggers isothermal self-assembly of a pre-designed, G-quadruplex sequence containing hairpin DNAs into ``DNAzyme ferris wheel''-like nanostructures (in association with hemin) with horseradish peroxidase mimicking activity. These DNAzyme nanostructures catalyze an intensified color transition of the probe solution for highly sensitive detection of miR-141 down to 0.5 pM with the naked eye, and the monitoring of as low as 283 human prostate cancer cells can also, theoretically, be achieved in a colorimetric approach. The work demonstrated here thus offers new opportunities for the construction of functional DNA nanostructures and for the application of these DNA nanostructures as an effective signal amplification means in the sensitive detection of nucleic acid biomarkers.
Modulation of RNA function by aminoglycoside antibiotics.

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Schroeder, R; Waldsich, C; Wank, H

2000-01-04

One of the most important families of antibiotics are the aminoglycosides, including drugs such as neomycin B, paromomycin, gentamicin and streptomycin. With the discovery of the catalytic potential of RNA, these antibiotics became very popular due to their RNA-binding capacity. They serve for the analysis of RNA function as well as for the study of RNA as a potential therapeutic target. Improvements in RNA structure determination recently provided first insights into the decoding site of the ribosome at high resolution and how aminoglycosides might induce misreading of the genetic code. In addition to inhibiting prokaryotic translation, aminoglycosides inhibit several catalytic RNAs such as self-splicing group I introns, RNase P and small ribozymes in vitro. Furthermore, these antibiotics interfere with human immunodeficiency virus (HIV) replication by disrupting essential RNA-protein contacts. Most exciting is the potential of many RNA-binding antibiotics to stimulate RNA activities, conceiving small-molecule partners for the hypothesis of an ancient RNA world. SELEX (systematic evolution of ligands by exponential enrichment) has been used in this evolutionary game leading to small synthetic RNAs, whose NMR structures gave valuable information on how aminoglycosides interact with RNA, which could possibly be used in applied science.
RNA signal amplifier circuit with integrated fluorescence output.

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Akter, Farhima; Yokobayashi, Yohei

2015-05-15

We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.
Involvement of the catalytic subunit of protein kinase A and of HA95 in pre-mRNA splicing

International Nuclear Information System (INIS)

Kvissel, Anne-Katrine; Orstavik, Sigurd; Eikvar, Sissel; Brede, Gaute; Jahnsen, Tore; Collas, Philippe; Akusjaervi, Goeran; Skalhegg, Bjorn Steen

2007-01-01

Protein kinase A (PKA) is a holoenzyme consisting of two catalytic (C) subunits bound to a regulatory (R) subunit dimer. Stimulation by cAMP dissociates the holoenzyme and causes translocation to the nucleus of a fraction of the C subunit. Apart from transcription regulation, little is known about the function of the C subunit in the nucleus. In the present report, we show that both Cα and Cβ are localized to spots in the mammalian nucleus. Double immunofluorescence analysis of splicing factor SC35 with the C subunit indicated that these spots are splicing factor compartments (SFCs). Using the E1A in vivo splicing assay, we found that catalytically active C subunits regulate alternative splicing and phosphorylate several members of the SR-protein family of splicing factors in vitro. Furthermore, nuclear C subunits co-localize with the C subunit-binding protein homologous to AKAP95, HA95. HA95 also regulates E1A alternative splicing in vivo, apparently through its N-terminal domain. Localization of the C subunit to SFCs and the E1A splicing pattern were unaffected by cAMP stimulation. Our findings demonstrate that the nuclear PKA C subunit co-locates with HA95 in SFCs and regulates pre-mRNA splicing, possibly through a cAMP-independent mechanism
Error baseline rates of five sample preparation methods used to characterize RNA virus populations.

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Jeffrey R Kugelman

Full Text Available Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses. However, both steps may lead to the introduction of artificial mutations, thereby skewing the data. To better understand how such errors are introduced during sample preparation, we determined and compared error baseline rates of five different sample preparation methods by analyzing in vitro transcribed Ebola virus RNA from an artificial plasmid-based system. These methods included: shotgun sequencing from plasmid DNA or in vitro transcribed RNA as a basic "no amplification" method, amplicon sequencing from the plasmid DNA or in vitro transcribed RNA as a "targeted" amplification method, sequence-independent single-primer amplification (SISPA as a "random" amplification method, rolling circle reverse transcription sequencing (CirSeq as an advanced "no amplification" method, and Illumina TruSeq RNA Access as a "targeted" enrichment method. The measured error frequencies indicate that RNA Access offers the best tradeoff between sensitivity and sample preparation error (1.4-5 of all compared methods.
Error baseline rates of five sample preparation methods used to characterize RNA virus populations

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Kugelman, Jeffrey R.; Wiley, Michael R.; Nagle, Elyse R.; Reyes, Daniel; Pfeffer, Brad P.; Kuhn, Jens H.; Sanchez-Lockhart, Mariano; Palacios, Gustavo F.

2017-01-01

Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses. However, both steps may lead to the introduction of artificial mutations, thereby skewing the data. To better understand how such errors are introduced during sample preparation, we determined and compared error baseline rates of five different sample preparation methods by analyzing in vitro transcribed Ebola virus RNA from an artificial plasmid-based system. These methods included: shotgun sequencing from plasmid DNA or in vitro transcribed RNA as a basic “no amplification” method, amplicon sequencing from the plasmid DNA or in vitro transcribed RNA as a “targeted” amplification method, sequence-independent single-primer amplification (SISPA) as a “random” amplification method, rolling circle reverse transcription sequencing (CirSeq) as an advanced “no amplification” method, and Illumina TruSeq RNA Access as a “targeted” enrichment method. The measured error frequencies indicate that RNA Access offers the best tradeoff between sensitivity and sample preparation error (1.4−5) of all compared methods. PMID:28182717
Insight into the recognition, binding, and reactivity of catalytic metallodrugs targeting stem loop IIb of hepatitis C IRES RNA.

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Bradford, Seth S; Ross, Martin James; Fidai, Insiya; Cowan, James A

2014-06-01

The complex Cu-GGHYrFK-amide (1-Cu) was previously reported as a novel metallotherapeutic that catalytically inactivates stem loop IIb (SLIIb) of the hepatitis C virus (HCV) internal ribosomal entry site (IRES) RNA and demonstrates significant antiviral activity in a cellular HCV replicon assay. Herein we describe additional studies focused on understanding the cleavage mechanism as well as the relationship of catalyst configuration to structural recognition and site-selective cleavage of the structured RNA motif. These are advanced by use of a combination of MALDI-TOF mass spectrometry, melting temperature determinations, and computational analysis to develop a structural model for binding and reactivity toward SLIIb of the IRES RNA. In addition, the binding, reactivity, and structural chemistry of the all-D-amino acid form of this metallopeptide, complex 2-Cu, are reported and compared with those of complex 1-Cu. In vitro RNA binding and cleavage assays for complex 2-Cu show a KD value of 76 ± 3 nM, and Michaelis-Menten parameters of kcat =0.14 ± 0.01 min(-1) and KM =7.9 ± 1.2 μM, with a turnover number exceeding 40. In a luciferase-based cellular replicon assay Cu-GGhyrfk-amide shows activity similar to that of the 1-Cu parent peptide, with an IC50 value of 1.9 ± 0.4 μM and cytotoxicity exceeding 100 μM. RT-PCR experiments confirm a significant decrease in HCV RNA levels in replicon assays for up to nine days when treated with complex 1-Cu in three-day dosing increments. This study shows the influence that the α-carbon stereocenter has for this new class of compounds, while detailed mass spectrometry and computational analyses provide new insight into the mechanisms of recognition, binding, and reactivity. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

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Zhu, Yanglong; Stribinskis, Vilius; Ramos, Kenneth S.; Li, Yong

2006-01-01

RNase MRP is a eukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase P is a ubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5′ termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata, the internal loop of helix P3 is 100% conserved between MRP and P RNAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of P RNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and P RNA, such as those from Dictyostelium discoideum. These conserved nucleotides between the MRP and P RNAs strongly support the hypothesis that the MRP RNA is derived from the P RNA molecule in early eukaryote evolution. PMID:16540690

Concerning RNA-guided gene drives for the alteration of wild populations.

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Esvelt, Kevin M; Smidler, Andrea L; Catteruccia, Flaminia; Church, George M

2014-07-17

Gene drives may be capable of addressing ecological problems by altering entire populations of wild organisms, but their use has remained largely theoretical due to technical constraints. Here we consider the potential for RNA-guided gene drives based on the CRISPR nuclease Cas9 to serve as a general method for spreading altered traits through wild populations over many generations. We detail likely capabilities, discuss limitations, and provide novel precautionary strategies to control the spread of gene drives and reverse genomic changes. The ability to edit populations of sexual species would offer substantial benefits to humanity and the environment. For example, RNA-guided gene drives could potentially prevent the spread of disease, support agriculture by reversing pesticide and herbicide resistance in insects and weeds, and control damaging invasive species. However, the possibility of unwanted ecological effects and near-certainty of spread across political borders demand careful assessment of each potential application. We call for thoughtful, inclusive, and well-informed public discussions to explore the responsible use of this currently theoretical technology.
Mutational analysis of Sep-tRNA:Cys-tRNA synthase reveals critical residues for tRNA-dependent cysteine formation.

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Helgadóttir, Sunna; Sinapah, Sylvie; Söll, Dieter; Ling, Jiqiang

2012-01-02

In methanogenic archaea, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys). The mechanism of tRNA-dependent cysteine formation remains unclear due to the lack of functional studies. In this work, we mutated 19 conserved residues in Methanocaldococcus jannaschii SepCysS, and employed an in vivo system to determine the activity of the resulting variants. Our results show that three active-site cysteines (Cys39, Cys42 and Cys247) are essential for SepCysS activity. In addition, combined with structural modeling, our mutational and functional analyses also reveal multiple residues that are important for the binding of PLP, Sep and tRNA. Our work thus represents the first systematic functional analysis of conserved residues in archaeal SepCysSs, providing insights into the catalytic and substrate binding mechanisms of this poorly characterized enzyme. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2

International Nuclear Information System (INIS)

Eckerle, Lance D.; Albarino, Cesar G.; Ball, L. Andrew.

2003-01-01

The nodavirus Flock House virus has a bipartite genome composed of RNAs 1 and 2, which encode the catalytic component of the RNA-dependent RNA polymerase (RdRp) and the capsid protein precursor, respectively. In addition to catalyzing replication of the viral genome, the RdRp also transcribes from RNA1 a subgenomic RNA3, which is both required for and suppressed by RNA2 replication. Here, we show that in the absence of RNA1 replication, FHV RdRp replicated positive-sense RNA3 transcripts fully and copied negative-sense RNA3 transcripts into positive strands. The two nonstructural proteins encoded by RNA3 were dispensable for replication, but sequences in the 3'-terminal 58 nucleotides were required. RNA3 variants that failed to replicate also failed to transactivate RNA2. These results imply that RNA3 is naturally produced both by transcription from RNA1 and by subsequent RNA1-independent replication and that RNA3 replication may be necessary for transactivation of RNA2
Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes.

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Cornelius Schneider

Full Text Available Little is known about contacts in the spliceosome between proteins and intron nucleotides surrounding the pre-mRNA branch-site and their dynamics during splicing. We investigated protein-pre-mRNA interactions by UV-induced crosslinking of purified yeast B(act spliceosomes formed on site-specifically labeled pre-mRNA, and analyzed their changes after conversion to catalytically-activated B* and step 1 C complexes, using a purified splicing system. Contacts between nucleotides upstream and downstream of the branch-site and the U2 SF3a/b proteins Prp9, Prp11, Hsh49, Cus1 and Hsh155 were detected, demonstrating that these interactions are evolutionarily conserved. The RES proteins Pml1 and Bud13 were shown to contact the intron downstream of the branch-site. A comparison of the B(act crosslinking pattern versus that of B* and C complexes revealed that U2 and RES protein interactions with the intron are dynamic. Upon step 1 catalysis, Cwc25 contacts with the branch-site region, and enhanced crosslinks of Prp8 and Prp45 with nucleotides surrounding the branch-site were observed. Cwc25's step 1 promoting activity was not dependent on its interaction with pre-mRNA, indicating it acts via protein-protein interactions. These studies provide important insights into the spliceosome's protein-pre-mRNA network and reveal novel RNP remodeling events during the catalytic activation of the spliceosome and step 1 of splicing.
Domain motions of Argonaute, the catalytic engine of RNA interference

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Wall Michael E

2007-11-01

Full Text Available Abstract Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. Results The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes – an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different. Conclusion Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.
Electrocatalytic miRNA Detection Using Cobalt Porphyrin-Modified Reduced Graphene Oxide

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Camille De Souza

2014-06-01

Full Text Available Metalated porphyrins have been described to bind nucleic acids. Additionally, cobalt porphyrins present catalytic properties towards oxygen reduction. In this work, a carboxylic acid-functionalized cobalt porphyrin was physisorbed on reduced graphene oxide, then immobilized on glassy carbon electrodes. The carboxylic groups were used to covalently graft amino-terminated oligonucleotide probes which are complementary to a short microRNA target. It was shown that the catalytic oxygen electroreduction on cobalt porphyrin increases upon hybridization of miRNA strand (“signal-on” response. Current changes are amplified compared to non-catalytic amperometric system. Apart from oxygen, no added reagent is necessary. A limit of detection in the sub-nanomolar range was reached. This approach has never been described in the literature.
Association of MiRNA-146a, MiRNA-499, IRAK1 and PADI4 Polymorphisms with Rheumatoid Arthritis in Egyptian Population

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Olfat Gamil Shaker

2018-05-01

Full Text Available Background/Aims: Rheumatoid arthritis (RA is a systemic autoimmune disease affecting up to 1% of the population worldwide. The aim of the present study was to investigate whether miRNA-146a rs2910164, miRNA-499 rs3746444, IRAK1 rs3027898 and PADI4 rs1748033 polymorphisms are associated with susceptibility to RA in Egyptians and whether they influence disease severity and activity. Methods: The study was performed on 104 unrelated RA patients and 112 healthy subjects. RA patients were further subdivided into active and inactive RA groups. Polymorphisms were genotyped by using real-time polymerase chain reaction with TaqMan allelic discrimination assay. Results: Significant differences in the frequency of miRNA-146a rs2910164, miRNA-499 rs3746444, IRAK1 rs3027898 and PADI4 rs1748033 alleles and genotypes were observed between RA patients and controls. Only CA and AA genotypes of IRAK1 rs3027898 shows a significant difference between active and inactive subgroups. MiRNA-146a rs2910164 and IRAK1 rs3027898 polymorphisms were a risk factor for predisposition to RA in codominant and dominant tested inheritance models, while, the miRNA-499 rs3746444 and PADI4 rs1748033 polymorphisms were a risk factor in codominant and recessive one. CG and GG genotypes of miRNA-146a rs2910164 were associated with positive erosions. CA genotype of IRAK1 rs3027898 was associated with low disease activity and negative erosions, while, the AA genotype was associated with high disease activity. CC genotype of PADI4 rs1748033 was associated with negative rheumatoid factor. Conclusion: The 4 studied SNPs were likely to play an important role in the susceptibility to RA and can influence disease severity and activity in Egyptian population.
Characterization of the catalytic center of the Ebola virus L polymerase.

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Schmidt, Marie Luisa; Hoenen, Thomas

2017-10-01

Ebola virus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates. While no licensed therapeutics are available, recently there has been tremendous progress in developing antivirals. Targeting the ribonucleoprotein complex (RNP) proteins, which facilitate genome replication and transcription, and particularly the polymerase L, is a promising antiviral approach since these processes are essential for the virus life cycle. However, until now little is known about L in terms of its structure and function, and in particular the catalytic center of the RNA-dependent RNA polymerase (RdRp) of L, which is one of the most promising molecular targets, has never been experimentally characterized. Using multiple sequence alignments with other negative sense single-stranded RNA viruses we identified the putative catalytic center of the EBOV RdRp. An L protein with mutations in this center was then generated and characterized using various life cycle modelling systems. These systems are based on minigenomes, i.e. miniature versions of the viral genome, in which the viral genes are exchanged against a reporter gene. When such minigenomes are coexpressed with RNP proteins in mammalian cells, the RNP proteins recognize them as authentic templates for replication and transcription, resulting in reporter activity reflecting these processes. Replication-competent minigenome systems indicated that our L catalytic domain mutant was impaired in genome replication and/or transcription, and by using replication-deficient minigenome systems, as well as a novel RT-qPCR-based genome replication assay, we showed that it indeed no longer supported either of these processes. However, it still showed similar expression to wild-type L, and retained its ability to be incorporated into inclusion bodies, which are the sites of EBOV genome replication. We have experimentally defined the catalytic center of the EBOV RdRp, and thus a promising antiviral target regulating an essential
Characterization of the catalytic center of the Ebola virus L polymerase.

Directory of Open Access Journals (Sweden)

Marie Luisa Schmidt

2017-10-01

Full Text Available Ebola virus (EBOV causes a severe hemorrhagic fever in humans and non-human primates. While no licensed therapeutics are available, recently there has been tremendous progress in developing antivirals. Targeting the ribonucleoprotein complex (RNP proteins, which facilitate genome replication and transcription, and particularly the polymerase L, is a promising antiviral approach since these processes are essential for the virus life cycle. However, until now little is known about L in terms of its structure and function, and in particular the catalytic center of the RNA-dependent RNA polymerase (RdRp of L, which is one of the most promising molecular targets, has never been experimentally characterized.Using multiple sequence alignments with other negative sense single-stranded RNA viruses we identified the putative catalytic center of the EBOV RdRp. An L protein with mutations in this center was then generated and characterized using various life cycle modelling systems. These systems are based on minigenomes, i.e. miniature versions of the viral genome, in which the viral genes are exchanged against a reporter gene. When such minigenomes are coexpressed with RNP proteins in mammalian cells, the RNP proteins recognize them as authentic templates for replication and transcription, resulting in reporter activity reflecting these processes. Replication-competent minigenome systems indicated that our L catalytic domain mutant was impaired in genome replication and/or transcription, and by using replication-deficient minigenome systems, as well as a novel RT-qPCR-based genome replication assay, we showed that it indeed no longer supported either of these processes. However, it still showed similar expression to wild-type L, and retained its ability to be incorporated into inclusion bodies, which are the sites of EBOV genome replication.We have experimentally defined the catalytic center of the EBOV RdRp, and thus a promising antiviral target
Clay catalyzed RNA synthesis under Martian conditions: Application for Mars return samples.

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Joshi, Prakash C; Dubey, Krishna; Aldersley, Michael F; Sausville, Meaghen

2015-06-26

Catalysis by montmorillonites clay minerals is regarded as a feasible mechanism for the abiotic production and polymerization of key biomolecules on early Earth. We have investigated a montmorillonite-catalyzed reaction of the 5'-phosphorimidazolide of nucleosides as a model to probe prebiotic synthesis of RNA-type oligomers. Here we show that this model is specific for the generation of RNA oligomers despite deoxy-mononucleotides adsorbing equally well onto the montmorillonite catalytic surfaces. Optimum catalytic activity was observed over a range of pH (6-9) and salinity (1 ± 0.2 M NaCl). When the weathering steps of early Earth that generated catalytic montmorillonite were modified to meet Martian soil conditions, the catalytic activity remained intact without altering the surface layer charge. Additionally, the formation of oligomers up to tetramer was detected using as little as 0.1 mg of Na⁺-montmorillonite, suggesting that the catalytic activity of a Martian clay return sample can be investigated with sub-milligram scale samples. Copyright © 2015 Elsevier Inc. All rights reserved.
Association between SNPs in microRNA-machinery genes and tuberculosis susceptibility in Chinese Tibetan population.

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Song, Xingbo; Li, Siyue; QuCuo, MeiLang; Zhou, MeiLang; Zhou, Yi; Hu, Xin; Zhou, Juan; Lu, Xiaojun; Wang, Jun; Hua, Wei; Ye, Yuanxin; Ying, Binwu; Wang, Lanlan

2013-10-01

Tuberculosis (TB) is caused by infection with Mycobacterium tuberculosis and remains a leading cause of morbidity and mortality caused by infectious agents worldwide. Although our current understanding of the pathogenesis of TB is far from clear, there is a growing body of evidence suggesting a genetic contribution to the etiology of TB. By analyzing 294 TB cases and 287 healthy controls in a Chinese Tibetan population, we used a candidate gene approach to evaluate the association between six single nucleotide polymorphisms (rs10719, rs3757, rs3742330, rs636832, rs7813, and rs3744741) in microRNA machinery genes and TB susceptibility. The genotypic distributions of rs3757 and rs3744741 in controls were not in accordance with the Hardy–Weinberg Equilibrium (P microRNA-632 (miR-632) and that the G allele alters the affinity of microRNA-mRNA binding by disrupting the local structure of dicer 1, ribonuclease type III (DICER) mRNA, presumably allowing for upregulated DICER expression. Taken together, our data suggest that common genetic variations DICER may influence TB risk, possibly through miR-632-mediated regulation. Replication of our studies in other populations will strengthen our understanding of this association.
The inhibitory effect of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) and its family members on the activity of cellular microRNAs.

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Zhang, Hui

2010-01-01

The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G or APOBEC3G) and its fellow cytidine deaminase family members are potent restrictive factors for human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. However, the cellular function of APOBEC3G remains to be further clarified. It has been reported that APOBEC3s can restrict the mobility of endogenous retroviruses and LTR-retrotransposons, suggesting that they can maintain stability in host genomes. However, APOBEC3G is normally cytoplasmic. Further studies have demonstrated that it is associated with an RNase-sensitive high molecular mass (HMM) and located in processing bodies (P-bodies) of replicating T-cells, indicating that the major cellular function of APOBEC3G seems to be related to P-body-related RNA processing and metabolism. As the function of P-body is closely related to miRNA activity, APOBEC3G could affect the miRNA function. Recent studies have demonstrated that APOBEC3G and its family members counteract miRNA-mediated repression of protein translation. Further, APOBEC3G enhances the association of miRNA-targeted mRNA with polysomes, and facilitates the dissociation of miRNA-targeted mRNA from P-bodies. As such, APOBEC3G regulate the activity of cellular miRNAs. Whether this function is related to its potent antiviral activity remains to be further determined.
Reexamining microRNA site accessibility in Drosophila: a population genomics study.

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Kevin Chen

Full Text Available Kertesz et al. (Nature Genetics 2008 described PITA, a miRNA target prediction algorithm based on hybridization energy and site accessibility. In this note, we used a population genomics approach to reexamine their data and found that the PITA algorithm had lower specificity than methods based on evolutionary conservation at comparable levels of sensitivity.We also showed that deeply conserved miRNAs tend to have stronger hybridization energies to their targets than do other miRNAs. Although PITA had higher specificity in predicting targets than a naïve seed-match method, this signal was primarily due to the use of a single cutoff score for all miRNAs and to the observed correlation between conservation and hybridization energy. Overall, our results clarify the accuracy of different miRNA target prediction algorithms in Drosophila and the role of site accessibility in miRNA target prediction.
Punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori in Colombian populations.

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Matta, Andrés Jenuer; Zambrano, Diana Carolina; Pazos, Alvaro Jairo

2018-04-14

To characterize punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori ( H. pylori ) and determine their association with therapeutic failure. PCR products of 23S rRNA gene V domain of 74 H. pylori isolates; 34 resistant to clarithromycin (29 from a low-risk gastric cancer (GC) population: Tumaco-Colombia, and 5 from a high-risk population: Tuquerres-Colombia) and 40 from a susceptible population (28 from Tumaco and 12 from Túquerres) were sequenced using capillary electrophoresis. The concordance between mutations of V domain 23S rRNA gene of H. pylori and therapeutic failure was determined using the Kappa coefficient and McNemar's test was performed to determine the relationship between H. pylori mutations and clarithromycin resistance. 23S rRNA gene from H. pylori was amplified in 56/74 isolates, of which 25 were resistant to clarithromycin (20 from Tumaco and 5 from Túquerres, respectively). In 17 resistant isolates (13 from Tumaco and 4 from Túquerres) the following mutations were found: A1593T1, A1653G2, C1770T, C1954T1, and G1827C in isolates from Tumaco, and A2144G from Túquerres. The mutations T2183C, A2144G and C2196T in H. pylori isolates resistant to clarithromycin from Colombia are reported for the first time. No association between the H. pylori mutations and in vitro clarithromycin resistance was found. However, therapeutic failure of eradication treatment was associated with mutations of 23S rRNA gene in clarithromycin-resistant H. pylori ( κ = 0.71). The therapeutic failure of eradication treatment in the two populations from Colombia was associated with mutations of the 23S rRNA gene in clarithromycin-resistant H. pylori .
Mechanism for Coordinated RNA Packaging and Genome Replication by Rotavirus Polymerase VP1

Energy Technology Data Exchange (ETDEWEB)

Lu, Xiaohui; McDonald, Sarah M.; Tortorici, M. Alejandra; Tao, Yizhi Jane; Vasquez-Del Carpio, Rodrigo; Nibert, Max L.; Patton, John T.; Harrison, Stephen C. (Harvard-Med); (NIH); (CH-Boston)

2009-04-08

Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 {angstrom} resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus {lambda}3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.
A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations.

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Remnant, Emily J; Shi, Mang; Buchmann, Gabriele; Blacquière, Tjeerd; Holmes, Edward C; Beekman, Madeleine; Ashe, Alyson

2017-08-15

Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees ( Apis mellifera ) has changed dramatically since the emergence of the parasitic mite Varroa destructor , which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management. IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa -infected colonies are often overwhelmed
A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

Science.gov (United States)

Shi, Mang; Buchmann, Gabriele; Blacquière, Tjeerd; Beekman, Madeleine; Ashe, Alyson

2017-01-01

ABSTRACT Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa. This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management. IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales. Collapsing Varroa-infected colonies are often
Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis.

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Javad Noorbakhsh

Full Text Available MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by prokaryotic small non-coding RNAs (sRNAs. Our model uses a combination of analytic techniques as well as computational simulations to calculate the mean-expression and noise profiles of genes regulated by both microRNAs and sRNAs. We find that despite very different molecular machinery and modes of action (catalytic vs stoichiometric, the mean expression levels and noise profiles of microRNA-regulated genes are almost identical to genes regulated by prokaryotic sRNAs. This behavior is extremely robust and persists across a wide range of biologically relevant parameters. We extend our model to study crosstalk between multiple mRNAs that are regulated by a single microRNA and show that noise is a sensitive measure of microRNA-mediated interaction between mRNAs. We conclude by discussing possible experimental strategies for uncovering the microRNA-mRNA interactions and testing the competing endogenous RNA (ceRNA hypothesis.
Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP.

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Perederina, Anna; Khanova, Elena; Quan, Chao; Berezin, Igor; Esakova, Olga; Krasilnikov, Andrey S

2011-10-01

Ribonuclease (RNase) MRP is a multicomponent ribonucleoprotein complex closely related to RNase P. RNase MRP and eukaryotic RNase P share most of their protein components, as well as multiple features of their catalytic RNA moieties, but have distinct substrate specificities. While RNase P is practically universally found in all three domains of life, RNase MRP is essential in eukaryotes. The structural organizations of eukaryotic RNase P and RNase MRP are poorly understood. Here, we show that Pop5 and Rpp1, protein components found in both RNase P and RNase MRP, form a heterodimer that binds directly to the conserved area of the putative catalytic domain of RNase MRP RNA. The Pop5/Rpp1 binding site corresponds to the protein binding site in bacterial RNase P RNA. Structural and evolutionary roles of the Pop5/Rpp1 heterodimer in RNases P and MRP are discussed.
Redox status affects the catalytic activity of glutamyl-tRNA synthetase

DEFF Research Database (Denmark)

Katz, Assaf; Banerjee, Rajat; de Armas, Merly

2010-01-01

Glutamyl-tRNA synthetases (GluRS) provide Glu-tRNA for different processes including protein synthesis, glutamine transamidation and tetrapyrrole biosynthesis. Many organisms contain multiple GluRSs, but whether these duplications solely broaden tRNA specificity or also play additional roles in t...... inactivation by hemin plus hydrogen peroxide. The sensitivity to oxidation of A. ferrooxidans GluRS1 might provide a means to regulate tetrapyrrole and protein biosynthesis in response to extreme changes in both the redox and heme status of the cell via a single enzyme....

RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway.

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Saito, Yuichiro; Takeda, Jun; Adachi, Kousuke; Nobe, Yuko; Kobayashi, Junya; Hirota, Kouji; Oliveira, Douglas V; Taoka, Masato; Isobe, Toshiaki

2014-01-01

Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNA(Ser-Met). To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNA(Ser-Met), suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry-based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute "Domain 1" in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.
New Catalytic DNA Biosensors for Radionuclides and Metal ions

International Nuclear Information System (INIS)

Lu, Yi

2003-01-01

The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize
Experimental evolution of an RNA virus in wild birds: evidence for host-dependent impacts on population structure and competitive fitness.

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Nathan D Grubaugh

2015-05-01

Full Text Available Within hosts, RNA viruses form populations that are genetically and phenotypically complex. Heterogeneity in RNA virus genomes arises due to error-prone replication and is reduced by stochastic and selective mechanisms that are incompletely understood. Defining how natural selection shapes RNA virus populations is critical because it can inform treatment paradigms and enhance control efforts. We allowed West Nile virus (WNV to replicate in wild-caught American crows, house sparrows and American robins to assess how natural selection shapes RNA virus populations in ecologically relevant hosts that differ in susceptibility to virus-induced mortality. After five sequential passages in each bird species, we examined the phenotype and population diversity of WNV through fitness competition assays and next generation sequencing. We demonstrate that fitness gains occur in a species-specific manner, with the greatest replicative fitness gains in robin-passaged WNV and the least in WNV passaged in crows. Sequencing data revealed that intrahost WNV populations were strongly influenced by purifying selection and the overall complexity of the viral populations was similar among passaged hosts. However, the selective pressures that control WNV populations seem to be bird species-dependent. Specifically, crow-passaged WNV populations contained the most unique mutations (~1.7× more than sparrows, ~3.4× more than robins and defective genomes (~1.4× greater than sparrows, ~2.7× greater than robins, but the lowest average mutation frequency (about equal to sparrows, ~2.6× lower than robins. Therefore, our data suggest that WNV replication in the most disease-susceptible bird species is positively associated with virus mutational tolerance, likely via complementation, and negatively associated with the strength of selection. These differences in genetic composition most likely have distinct phenotypic consequences for the virus populations. Taken together
Mammalian α-polymerase: cloning of partial complementary DNA and immunobinding of catalytic subunit in crude homogenate protein blots

International Nuclear Information System (INIS)

SenGupta, D.N.; Kumar, P.; Zmudzka, B.Z.; Coughlin, S.; Vishwanatha, J.K.; Robey, F.A.; Parrott, C.; Wilson, S.H.

1987-01-01

A new polyclonal antibody against the α-polymerase catalytic polypeptide was prepared by using homogeneous HeLa cellα-polymerase. The antibody neutralized α-polymerase activity and was strong and specific for the α-polymerase catalytic polypeptide (M/sub r/ 183,000) in Western blot analysis of crude extracts of HeLa cells. The antibody was used to screen a cDNA library of newborn rat brain poly(A+) RNA in λgt11. A positive phage was identified and plaque purified. This phage, designated λpolα1.2, also was found to be positive with an antibody against Drosophila α-polymerase. The insert in λpolα1.2 (1183 base pairs) contained a poly(A) sequence at the 3' terminus and a short in-phase open reading frame at the 5' terminus. A synthetic oligopeptide (eight amino acids) corresponding to the open reading frame was used to raise antiserum in rabbits. Antibody affinity purified from this serum was found to be immunoreactive against purified α-polymerase by enzyme-linked immunosorbent assay and was capable of immunoprecipitating α-polymerase. This indicated the λpolα1.2 insert encoded an α-polymerase epitope and suggested that the cDNA corresponded to an α-polymerase mRNA. This was confirmed in hybrid selection experiments using pUC9 containing the cDNA insert and poly(A+) RNA from newborn rat brain; the insert hybridized to mRNA capable of encoding α-polymerase catalytic polypeptides. Northern blot analysis of rat brain poly(A+) RNA revealed that this mRNA is ∼5.4 kilobases
Catalytic mechanism of Sep-tRNA:Cys-tRNA synthase: sulfur transfer is mediated by disulfide and persulfide.

Science.gov (United States)

Liu, Yuchen; Dos Santos, Patricia C; Zhu, Xiang; Orlando, Ron; Dean, Dennis R; Söll, Dieter; Yuan, Jing

2012-02-17

Sep-tRNA:Cys-tRNA synthase (SepCysS) catalyzes the sulfhydrylation of tRNA-bound O-phosphoserine (Sep) to form cysteinyl-tRNA(Cys) (Cys-tRNA(Cys)) in methanogens that lack the canonical cysteinyl-tRNA synthetase (CysRS). A crystal structure of the Archaeoglobus fulgidus SepCysS apoenzyme provides information on the binding of the pyridoxal phosphate cofactor as well as on amino acid residues that may be involved in substrate binding. However, the mechanism of sulfur transfer to form cysteine was not known. Using an in vivo Escherichia coli complementation assay, we showed that all three highly conserved Cys residues in SepCysS (Cys(64), Cys(67), and Cys(272) in the Methanocaldococcus jannaschii enzyme) are essential for the sulfhydrylation reaction in vivo. Biochemical and mass spectrometric analysis demonstrated that Cys(64) and Cys(67) form a disulfide linkage and carry a sulfane sulfur in a portion of the enzyme. These results suggest that a persulfide group (containing a sulfane sulfur) is the proximal sulfur donor for cysteine biosynthesis. The presence of Cys(272) increased the amount of sulfane sulfur in SepCysS by 3-fold, suggesting that this Cys residue facilitates the generation of the persulfide group. Based upon these findings, we propose for SepCysS a sulfur relay mechanism that recruits both disulfide and persulfide intermediates.
Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors.

Science.gov (United States)

Gerasimova, Yulia V; Yakovchuk, Petro; Dedkova, Larisa M; Hecht, Sidney M; Kolpashchikov, Dmitry M

2015-10-01

Mutations in ribosomal RNA (rRNA) have traditionally been detected by the primer extension assay, which is a tedious and multistage procedure. Here, we describe a simple and straightforward fluorescence assay based on binary deoxyribozyme (BiDz) sensors. The assay uses two short DNA oligonucleotides that hybridize specifically to adjacent fragments of rRNA, one of which contains a mutation site. This hybridization results in the formation of a deoxyribozyme catalytic core that produces the fluorescent signal and amplifies it due to multiple rounds of catalytic action. This assay enables us to expedite semi-quantification of mutant rRNA content in cell cultures starting from whole cells, which provides information useful for optimization of culture preparation prior to ribosome isolation. The method requires less than a microliter of a standard Escherichia coli cell culture and decreases analysis time from several days (for primer extension assay) to 1.5 h with hands-on time of ∼10 min. It is sensitive to single-nucleotide mutations. The new assay simplifies the preliminary analysis of RNA samples and cells in molecular biology and cloning experiments and is promising in other applications where fast detection/quantification of specific RNA is required. © 2015 Gerasimova et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Conserved and variable domains of RNase MRP RNA.

Science.gov (United States)

Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

2009-01-01

Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.
Programmed self-assembly of DNA/RNA for biomedical applications

Science.gov (United States)

Wang, Pengfei

Three self-assembly strategies were utilized for assembly of novel functional DNA/RNA nanostructures. RNA-DNA hybrid origami method was developed to fabricate nano-objects (ribbon, rectangle, and triangle) with precisely controlled geometry. Unlike conventional DNA origami which use long DNA single strand as scaffold, a long RNA single strand was used instead, which was folded by short DNA single strands (staples) into prescribed objects through sequence specific hybridization between RNA and DNA. Single stranded tiles (SST) and RNA-DNA hybrid origami were utilized to fabricate a variety of barcode-like nanostructures with unique patterns by expanding a plain rectangle via introducing spacers (10-bp dsDNA segment) between parallel duplexes. Finally, complex 2D array and 3D polyhedrons with multiple patterns within one structure were assembled from simple DNA motifs. Two demonstrations of biomedical applications of DNA nanotechnology were presented. Firstly, lambda-DNA was used as template to direct the fabrication of multi-component magnetic nanoparticle chains. Nuclear magnetic relaxation (NMR) characterization showed superb magnetic relaxativity of the nanoparticle chains which have large potential to be utilized as MRI contrast agents. Secondly, DNA nanotechnology was introduced into the conformational study of a routinely used catalytic DNAzyme, the RNA-cleaving 10-23 DNAzyme. The relative angle between two flanking duplexes of the catalytic core was determined (94.8°), which shall be able to provide a clue to further understanding of the cleaving mechanism of this DNAzyme from a conformational perspective.
Identification of active dehalorespiring microbial populations in anoxic river sediment by RNA-based stable isotope probing

Science.gov (United States)

Kittelmann, S.; Friedrich, M. W.

2005-12-01

Tetrachloroethene (perchloroethylene, PCE), a persistent contaminant in aquifers, soils and sediments, can be reductively dechlorinated by anaerobic microorganisms in a process referred to as dehalorespiration. However, the biodiversity of dehalorespiring microorganisms and their distribution especially in pristine environments is largely unexplored. Therefore, the aim of this study was to detect potentially novel PCE-dehalorespiring microorganisms by using stable isotope probing (SIP), a technique that allows to directly identify the function of uncultivated microbial populations. We simulated a PCE contamination by incubating pristine river sediment in the presence of PCE at a steady, low aqueous concentration (20 μM). Dehalogenation activity in microcosms (20 nmol cis-dichloroethene per ml slurry per day formed) was detected already after 4 weeks at 20°C with sediment indigenous electron donors. The microbial community in sediment incubations was probed with 13C-labelled acetate (0.5 mM) as electron donor and carbon source at 15°C for 3 days. After RNA extraction, "heavy" 13C-rRNA and light 12C-rRNA were separated by isopycnic centrifugation, and Bacteria-related populations in gradient fractions were characterised by terminal restriction fragment length polymorphism analysis and cloning. In heavy gradient fractions from the microcosm with PCE, we detected a prominent 506-bp terminal restriction fragment (T-RF) and a few minor T-RFs only. In contrast, in the control without PCE, Bacteria-specific rRNA was restricted to light gradient fractions, and the prominent T-RFs found in the PCE-dechlorinating microcosm were of minor importance. Apparently, 13C-acetate was incorporated into bacterial rRNA more effectively in PCE-respiring microcosms. Thus, rRNA-SIP provides strong evidence for the presence of PCE-dehalorespiring, 13C-acetate-utilising populations in river sediment microcosms. Cloning/sequencing analysis identified the prominent members of the heavy
Catalytic mechanism and inhibition of tRNA (Uracil-5-)methyltransferase: evidence for covalent catalysis

International Nuclear Information System (INIS)

Santi, D.V.; Hardy, L.W.

1987-01-01

tRNA (Ura-5-) methyltransferase catalyzes the transfer of a methyl group from S-adenosylmethionine (AdoMet) to the 5-carbon of a specific Urd residue in tRNA. This results in stoichiometric release of tritium from [5- 3 H] Urd-labeled substrate tRNA isolated from methyltransferase-deficient Escherichia coli. The enzyme also catalyzes an AdoMet-independent exchange reaction between [5- 3 H]-Urd-labeled substrate tRNA and protons of water at a rate that is about 1% that of the normal methylation reaction, but with identical stoichiometry. S-Adenosylhomocysteine inhibits the rate of the exchange reaction by 2-3-fold, whereas an analog having the sulfur of AdoMet replaced by nitrogen accelerates the exchange reaction 9-fold. In the presence (but not absence) of AdoMet, 5-fluorouracil-substituted tRNA (FUra-tRNA) leads to the first-order inactivation of the enzyme. This is accompanied by the formation of a stable covalent complex containing the enzyme, FUra-tRNA, and the methyl group AdoMet. A mechanism for catalysis is proposed that explains both the 5-H exchange reaction and the inhibition by FUra-tRNA: the enzyme forms a covalent Michael adduct with substrate or inhibitor tRNA by attack of a nucleophilic group of the enzyme at carbon 6 of the pyrimidine residue to be modified. As a result, an anion equivalent is generated at carbon 5 that is sufficiently reactive to be methylated by AdoMet. Preliminary experiments and precedents suggest that the nucleophilic catalyst of the enzyme is a thiol group of cysteine. The potent irreversible inhibition by FUra-tRNA suggest that a mechanism for the RNA effects of FUra may also involve irreversible inhibition of RNA-modifying enzymes
Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I.

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Lama, Lodoe; Ryan, Kevin

2016-01-01

Many high-throughput small RNA next-generation sequencing protocols use 5' preadenylylated DNA oligonucleotide adapters during cDNA library preparation. Preadenylylation of the DNA adapter's 5' end frees from ATP-dependence the ligation of the adapter to RNA collections, thereby avoiding ATP-dependent side reactions. However, preadenylylation of the DNA adapters can be costly and difficult. The currently available method for chemical adenylylation of DNA adapters is inefficient and uses techniques not typically practiced in laboratories profiling cellular RNA expression. An alternative enzymatic method using a commercial RNA ligase was recently introduced, but this enzyme works best as a stoichiometric adenylylating reagent rather than a catalyst and can therefore prove costly when several variant adapters are needed or during scale-up or high-throughput adenylylation procedures. Here, we describe a simple, scalable, and highly efficient method for the 5' adenylylation of DNA oligonucleotides using the thermostable RNA ligase 1 from bacteriophage TS2126. Adapters with 3' blocking groups are adenylylated at >95% yield at catalytic enzyme-to-adapter ratios and need not be gel purified before ligation to RNA acceptors. Experimental conditions are also reported that enable DNA adapters with free 3' ends to be 5' adenylylated at >90% efficiency. © 2015 Lama and Ryan; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
The Structure of the RNA m5C Methyltransferase YebU from Escherichia coli Reveals a C-terminal RNA-recruiting PUA Domain

DEFF Research Database (Denmark)

Hallberg, B. Martin; Ericsson, Ulrika B.; Johnson, Kenneth A

2006-01-01

potential that differ from other RNA-MTase structures, suggesting that YebU interacts with its RNA target in a different manner. Docking of YebU onto the 30 S subunit indicates that the PUA and MTase domains make several contacts with 16 S rRNA as well as with the ribosomal protein S12. The ribosomal...... protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU....... by X-ray crystallography, and we present a molecular model for how YebU specifically recognizes, binds and methylates its ribosomal substrate. The YebU protein has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other m(5)C RNA MTases including...
Generation and Development of RNA Ligase Ribozymes with Modular Architecture Through “Design and Selection”

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Yuki Fujita

2010-08-01

Full Text Available In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed “design and selection,” new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis

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Obarska Agnieszka

2006-01-01

Full Text Available Abstract Background Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential enzyme in plant microRNA (miRNA biogenesis. HEN1 transfers a methyl group from S-adenosylmethionine to the 2'-OH or 3'-OH group of the last nucleotide of miRNA/miRNA* duplexes produced by the nuclease Dicer. Previously it was found that HEN1 possesses a Rossmann-fold methyltransferase (RFM domain and a long N-terminal extension including a putative double-stranded RNA-binding motif (DSRM. However, little is known about the details of the structure and the mechanism of action of this enzyme, and about its phylogenetic origin. Results Extensive database searches were carried out to identify orthologs and close paralogs of HEN1. Based on the multiple sequence alignment a phylogenetic tree of the HEN1 family was constructed. The fold-recognition approach was used to identify related methyltransferases with experimentally solved structures and to guide the homology modeling of the HEN1 catalytic domain. Additionally, we identified a La-like predicted RNA binding domain located C-terminally to the DSRM domain and a domain with a peptide prolyl cis/trans isomerase (PPIase fold, but without the conserved PPIase active site, located N-terminally to the catalytic domain. Conclusion The bioinformatics analysis revealed that the catalytic domain of HEN1 is not closely related to any known RNA:2'-OH methyltransferases (e.g. to the RrmJ/fibrillarin superfamily, but rather to small-molecule methyltransferases. The structural model was used as a platform to identify the putative active site and substrate-binding residues of HEN and to propose its mechanism of action.
The pre-existing population of 5S rRNA effects p53 stabilization during ribosome biogenesis inhibition.

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Onofrillo, Carmine; Galbiati, Alice; Montanaro, Lorenzo; Derenzini, Massimo

2017-01-17

Pre-ribosomal complex RPL5/RPL11/5S rRNA (5S RNP) is considered the central MDM2 inhibitory complex that control p53 stabilization during ribosome biogenesis inhibition. Despite its role is well defined, the dynamic of 5S RNP assembly still requires further characterization. In the present work, we report that MDM2 inhibition is dependent by a pre-existing population of 5S rRNA.
Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.

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Noah Fahlgren

Full Text Available In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.
Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.

Science.gov (United States)

Fahlgren, Noah; Bollmann, Stephanie R; Kasschau, Kristin D; Cuperus, Josh T; Press, Caroline M; Sullivan, Christopher M; Chapman, Elisabeth J; Hoyer, J Steen; Gilbert, Kerrigan B; Grünwald, Niklaus J; Carrington, James C

2013-01-01

In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.
Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

Science.gov (United States)

Fahlgren, Noah; Bollmann, Stephanie R.; Kasschau, Kristin D.; Cuperus, Josh T.; Press, Caroline M.; Sullivan, Christopher M.; Chapman, Elisabeth J.; Hoyer, J. Steen; Gilbert, Kerrigan B.; Grünwald, Niklaus J.; Carrington, James C.

2013-01-01

In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work. PMID:24204767
Multiple isoforms for the catalytic subunit of PKA in the basal fungal lineage Mucor circinelloides.

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Fernández Núñez, Lucas; Ocampo, Josefina; Gottlieb, Alexandra M; Rossi, Silvia; Moreno, Silvia

2016-12-01

Protein kinase A (PKA) activity is involved in dimorphism of the basal fungal lineage Mucor. From the recently sequenced genome of Mucor circinelloides we could predict ten catalytic subunits of PKA. From sequence alignment and structural prediction we conclude that the catalytic core of the isoforms is conserved, and the difference between them resides in their amino termini. This high number of isoforms is maintained in the subdivision Mucoromycotina. Each paralogue, when compared to the ones form other fungi is more homologous to one of its orthologs than to its paralogs. All of these fungal isoforms cannot be included in the class I or II in which fungal protein kinases have been classified. mRNA levels for each isoform were measured during aerobic and anaerobic growth. The expression of each isoform is differential and associated to a particular growth stage. We reanalyzed the sequence of PKAC (GI 20218944), the only cloned sequence available until now for a catalytic subunit of M. circinelloides. PKAC cannot be classified as a PKA because of its difference in the conserved C-tail; it shares with PKB a conserved C2 domain in the N-terminus. No catalytic activity could be measured for this protein nor predicted bioinformatically. It can thus be classified as a pseudokinase. Its importance can not be underestimated since it is expressed at the mRNA level in different stages of growth, and its deletion is lethal. Copyright Â© 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.
Studies on the catalytic rate constant of ribosomal peptidyltransferase.

Science.gov (United States)

Synetos, D; Coutsogeorgopoulos, C

1987-02-20

A detailed kinetic analysis of a model reaction for the ribosomal peptidyltransferase is described, using fMet-tRNA or Ac-Phe-tRNA as the peptidyl donor and puromycin as the acceptor. The initiation complex (fMet-tRNA X AUG X 70 S ribosome) or (Ac-Phe-tRNA X poly(U) X 70 S ribosome) (complex C) is isolated and then reacted with excess puromycin (S) to give fMet-puromycin or Ac-Phe-puromycin. This reaction (puromycin reaction) is first order at all concentrations of S tested. An important asset of this kinetic analysis is the fact that the relationship between the first order rate constant kobs and [S] shows hyperbolic saturation and that the value of kobs at saturating [S] is a measure of the catalytic rate constant (k cat) of peptidyltransferase in the puromycin reaction. With fMet-tRNA as the donor, this kcat of peptidyltransferase is 8.3 min-1 when the 0.5 M NH4Cl ribosomal wash is present, compared to 3.8 min-1 in its absence. The kcat of peptidyltransferase is 2.0 min-1 when Ac-Phe-tRNA replaces fMet-tRNA in the presence of the ribosomal wash and decreases to 0.8 min-1 in its absence. This kinetic procedure is the best method available for evaluating changes in the activity of peptidyltransferase in vitro. The results suggest that peptidyltransferase is subjected to activation by the binding of fMet-tRNA to the 70 S initiation complex.

Structural insights into RNA processing by the human RISC-loading complex.

Science.gov (United States)

Wang, Hong-Wei; Noland, Cameron; Siridechadilok, Bunpote; Taylor, David W; Ma, Enbo; Felderer, Karin; Doudna, Jennifer A; Nogales, Eva

2009-11-01

Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2.
Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase.

Science.gov (United States)

Poranen, Minna M; Salgado, Paula S; Koivunen, Minni R L; Wright, Sam; Bamford, Dennis H; Stuart, David I; Grimes, Jonathan M

2008-11-01

The biological role of manganese (Mn(2+)) has been a long-standing puzzle, since at low concentrations it activates several polymerases whilst at higher concentrations it inhibits. Viral RNA polymerases possess a common architecture, reminiscent of a closed right hand. The RNA-dependent RNA polymerase (RdRp) of bacteriophage 6 is one of the best understood examples of this important class of polymerases. We have probed the role of Mn(2+) by biochemical, biophysical and structural analyses of the wild-type enzyme and of a mutant form with an altered Mn(2+)-binding site (E491 to Q). The E491Q mutant has much reduced affinity for Mn(2+), reduced RNA binding and a compromised elongation rate. Loss of Mn(2+) binding structurally stabilizes the enzyme. These data and a re-examination of the structures of other viral RNA polymerases clarify the role of manganese in the activation of polymerization: Mn(2+) coordination of a catalytic aspartate is necessary to allow the active site to properly engage with the triphosphates of the incoming NTPs. The structural flexibility caused by Mn(2+) is also important for the enzyme dynamics, explaining the requirement for manganese throughout RNA polymerization.
Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components.

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Fagerlund, Robert D; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2015-09-01

Ribonuclease (RNase) P and RNase MRP are closely related catalytic ribonucleoproteins involved in the metabolism of a wide range of RNA molecules, including tRNA, rRNA, and some mRNAs. The catalytic RNA component of eukaryotic RNase P retains the core elements of the bacterial RNase P ribozyme; however, the peripheral RNA elements responsible for the stabilization of the global architecture are largely absent in the eukaryotic enzyme. At the same time, the protein makeup of eukaryotic RNase P is considerably more complex than that of the bacterial RNase P. RNase MRP, an essential and ubiquitous eukaryotic enzyme, has a structural organization resembling that of eukaryotic RNase P, and the two enzymes share most of their protein components. Here, we present the results of the analysis of interactions between the largest protein component of yeast RNases P/MRP, Pop1, and the RNA moieties of the enzymes, discuss structural implications of the results, and suggest that Pop1 plays the role of a scaffold for the stabilization of the global architecture of eukaryotic RNase P RNA, substituting for the network of RNA-RNA tertiary interactions that maintain the global RNA structure in bacterial RNase P. © 2015 Fagerlund et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
miRNA Expression Profiles of HPV-Infected Patients with Cervical Cancer in the Uyghur Population in China.

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Dongmei Gao

Full Text Available The study aimed to investigate the state of human papillomavirus (HPV infection in patients with cervical cancer in the Uyghur population in China and to identify miRNA as biomarker for cervical cancer and HPV infection. We also performed genotyping to determine the variation in the types of HPV. Using microRNA (miRNA microarray technology, differential miRNA expression between HPV-infected cervical cancer and uninfected normal cervical tissues was determined; the microarray results were verified by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR using 20 samples of both the tissues. The infection rate of HPV in patients with cervical cancer was 96.7% (29 of 30, and the main subtype identified was HPV16 (29 of 29. HPV16 integration assay demonstrated that the majority of infectious cases were of the integrated form (26 of 29. Analysis of 140 miRNAs demonstrated greater than two-fold change in miRNA expression in HPV-infected cervical cancer tissue as compared to that in uninfected cervical tissue. The qRT-PCR analysis verified that the expression of miR-15a-5p, miR-17-5p, miR-20a-5p, miR-21-5p, miR-96, miR-106b-5p, and miR-3653 was higher, while the expression of miR-497-5p was lower in cancer tissues than in normal tissues. The results demonstrate significant changes in miRNA expression in cervical cancer tissues associated with HPV infection as compared to that in normal tissues. These molecular markers may be useful for an early diagnosis and prognosis of cervical cancer in specific human populations.
Role of RNA structure and RNA binding activity of foot-and-mouth disease virus 3C protein in VPg uridylylation and virus replication

DEFF Research Database (Denmark)

Nayak, A.; Goodfellow, I. G.; Woolaway, K. E.

2006-01-01

The uridylylation of the VPg peptide primer is the first stage in the replication of picornavirus RNA. This process can be achieved in vitro using purified components, including 3B (VPg) with the RNA dependent RNA polymerase (3D(pol)), the precursor 3CD, and an RNA template containing the cre....../bus. We show that certain RNA sequences within the foot-and-mouth disease virus (FMDV) 5' untranslated region but outside of the cre/bus can enhance VPg uridylylation activity. Furthermore, we have shown that the FMDV X protein alone can substitute for 3CD, albeit less efficiently. In addition, the VPg...... precursors, 3B(3)3C and 3B(123)3C, can function as substrates for uridylylation in the absence of added 3C or 3CD. Residues within the FMDV 3C protein involved in interaction with the cre/bus RNA have been identified and are located on the face of the protein opposite from the catalytic site. These residues...
Snapshots of Dynamics in Synthesizing N6-isopentenyladenosine at tRNA Anticodon†,‡

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Chimnaronk, Sarin; Forouhar, Farhad; Sakai, Junichi; Yao, Min; Tron, Cecile M.; Atta, Mohamed; Fontecave, Marc; Hunt, John F.; Tanaka, Isao

2009-01-01

Bacterial and eukaryotic transfer RNAs that decode codons starting with uridine have a hydrophobically-hypermodified adenosine at the position 37 (A37) adjacent to the 3′-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of the crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during modification of RNA. A compact evolutionary inserted domain (herein ‘swinging domain’) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A36 and A38 together to squeeze out A37 into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate-binding of MiaA. PMID:19435325
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

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Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A

2014-03-06

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

Science.gov (United States)

Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

2014-03-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.
A Structural Overview of RNA-Dependent RNA Polymerases from the Flaviviridae Family

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Jiqin Wu

2015-06-01

Full Text Available RNA-dependent RNA polymerases (RdRPs from the Flaviviridae family are representatives of viral polymerases that carry out RNA synthesis through a de novo initiation mechanism. They share a ≈ 600-residue polymerase core that displays a canonical viral RdRP architecture resembling an encircled right hand with palm, fingers, and thumb domains surrounding the active site. Polymerase catalytic motifs A–E in the palm and motifs F/G in the fingers are shared by all viral RdRPs with sequence and/or structural conservations regardless of the mechanism of initiation. Different from RdRPs carrying out primer-dependent initiation, Flaviviridae and other de novo RdRPs utilize a priming element often integrated in the thumb domain to facilitate primer-independent initiation. Upon the transition to the elongation phase, this priming element needs to undergo currently unresolved conformational rearrangements to accommodate the growth of the template-product RNA duplex. In the genera of Flavivirus and Pestivirus, the polymerase module in the C-terminal part of the RdRP protein may be regulated in cis by the N-terminal region of the same polypeptide. Either being a methyltransferase in Flavivirus or a functionally unclarified module in Pestivirus, this region could play auxiliary roles for the canonical folding and/or the catalysis of the polymerase, through defined intra-molecular interactions.
Computational Insights into the High-Fidelity Catalysis of Aminoacyl-tRNA Synthetases

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Aboelnga, Mohamed M.

Obtaining insights into the catalytic function of enzymes is an important area of research due to their widespread applications in the biotechnology and pharmaceutical industries. Among these enzymes, the aminoacyl-tRNA synthetases (aaRSs) are known for their remarkable fidelity in catalyzing the aminoacylation reactions of tRNA in protein biosynthesis. Despite the exceptional execution of this critical function, mechanistic details of the reactions catalyzed by aminoacyl-tRNA synthetases remain elusive demonstrating the obvious need to explore their remarkable chemistry. During the PhD studies reported in this thesis the mechanism of aminoacylation, pre?transfer editing and post?transfer editing catalyzed by different aaRS have been established using multi-scale computational enzymology. In the first two chapters a detailed information about aaRS and the addressed questions was given in addition to an overview of the used computational methodology currently used to investigate the enzymatic mechanisms. The aminoacylation mechanism of threonine by Threonyl-tRNA synthetases, glutamine by Glutaminyl-tRNA synthetases and glutamate by Glutamyl-tRNA synthetases have been clearly unveiled in chapter 3 and 4. Also, valuable information regarding the role of cofactors and active site residues has been obtained. While investigating the post-transfer editing mechanisms, which proceed in a remote and distinct active site, two different scenarios were experimentally suggested for two types of threonyl-tRNA synthetase species to correct the misacylation of the structurally related serine. We explored these two mechanisms as in chapters 5 and 6. Moreover, the synthetic site in which the aminoacylation reaction is catalyzed, is also responsible for a second type of proofreading reaction called pre-transfer editing mechanism. In chapter 7, this latter mechanism has been elucidated for both Seryl-tRNA synthetases and Isoleucyl-tRNA synthetases against their non-cognate substrates
Cytoplasmic viral RNA-dependent RNA polymerase disrupts the intracellular splicing machinery by entering the nucleus and interfering with Prp8.

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Yen-Chin Liu

2014-06-01

Full Text Available The primary role of cytoplasmic viral RNA-dependent RNA polymerase (RdRp is viral genome replication in the cellular cytoplasm. However, picornaviral RdRp denoted 3D polymerase (3D(pol also enters the host nucleus, where its function remains unclear. In this study, we describe a novel mechanism of viral attack in which 3D(pol enters the nucleus through the nuclear localization signal (NLS and targets the pre-mRNA processing factor 8 (Prp8 to block pre-mRNA splicing and mRNA synthesis. The fingers domain of 3D(pol associates with the C-terminal region of Prp8, which contains the Jab1/MPN domain, and interferes in the second catalytic step, resulting in the accumulation of the lariat form of the splicing intermediate. Endogenous pre-mRNAs trapped by the Prp8-3D(pol complex in enterovirus-infected cells were identified and classed into groups associated with cell growth, proliferation, and differentiation. Our results suggest that picornaviral RdRp disrupts pre-mRNA splicing processes, that differs from viral protease shutting off cellular transcription and translation which contributes to the pathogenesis of viral infection.
Differential distribution of calcineurin Aα isoenzyme mRNA's in rat brain

NARCIS (Netherlands)

Buttini, M.; Limonta, S.; Luyten, M.; Boddeke, H.

1993-01-01

Specific antisense oligonucleotide probes for the α isoforms of the catalytic subunit (A-subunit) of calcineurin were prepared and the distribution of Aα1 and Aα2 mRNA's has been studied in rat brain using in situ hybridization histochemistry. Clear regional differences have been observed for the
Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing.

Science.gov (United States)

Cornman, Robert Scott; Boncristiani, Humberto; Dainat, Benjamin; Chen, Yanping; vanEngelsdorp, Dennis; Weaver, Daniel; Evans, Jay D

2013-03-07

Deep sequencing of viruses isolated from infected hosts is an efficient way to measure population-genetic variation and can reveal patterns of dispersal and natural selection. In this study, we mined existing Illumina sequence reads to investigate single-nucleotide polymorphisms (SNPs) within two RNA viruses of the Western honey bee (Apis mellifera), deformed wing virus (DWV) and Israel acute paralysis virus (IAPV). All viral RNA was extracted from North American samples of honey bees or, in one case, the ectoparasitic mite Varroa destructor. Coverage depth was generally lower for IAPV than DWV, and marked gaps in coverage occurred in several narrow regions (selection. The Kakugo strain of DWV fell outside of all other DWV sequences at 100% bootstrap support. IAPV consensus sequences supported the existence of multiple clades as had been previously reported, and Fu and Li's D was closer to neutral expectation overall, although a sliding-window analysis identified a significantly positive D within the protease region, suggesting selection maintains diversity in that region. Within-sample mean diversity was comparable between the two viruses on average, although for both viruses there was substantial variation among samples in mean diversity at third codon positions and in the number of high-diversity sites. FST values were bimodal for DWV, likely reflecting neutral divergence in two low-diversity populations, whereas IAPV had several sites that were strong outliers with very low FST. This initial survey of genetic variation within honey bee RNA viruses suggests future directions for studies examining the underlying causes of population-genetic structure in these economically important pathogens.
Nonlinear physics approach to RNA cross-replication: Marginal stability, generalized logistic growth, and impacts of degradation

Energy Technology Data Exchange (ETDEWEB)

Frank, T.D., E-mail: till.frank@ucd.ie [UCD School of Physics, University College Dublin, Belfield, Dublin 4 (Ireland); Systems Biology Ireland, University College Dublin, Belfield, Dublin 4 (Ireland); Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269 (United States)

2011-10-24

Highlights: → RNA cross-replication is a marginally stable but not asymptotically stable process. → RNA enzymes exhibits a generalized logistic growth pattern with exponent equal to 2. → Degradation results in non-symmetric saturation levels of cross-replicating RNAs. -- Abstract: It is nowadays believed that the evolution of life involved as an intermediate step an RNA world. In such an RNA world RNA molecules replicate themselves in catalytic reactions. Recent experiments on cross-replicating RNA support the RNA world hypothesis. We derive a nonlinear mass-action kinetics model to explain logistic growth patterns and non-symmetric saturation levels observed in those experiments. We also demonstrate that fixed points of the RNA growth process are only marginally stable rather than asymptotically stable.
Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.

Science.gov (United States)

Sauguet, Ludovic; Raia, Pierre; Henneke, Ghislaine; Delarue, Marc

2016-08-22

Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 Å resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same 'double-psi β-barrel' architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs.
Steam reformer with catalytic combustor

Science.gov (United States)

Voecks, Gerald E. (Inventor)

1990-01-01

A steam reformer is disclosed having an annular steam reforming catalyst bed formed by concentric cylinders and having a catalytic combustor located at the center of the innermost cylinder. Fuel is fed into the interior of the catalytic combustor and air is directed at the top of the combustor, creating a catalytic reaction which provides sufficient heat so as to maintain the catalytic reaction in the steam reforming catalyst bed. Alternatively, air is fed into the interior of the catalytic combustor and a fuel mixture is directed at the top. The catalytic combustor provides enhanced radiant and convective heat transfer to the reformer catalyst bed.
An anti-HIV-1 compound that increases steady-state expression of apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G.

Science.gov (United States)

Ejima, Tomohiko; Hirota, Mayuko; Mizukami, Tamio; Otsuka, Masami; Fujita, Mikako

2011-10-01

Human apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) 3G (A3G) is an antiviral protein that blocks HIV-1 replication. However, the antiviral activity of A3G is overcome by the HIV-1 protein Vif. This inhibitory function of Vif is related to its ability to degrade A3G in the proteasome. This finding prompted us to examine the activities of 4-(dimethylamino)-2,6-bis[(N-(2-[(2-nitrophenyl)dithio]ethyl)amino)methyl]pyridine (SN-2) and SN-3. We found that 5 µM SN-2 increases the expression of A3G to a level much higher than that observed in the absence of Vif, without affecting the level of Vif expression. The proteasome inhibitor MG-132 increased the level of both A3G and Vif expression. These results demonstrate that A3G is ubiquitinated and degraded in the proteasome by a factor other than Vif, and that SN-2 selectively inhibits these processes. Furthermore, 5 µM SN-2 significantly inhibited the MAGI cell infectivity of wild-type HIV-1. These findings may contribute to the development of a novel anti-HIV-1 drug.
Theoretical studies on sRNA-mediated regulation in bacteria

Science.gov (United States)

Chang, Xiao-Xue; Xu, Liu-Fang; Shi, Hua-Lin

2015-12-01

Small RNA(sRNA)-mediated post-transcriptional regulation differs from protein-mediated regulation. Through base-pairing, sRNA can regulate the target mRNA in a catalytic or stoichiometric manner. Some theoretical models were built for comparison of the protein-mediated and sRNA-mediated modes in the steady-state behaviors and noise properties. Many experiments demonstrated that a single sRNA can regulate several mRNAs, which causes crosstalk between the targets. Here, we focus on some models in which two target mRNAs are silenced by the same sRNA to discuss their crosstalk features. Additionally, the sequence-function relationship of sRNA and its role in the kinetic process of base-pairing have been highlighted in model building. Project supported by the National Basic Research Program of China (Grant No. 2013CB834100), the National Natural Science Foundation of China (Grant Nos. 11121403 and 11274320), the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y4KF171CJ1), the National Natural Science Foundation for Young Scholar of China (Grant No. 11304115), and the China Postdoctoral Science Foundation (Grant No. 2013M541282).
Associations of ACE Gene Insertion/Deletion Polymorphism, ACE Activity, and ACE mRNA Expression with Hypertension in a Chinese Population

Science.gov (United States)

He, Qingfang; Fan, Chunhong; Yu, Min; Wallar, Gina; Zhang, Zuo-Feng; Wang, Lixin; Zhang, Xinwei; Hu, Ruying

2013-01-01

Background The present study was designed to explore the association of angiotensin converting enzyme (ACE) gene insertion/deletion (I/D, rs4646994) polymorphism, plasma ACE activity, and circulating ACE mRNA expression with essential hypertension (EH) in a Chinese population. In addition, a new detection method for circulating ACE mRNA expression was explored. Methods The research was approved by the ethics committee of Zhejiang Provincial Center for Disease Prevention and Control. Written informed consent was obtained prior to the investigation. 221 hypertensives (cases) and 221 normotensives (controls) were interviewed, subjected to a physical examination, and provided blood for biochemical and genetic tests. The ACE mRNA expression was analyzed by real time fluorescent quantitative Reverse Transcription PCR (FQ-RT-PCR). We performed logistic regression to assess associations of ACE I/D genotypes, ACE activity, and ACE mRNA expression levels with hypertension. Results The results of the multivariate logistic regression analysis showed that the additive model (ID, DD versus II) of the ACE genotype revealed an association with hypertension with adjusted OR of 1.43(95% CI: 1.04-1.97), and ACE ID genotype with adjusted OR of 1.72(95% CI: 1.01-2.92), DD genotype with adjusted OR of 1.94(95% CI: 1.01-3.73), respectively. In addition, our data also indicate that plasma ACE activity (adjusted OR was 1.13(95% CI: 1.08-1.18)) was significantly related to hypertension. However, the plasma ACE mRNA expressions were not different between the cases and controls. Conclusion ACE I/D polymorphism and ACE activity revealed significant influence on hypertension, while circulating ACE mRNA expression was not important factors associated with hypertension in this Chinese population. The detection of circulating ACE mRNA expression by FQ-RT-PCR might be a useful method for early screening and monitoring of EH. PMID:24098401
A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

International Nuclear Information System (INIS)

Yap, Thai Leong; Chen, Yen Liang; Xu, Ting; Wen, Daying; Vasudevan, Subhash G.; Lescar, Julien

2007-01-01

Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents an interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration

A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

Energy Technology Data Exchange (ETDEWEB)

Yap, Thai Leong [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); Chen, Yen Liang; Xu, Ting; Wen, Daying; Vasudevan, Subhash G. [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); Lescar, Julien, E-mail: julien@ntu.edu.sg [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)

2007-02-01

Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents an interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.
Catalytic nanoporous membranes

Science.gov (United States)

Pellin, Michael J; Hryn, John N; Elam, Jeffrey W

2013-08-27

A nanoporous catalytic membrane which displays several unique features Including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity. Also provided is a method for producing a catalytic membrane having flow-through pores and discreet catalytic clusters adhering to the inside surfaces of the pores.
Associations of ACE Gene Insertion/Deletion Polymorphism, ACE Activity, and ACE mRNA Expression with Hypertension in a Chinese Population

OpenAIRE

He, Qingfang; Fan, Chunhong; Yu, Min; Wallar, Gina; Zhang, Zuo-Feng; Wang, Lixin; Zhang, Xinwei; Hu, Ruying

2013-01-01

Background The present study was designed to explore the association of angiotensin converting enzyme (ACE) gene insertion/deletion (I/D, rs4646994) polymorphism, plasma ACE activity, and circulating ACE mRNA expression with essential hypertension (EH) in a Chinese population. In addition, a new detection method for circulating ACE mRNA expression was explored. Methods The research was approved by the ethics committee of Zhejiang Provincial Center for Disease Prevention and Control. Written i...
RNA interference of three up-regulated transcripts associated with insecticide resistance in an imidacloprid resistant population of Leptinotarsa decemlineata.

Science.gov (United States)

Clements, Justin; Schoville, Sean; Peterson, Nathan; Huseth, Anders S; Lan, Que; Groves, Russell L

2017-01-01

The Colorado potato beetle, Leptinotarsa decemlineata (Say), is a major agricultural pest of potatoes in the Central Sands production region of Wisconsin. Previous studies have shown that populations of L. decemlineata have become resistant to many classes of insecticides, including the neonicotinoid insecticide, imidacloprid. Furthermore, L. decemlineata has multiple mechanisms of resistance to deal with a pesticide insult, including enhanced metabolic detoxification by cytochrome p450s and glutathione S-transferases. With recent advances in the transcriptomic analysis of imidacloprid susceptible and resistant L. decemlineata populations, it is possible to investigate the role of candidate genes involved in imidacloprid resistance. A recently annotated transcriptome analysis of L. decemlineata was obtained from select populations of L. decemlineata collected in the Central Sands potato production region, which revealed a subset of mRNA transcripts constitutively up-regulated in resistant populations. We hypothesize that a portion of the up-regulated transcripts encoding for genes within the resistant populations also encode for pesticide resistance and can be suppressed to re-establish a susceptible phenotype. In this study, a discrete set of three up-regulated targets were selected for RNA interference experiments using a resistant L. decemlineata population. Following the successful suppression of transcripts encoding for a cytochrome p450, a cuticular protein, and a glutathione synthetase protein in a select L. decemlineata population, we observed reductions in measured resistance to imidacloprid that strongly suggest these genes control essential steps in imidacloprid metabolism in these field populations. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Structural and functional basis for RNA cleavage by Ire1

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Stroud Robert M

2011-07-01

Full Text Available Abstract Background The unfolded protein response (UPR controls the protein folding capacity of the endoplasmic reticulum (ER. Central to this signaling pathway is the ER-resident bifunctional transmembrane kinase/endoribonuclease Ire1. The endoribonuclease (RNase domain of Ire1 initiates a non-conventional mRNA splicing reaction, leading to the production of a transcription factor that controls UPR target genes. The mRNA splicing reaction is an obligatory step of Ire1 signaling, yet its mechanism has remained poorly understood due to the absence of substrate-bound crystal structures of Ire1, the lack of structural similarity between Ire1 and other RNases, and a scarcity of quantitative enzymological data. Here, we experimentally define the active site of Ire1 RNase and quantitatively evaluate the contribution of the key active site residues to catalysis. Results This analysis and two new crystal structures suggest that Ire1 RNase uses histidine H1061 and tyrosine Y1043 as the general acid-general base pair contributing ≥ 7.6 kcal/mol and 1.4 kcal/mol to transition state stabilization, respectively, and asparagine N1057 and arginine R1056 for coordination of the scissile phosphate. Investigation of the stem-loop recognition revealed that additionally to the stem-loops derived from the classic Ire1 substrates HAC1 and Xbp1 mRNA, Ire1 can site-specifically and rapidly cleave anticodon stem-loop (ASL of unmodified tRNAPhe, extending known substrate specificity of Ire1 RNase. Conclusions Our data define the catalytic center of Ire1 RNase and suggest a mechanism of RNA cleavage: each RNase monomer apparently contains a separate catalytic apparatus for RNA cleavage, whereas two RNase subunits contribute to RNA stem-loop docking. Conservation of the key residues among Ire1 homologues suggests that the mechanism elucidated here for yeast Ire1 applies to Ire1 in metazoan cells, and to the only known Ire1 homologue RNase L.
The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module

Science.gov (United States)

Dilworth, David; Bonnafous, Pierre; Edoo, Amiirah Bibi; Bourbigot, Sarah; Pesek-Jardim, Francy; Gudavicius, Geoff; Serpa, Jason J.; Petrotchenko, Evgeniy V.; Borchers, Christoph H.

2017-01-01

Abstract Prolyl isomerases are defined by a catalytic domain that facilitates the cis–trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors. An independent mobility of the BTHB and FKBP catalytic domains supports a model by which the N-terminus of FKBP25 is anchored to regions of dsRNA, whereas the FKBP domain is free to interact with neighboring proteins. Apart from the identification of the BTHB as a new dsRNA-binding module, this domain adds to the growing list of auxiliary functions used by prolyl isomerases to define their primary cellular targets. PMID:29036638
Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae

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Venanzetti Federica

2010-01-01

Full Text Available Abstract Background The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH ribozyme structure and activity embedded within each repeat. Results We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. Conclusions The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.
RNase MRP RNA and RNase P activity in plants are associated with a Pop1p containing complex.

Science.gov (United States)

Krehan, Mario; Heubeck, Christian; Menzel, Nicolas; Seibel, Peter; Schön, Astrid

2012-09-01

RNase P processes the 5'-end of tRNAs. An essential catalytic RNA has been demonstrated in Bacteria, Archaea and the nuclei of most eukaryotes; an organism-specific number of proteins complement the holoenzyme. Nuclear RNase P from yeast and humans is well understood and contains an RNA, similar to the sister enzyme RNase MRP. In contrast, no protein subunits have yet been identified in the plant enzymes, and the presence of a nucleic acid in RNase P is still enigmatic. We have thus set out to identify and characterize the subunits of these enzymes in two plant model systems. Expression of the two known Arabidopsis MRP RNA genes in vivo was verified. The first wheat MRP RNA sequences are presented, leading to improved structure models for plant MRP RNAs. A novel mRNA encoding the central RNase P/MRP protein Pop1p was identified in Arabidopsis, suggesting the expression of distinct protein variants from this gene in vivo. Pop1p-specific antibodies precipitate RNase P activity and MRP RNAs from wheat extracts. Our results provide evidence that in plants, Pop1p is associated with MRP RNAs and with the catalytic subunit of RNase P, either separately or in a single large complex.
Non-thermal plasmas for non-catalytic and catalytic VOC abatement

International Nuclear Information System (INIS)

Vandenbroucke, Arne M.; Morent, Rino; De Geyter, Nathalie; Leys, Christophe

2011-01-01

Highlights: → We review the current status of catalytic and non-catalytic VOC abatement based on a vast number of research papers. → The underlying mechanisms of plasma-catalysis for VOC abatement are discussed. → Critical process parameters that determine the influent are discussed and compared. - Abstract: This paper reviews recent achievements and the current status of non-thermal plasma (NTP) technology for the abatement of volatile organic compounds (VOCs). Many reactor configurations have been developed to generate a NTP at atmospheric pressure. Therefore in this review article, the principles of generating NTPs are outlined. Further on, this paper is divided in two equally important parts: plasma-alone and plasma-catalytic systems. Combination of NTP with heterogeneous catalysis has attracted increased attention in order to overcome the weaknesses of plasma-alone systems. An overview is given of the present understanding of the mechanisms involved in plasma-catalytic processes. In both parts (plasma-alone systems and plasma-catalysis), literature on the abatement of VOCs is reviewed in close detail. Special attention is given to the influence of critical process parameters on the removal process.
Catalytic distillation process

Science.gov (United States)

Smith, L.A. Jr.

1982-06-22

A method is described for conducting chemical reactions and fractionation of the reaction mixture comprising feeding reactants to a distillation column reactor into a feed zone and concurrently contacting the reactants with a fixed bed catalytic packing to concurrently carry out the reaction and fractionate the reaction mixture. For example, a method for preparing methyl tertiary butyl ether in high purity from a mixed feed stream of isobutene and normal butene comprising feeding the mixed feed stream to a distillation column reactor into a feed zone at the lower end of a distillation reaction zone, and methanol into the upper end of said distillation reaction zone, which is packed with a properly supported cationic ion exchange resin, contacting the C[sub 4] feed and methanol with the catalytic distillation packing to react methanol and isobutene, and concurrently fractionating the ether from the column below the catalytic zone and removing normal butene overhead above the catalytic zone.
iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

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Jittrawan Thaiprasit

2016-03-01

Full Text Available RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA
Catalytic Combustion of Gasified Waste

Energy Technology Data Exchange (ETDEWEB)

Kusar, Henrik

2003-09-01

This thesis concerns catalytic combustion for gas turbine application using a low heating-value (LHV) gas, derived from gasified waste. The main research in catalytic combustion focuses on methane as fuel, but an increasing interest is directed towards catalytic combustion of LHV fuels. This thesis shows that it is possible to catalytically combust a LHV gas and to oxidize fuel-bound nitrogen (NH{sub 3}) directly into N{sub 2} without forming NO{sub x} The first part of the thesis gives a background to the system. It defines waste, shortly describes gasification and more thoroughly catalytic combustion. The second part of the present thesis, paper I, concerns the development and testing of potential catalysts for catalytic combustion of LHV gases. The objective of this work was to investigate the possibility to use a stable metal oxide instead of noble metals as ignition catalyst and at the same time reduce the formation of NO{sub x} In paper II pilot-scale tests were carried out to prove the potential of catalytic combustion using real gasified waste and to compare with the results obtained in laboratory scale using a synthetic gas simulating gasified waste. In paper III, selective catalytic oxidation for decreasing the NO{sub x} formation from fuel-bound nitrogen was examined using two different approaches: fuel-lean and fuel-rich conditions. Finally, the last part of the thesis deals with deactivation of catalysts. The various deactivation processes which may affect high-temperature catalytic combustion are reviewed in paper IV. In paper V the poisoning effect of low amounts of sulfur was studied; various metal oxides as well as supported palladium and platinum catalysts were used as catalysts for combustion of a synthetic gas. In conclusion, with the results obtained in this thesis it would be possible to compose a working catalytic system for gas turbine application using a LHV gas.
Redefining high-risk patients with stage II colon cancer by risk index and microRNA-21: results from a population-based cohort

DEFF Research Database (Denmark)

Hansen, T F; Kjær-Frifeldt, S; Christensen, R D

2014-01-01

Background:The aim of the present study was to analyse the prognostic value of microRNA-21 (miRNA-21) in patients with stage II colon cancer aiming at a risk index for this group of patients.Methods:A population-based cohort of 554 patients was included. MicroRNA-21 was analysed by qPCR based.......001). The overall survival (OS) index identified three different subgroups (Pcolon cancer. Furthermore...... on tumour tissue. An index was created using the coefficients obtained from a collective multiple Cox regression. The entire procedure was cross-validated (10-fold). The performance of the index was quantified by time-dependent receiver operating characteristics curves.Results:High miRNA-21 expression...
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.
Structure of Drosophila Oskar reveals a novel RNA binding protein

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Yang, Na; Yu, Zhenyu; Hu, Menglong; Wang, Mingzhu; Lehmann, Ruth; Xu, Rui-Ming

2015-01-01

Oskar (Osk) protein plays critical roles during Drosophila germ cell development, yet its functions in germ-line formation and body patterning remain poorly understood. This situation contrasts sharply with the vast knowledge about the function and mechanism of osk mRNA localization. Osk is predicted to have an N-terminal LOTUS domain (Osk-N), which has been suggested to bind RNA, and a C-terminal hydrolase-like domain (Osk-C) of unknown function. Here, we report the crystal structures of Osk-N and Osk-C. Osk-N shows a homodimer of winged-helix–fold modules, but without detectable RNA-binding activity. Osk-C has a lipase-fold structure but lacks critical catalytic residues at the putative active site. Surprisingly, we found that Osk-C binds the 3′UTRs of osk and nanos mRNA in vitro. Mutational studies identified a region of Osk-C important for mRNA binding. These results suggest possible functions of Osk in the regulation of stability, regulation of translation, and localization of relevant mRNAs through direct interaction with their 3′UTRs, and provide structural insights into a novel protein–RNA interaction motif involving a hydrolase-related domain. PMID:26324911
The RNA Exosome Channeling and Direct Access Conformations Have Distinct In Vivo Functions

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Jaeil Han

2016-09-01

Full Text Available The RNA exosome is a 3′–5′ ribonuclease complex that is composed of nine core subunits and an essential catalytic subunit, Rrp44. Two distinct conformations of Rrp44 were revealed in previous structural studies, suggesting that Rrp44 may change its conformation to exert its function. In the channeling conformation, (Rrp44ch, RNA accesses the active site after traversing the central channel of the RNA exosome, whereas in the other conformation, (Rrp44da, RNA gains direct access to the active site. Here, we show that the Rrp44da exosome is important for nuclear function of the RNA exosome. Defects caused by disrupting the direct access conformation are distinct from those caused by channel-occluding mutations, indicating specific functions for each conformation. Our genetic analyses provide in vivo evidence that the RNA exosome employs a direct-access route to recruit specific substrates, indicating that the RNA exosome uses alternative conformations to act on different RNA substrates.
rRNA fragmentation induced by a yeast killer toxin.

Science.gov (United States)

Kast, Alene; Klassen, Roland; Meinhardt, Friedhelm

2014-02-01

Virus like dsDNA elements (VLE) in yeast were previously shown to encode the killer toxins PaT and zymocin, which target distinct tRNA species via specific anticodon nuclease (ACNase) activities. Here, we characterize a third member of the VLE-encoded toxins, PiT from Pichia inositovora, and identify PiOrf4 as the cytotoxic subunit by conditional expression in Saccharomyces cerevisiae. In contrast to the tRNA targeting toxins, however, neither a change of the wobble uridine modification status by introduction of elp3 or trm9 mutations nor tRNA overexpression rescued from PiOrf4 toxicity. Consistent with a distinct RNA target, expression of PiOrf4 causes specific fragmentation of the 25S and 18S rRNA. A stable cleavage product comprising the first ∼ 130 nucleotides of the 18S rRNA was purified and characterized by linker ligation and subsequent reverse transcription; 3'-termini were mapped to nucleotide 131 and 132 of the 18S rRNA sequence, a region showing some similarity to the anticodon loop of tRNA(Glu)(UUC), the zymocin target. PiOrf4 residues Glu9 and His214, corresponding to catalytic sites Glu9 and His209 in the ACNase subunit of zymocin are essential for in vivo toxicity and rRNA fragmentation, raising the possibility of functionally conserved RNase modules in both proteins. © 2013 John Wiley & Sons Ltd.
Catalytic bioreactors and methods of using same

Science.gov (United States)

Worden, Robert Mark; Liu, Yangmu Chloe

2017-07-25

Various embodiments provide a bioreactor for producing a bioproduct comprising one or more catalytically active zones located in a housing and adapted to keep two incompatible gaseous reactants separated when in a gas phase, wherein each of the one or more catalytically active zones may comprise a catalytic component retainer and a catalytic component retained within and/or thereon. Each of the catalytically active zones may additionally or alternatively comprise a liquid medium located on either side of the catalytic component retainer. Catalytic component may include a microbial cell culture located within and/or on the catalytic component retainer, a suspended catalytic component suspended in the liquid medium, or a combination thereof. Methods of using various embodiments of the bioreactor to produce a bioproduct, such as isobutanol, are also provided.
Host apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3G is an innate defensive factor and drug target against hepatitis C virus.

Science.gov (United States)

Peng, Zong-Gen; Zhao, Zhi-Yun; Li, Yan-Ping; Wang, Yu-Ping; Hao, Lan-Hu; Fan, Bo; Li, Yu-Huan; Wang, Yue-Ming; Shan, Yong-Qiang; Han, Yan-Xing; Zhu, Yan-Ping; Li, Jian-Rui; You, Xue-Fu; Li, Zhuo-Rong; Jiang, Jian-Dong

2011-04-01

Host cellular factor apolipoprotein B messenger RNA (mRNA)-editing enzyme catalytic polypeptide-like 3G (hA3G) is a cytidine deaminase that inhibits a group of viruses including human immunodeficiency virus-1 (HIV-1). In the continuation of our research on hA3G, we found that hA3G stabilizing compounds significantly inhibited hepatitis C virus (HCV) replication. Therefore, this study investigated the role of hA3G in HCV replication. Introduction of external hA3G into HCV-infected Huh7.5 human hepatocytes inhibited HCV replication; knockdown of endogenous hA3G enhanced HCV replication. Exogenous HIV-1 virion infectivity factor (Vif) decreased intracellular hA3G and therefore enhanced HCV proliferation, suggesting that the presence of Vif might be an explanation for the HIV-1/HCV coinfection often observed in HIV-1(+) individuals. Treatment of the HCV-infected Huh7.5 cells with RN-5 or IMB-26, two known hA3G stabilizing compounds, increased intracellular hA3G and accordingly inhibited HCV replication. The compounds inhibit HCV through increasing the level of hA3G incorporated into HCV particles, but not through inhibiting HCV enzymes. However, G/A hypermutation in the HCV genome were not detected, suggesting a new antiviral mechanism of hA3G in HCV, different from that in HIV-1. Stabilization of hA3G by RN-5 was safe in vivo. hA3G appears to be a cellular restrict factor against HCV and could be a potential target for drug discovery. 2011 American Association for the Study of Liver Diseases.
A Multisampling Reporter System for Monitoring MicroRNA Activity in the Same Population of Cells

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Pei-Chen Huang

2009-01-01

Full Text Available MicroRNAs (miRNAs downregulate gene expression by binding to the partially complementary sites in the 3′ untranslated region (UTR of target mRNAs. Several methods, such as Northern blot analysis, quantitative real-time RT-PCR, microarray, and the luciferase reporter system, are commonly used to quantify the relative level or activity of miRNAs. The disadvantage of these methods is the requirement for cell lysis, which means that several sets of wells/dishes of cells must be prepared to monitor changes in miRNA activity in time-course studies. In this study, we developed a multisampling reporter system in which two secretable bioluminescence-generating enzymes are employed, one as a reporter and the other as an internal control. The reporters consist of a pair of vectors containing the Metridia luciferase gene, one with and one without a duplicated miRNA targeting sequence at their 3′UTR, while the other vector coding for the secreted alkaline phosphatase gene is used as an internal control. This method allows miRNA activity to be monitored within the same population of cells over time by withdrawing aliquots of the culture medium. The practicability and benefits of this system are addressed in this report.

Catalytic process for tritium exchange reaction

International Nuclear Information System (INIS)

Hansoo Lee; Kang, H.S.; Paek, S.W.; Hongsuk Chung; Yang Geun Chung; Sook Kyung Lee

2001-01-01

The catalytic activities for a hydrogen isotope exchange were measured through the reaction of a vapor and gas mixture. The catalytic activity showed to be comparable with the published data. Since the gas velocity is relatively low, the deactivation was not found clearly during the 5-hour experiment. Hydrogen isotope transfer experiments were also conducted through the liquid phase catalytic exchange reaction column that consisted of a catalytic bed and a hydrophilic bed. The efficiencies of both the catalytic and hydrophilic beds were higher than 0.9, implying that the column performance was excellent. (author)
Contributions to the theory of catalytic titrations-III Neutralization catalytic titrations.

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Gaál, F F; Abramović, B F

1985-07-01

Neutralization catalytic titrations of weak monoprotic adds and bases with both volumetric and coulometric addition of the titrant (strong base/acid) have been simulated by taking into account the equilibrium concentration of the catalyst during the titration. The influence of several factors on the shape of the simulated catalytic titration curve has been investigated and is discussed.
Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world.

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Soslau, Gerald

2018-06-14

The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang. Perhaps the most important support for the concept comes from the fact that some RNA species possess catalytic activity, ribozymes, and that RNA could be reverse transcribe to DNA. The thrust of numerous papers on this topic has been to explore how the available molecules on Earth, at its birth, gave rise to life as we know it today. This paper focuses more on a reverse view of the topic. The "how" molecular building blocks were synthesized is not addressed nor how the "first" RNA molecules were synthesized. We can clearly speculate on the variable environmental conditions and chemistry available on Earth billions of years ago. However, we can never truly replicate the changing conditions or know the chemical composition of Earth at the beginning of time. We can, however, confirm that over millions, perhaps billions of years the basic building blocks for life accumulated sufficiently to initiate evolution to an RNA world followed by our RNA/DNA world. Here we are attempting to take the information from our current knowledge of biology and by inference and extrapolation work backward to hypothesize biological events in the march forward from RNA to DNA. It is proposed that the primordial replicating RNA cell, the ribocyte, evolved from liposomes encompassing required reactants and products for "life" and that ribonucleopeptide complexes formed membrane pores to support bidirectional ion and molecular transport to maintain biological functions and
Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex

Energy Technology Data Exchange (ETDEWEB)

Cocozaki, Alexis I.; Ramia, Nancy F.; Shao, Yaming; Hale, Caryn R.; Terns, Rebecca M.; Terns, Michael P.; Li, Hong (FSU); (Georgia)

2012-08-10

Cmr2 is the largest and an essential subunit of a CRISPR RNA-Cas protein complex (the Cmr complex) that cleaves foreign RNA to protect prokaryotes from invading genetic elements. Cmr2 is thought to be the catalytic subunit of the effector complex because of its N-terminal HD nuclease domain. Here, however, we report that the HD domain of Cmr2 is not required for cleavage by the complex in vitro. The 2.3 {angstrom} crystal structure of Pyrococcus furiosus Cmr2 (lacking the HD domain) reveals two adenylyl cyclase-like and two {alpha}-helical domains. The adenylyl cyclase-like domains are arranged as in homodimeric adenylyl cyclases and bind ADP and divalent metals. However, mutagenesis studies show that the metal- and ADP-coordinating residues of Cmr2 are also not critical for cleavage by the complex. Our findings suggest that another component provides the catalytic function and that the essential role by Cmr2 does not require the identified ADP- or metal-binding or HD domains in vitro.
The microRNA effector RNA-induced silencing complex in hidradenitis suppurativa: a significant dysregulation within active inflammatory lesions.

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Hessam, S; Sand, M; Skrygan, M; Bechara, Falk G

2017-09-01

Recently, we could show that the expression levels of the key regulators of the microRNA (miRNA) maturation and transport were dysregulated in inflamed hidradenitis suppurativa (HS) tissue (Heyam et al. in Wiley Interdiscip Rev RNA 6:271-289, 2015). The RNA-induced silencing complex (RISC) is the central element of the miRNA pathway and regulates miRNA formation and function. We investigated the expression of the RISC components, namely transactivation-responsive RNA-binding protein-1 (TRBP1), TRBP2, protein activator (PACT) of the interferon-induced protein kinase R, Argonaute RISC Catalytic Component-1 (AGO1) and Component-2 (AGO2), metadherin, and staphylococcal nuclease and Tudor domain-containing-1 (SND1) in inflamed HS tissue compared to healthy and psoriatic controls by real-time reverse transcription polymerase chain reaction. Expression levels of all investigated components were significantly lower in lesional HS skin (n = 18) compared to healthy controls (n = 10). TRBP1, PACT, AGO1, AGO2, and SND1 expression levels were significantly down-regulated in lesional HS skin compared to healthy-appearing perilesional skin (n = 7). TRBP2 and SND1 expression levels were significantly lower in healthy-appearing perilesional skin compared to healthy controls. In lesional HS skin, expression levels of PACT, AGO1, and AGO2 were significantly lower compared to psoriatic skin (n = 10). In summary, our data showed that all investigated components of RISC are dysregulated in the skin of HS patients, providing support for the hypothesis that miRNAs may have a pathological role in the inflammatory pathogenesis of HS.
Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI.

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Mohan Zhao

Full Text Available RsmI and RsmH are conserved S-Adenosylmethionine (AdoMet-dependent methyltransferases (MTases that are responsible for the 2'-O-methylation and N4-methylation of C1402 in bacterial 16S rRNA, respectively. Methylation of m4Cm1402 plays a role in fine-tuning the shape and functions of the P-site to increase the decoding fidelity, and was recently found to contribute to the virulence of Staphylococcus aureus in host animals. Here we report the 2.20-Å crystal structure of homodimeric RsmI from Escherichia coli in complex with the cofactor AdoMet. RsmI consists of an N-terminal putative RNA-binding domain (NTD and a C-terminal catalytic domain (CTD with a Rossmann-like fold, and belongs to the class III MTase family. AdoMet is specifically bound into a negatively charged deep pocket formed by both domains by making extensive contacts. Structure-based mutagenesis and isothermal titration calorimetry (ITC assays revealed Asp100 and Ala124 are vital for AdoMet-binding. Although the overall fold of RsmI shows remarkable similarities to the characterized MTases involved in vitamin B12 biosynthesis, it exhibits a distinct charge distribution especially around the AdoMet-binding pocket because of different substrate specificity. The docking model of RsmI-AdoMet-RNA ternary complex suggested a possible base-flipping mechanism of the substrate RNA that has been observed in several known RNA MTases. Our structural and biochemical studies provide novel insights into the catalytic mechanism of C1402 methylation in 16S rRNA.
The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during MicroRNA biogenesis

KAUST Repository

Liu, Chenggang; Axtell, Michael J.; Fedoroff, Nina V.

2012-01-01

Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 mutants accumulate low levels of miRNAs and display
Nature of the Nucleosomal Barrier to RNA Polymerase II | Center for Cancer Research

Science.gov (United States)

In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged into nucleosomes, but in vitro encounters with the nucleosomes induce catalytic inactivation (arrest) of the pol II core enzyme. To determine potential mechanisms making nucleosomes transparent to transcription in vivo, we analyzed the nature of the nucleosome-induced arrest. We found that the arrests
Particle size effects in the catalytic electroreduction of CO₂ on Cu nanoparticles.

Science.gov (United States)

Reske, Rulle; Mistry, Hemma; Behafarid, Farzad; Roldan Cuenya, Beatriz; Strasser, Peter

2014-05-14

A study of particle size effects during the catalytic CO2 electroreduction on size-controlled Cu nanoparticles (NPs) is presented. Cu NP catalysts in the 2-15 nm mean size range were prepared, and their catalytic activity and selectivity during CO2 electroreduction were analyzed and compared to a bulk Cu electrode. A dramatic increase in the catalytic activity and selectivity for H2 and CO was observed with decreasing Cu particle size, in particular, for NPs below 5 nm. Hydrocarbon (methane and ethylene) selectivity was increasingly suppressed for nanoscale Cu surfaces. The size dependence of the surface atomic coordination of model spherical Cu particles was used to rationalize the experimental results. Changes in the population of low-coordinated surface sites and their stronger chemisorption were linked to surging H2 and CO selectivities, higher catalytic activity, and smaller hydrocarbon selectivity. The presented activity-selectivity-size relations provide novel insights in the CO2 electroreduction reaction on nanoscale surfaces. Our smallest nanoparticles (~2 nm) enter the ab initio computationally accessible size regime, and therefore, the results obtained lend themselves well to density functional theory (DFT) evaluation and reaction mechanism verification.
Catalytic distillation structure

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Smith, L.A. Jr.

1984-04-17

Catalytic distillation structure is described for use in reaction distillation columns, and provides reaction sites and distillation structure consisting of a catalyst component and a resilient component intimately associated therewith. The resilient component has at least about 70 volume % open space and is present with the catalyst component in an amount such that the catalytic distillation structure consists of at least 10 volume % open space. 10 figs.
Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

Science.gov (United States)

Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

2013-01-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785
The RNA world hypothesis: the worst theory of the early evolution of life (except for all the othersa

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Bernhardt Harold S

2012-07-01

Full Text Available Abstract The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems with these alternative models. From a biosynthetic – as well as, arguably, evolutionary – perspective, DNA is a modified RNA, and so the chicken-and-egg dilemma of “which came first?” boils down to a choice between RNA and protein. This is not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such different types of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example of a ‘top down’ (or should it be ‘present back’? approach to early evolution: how can we simplify modern biological systems to give a plausible evolutionary pathway that preserves continuity of function? The discovery that RNA possesses catalytic ability provides a potential solution: a single macromolecule could have originally carried out both replication and catalysis. RNA – which constitutes the genome of RNA viruses, and catalyzes peptide synthesis on the ribosome – could have been both the chicken and the egg! However, the following objections have been raised to the RNA world hypothesis: (i RNA is too complex a molecule to have arisen prebiotically; (ii RNA is inherently unstable; (iii catalysis is a relatively rare property of long RNA sequences only; and (iv the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as ‘proteins first’, which holds that proteins either preceded RNA in evolution, or – at the very least – that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA
Viral replication. Structural basis for RNA replication by the hepatitis C virus polymerase.

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Appleby, Todd C; Perry, Jason K; Murakami, Eisuke; Barauskas, Ona; Feng, Joy; Cho, Aesop; Fox, David; Wetmore, Diana R; McGrath, Mary E; Ray, Adrian S; Sofia, Michael J; Swaminathan, S; Edwards, Thomas E

2015-02-13

Nucleotide analog inhibitors have shown clinical success in the treatment of hepatitis C virus (HCV) infection, despite an incomplete mechanistic understanding of NS5B, the viral RNA-dependent RNA polymerase. Here we study the details of HCV RNA replication by determining crystal structures of stalled polymerase ternary complexes with enzymes, RNA templates, RNA primers, incoming nucleotides, and catalytic metal ions during both primed initiation and elongation of RNA synthesis. Our analysis revealed that highly conserved active-site residues in NS5B position the primer for in-line attack on the incoming nucleotide. A β loop and a C-terminal membrane-anchoring linker occlude the active-site cavity in the apo state, retract in the primed initiation assembly to enforce replication of the HCV genome from the 3' terminus, and vacate the active-site cavity during elongation. We investigated the incorporation of nucleotide analog inhibitors, including the clinically active metabolite formed by sofosbuvir, to elucidate key molecular interactions in the active site. Copyright © 2015, American Association for the Advancement of Science.
Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase

International Nuclear Information System (INIS)

Guo, Min; Shapiro, Ryan; Schimmel, Paul; Yang, Xiang-Lei

2010-01-01

E. coli alanyl-tRNA synthetase is recalcitrant to crystallization. A group of leucine substitutions has transformed the protein. Although Escherichia coli alanyl-tRNA synthetase was among the first tRNA synthetases to be sequenced and extensively studied by functional analysis, it has proved to be recalcitrant to crystallization. This challenge remained even for crystallization of the catalytic fragment. By mutationally introducing three stacked leucines onto the solvent-exposed side of an α-helix, an engineered catalytic fragment of the synthetase was obtained that yielded multiple high-quality crystals and cocrystals with different ligands. The engineered α-helix did not form a leucine zipper that interlocked with the same α-helix from another molecule. Instead, using the created hydrophobic spine, it interacted with other surfaces of the protein as a leucine half-zipper (LHZ) to enhance the crystal lattice interactions. The LHZ made crystal lattice contacts in all crystals of different space groups. These results illustrate the power of introducing an LHZ into helices to facilitate crystallization. The authors propose that the method can be unified with surface-entropy reduction and can be broadly used for protein-surface optimization in crystallization
Probes of eukaryotic DNA-dependent RNA polymerase II-I. Binding of 9-beta-D-arabinofuranosyl-6-mercaptopurine to the elongation subsite.

Science.gov (United States)

Cho, J M; Kimball, A P

1982-08-15

9-beta-D-Arabinofuranosyl-6-mercaptopurine (ara-6-MP) was used to affinity-label wheat germ DNA-dependent RNA polymerase II (or B) (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). This nucleoside analogue was found to be a competitive inhibitor with respect to [3H]UMP incorporation. Natural substrates protected the enzyme from inactivation by ara-6-MP when the enzyme was preincubated with excess concentrations of substrates, suggesting that the inhibitor binds at the elongation subsite. The inhibitor bound the catalytic center of the enzyme with a stoichiometry of 0.6:1. The sulfhydryl reagent, dithiothreitol, reversed the inhibition by ara-6-MP, suggesting that the 6-thiol group of the inhibitor was interacting closely with an essential cysteine residue in the catalytic center of the enzyme. Chromatographic analysis of the pronase-digestion products of the RNA polymerase II-ara-6-MP complex also showed that ara-6-MP had bound a cysteine residue. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the denatured [6-35S]ara-6-MP-labeled RNA polymerase II revealed that over 80% of the radioactivity was associated with the IIb subunit of the enzyme.
The evolution of catalytic function

Science.gov (United States)

Maurel, Marie-Christine; Ricard, Jacques

2006-03-01

It is very likely that the main driving force of enzyme evolution is the requirement to improve catalytic and regulatory efficiency which results from the intrinsic performance as well as from the spatial and functional organization of enzymes in living cells. Kinetic co-operativity may occur in simple monomeric proteins if they display “slow” conformational transitions, at the cost of catalytic efficiency. Oligomeric enzymes on the other hand can be both efficient and co-operative. We speculate that the main reason for the emergence of co-operative oligomeric enzymes is the need for catalysts that are both cooperative and efficient. As it is not useful for an enzyme to respond to a change of substrate concentration in a complex kinetic way, the emergence of symmetry has its probable origin in a requirement for “functional simplicity”. In a living cell, enzyme are associated with other macromolecules and membranes. The fine tuning of their activity may also be reached through mutations of the microenvironment. Our hypothesis is that these mutations are related to the vectorial transport of molecules, to achieve the hysteresis loops of enzyme reactions generated by the coupling of reaction and diffusion, through the co-operativity brought about by electric interactions between a charged substrate and a membrane, and last but not least, through oscillations. As the physical origins of these effects are very simple and do not require complex molecular devices, it is very likely that the functional advantage generated by the spatial and functional organization of enzyme molecules within the cell have appeared in prebiotic catalysis or very early during the primeval stages of biological evolution. We shall began this paper by presenting the nature of the probable earliest catalysts in the RNA world.
Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

Science.gov (United States)

Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca

2015-01-01

In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.
Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

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Ilario Ferrocino

Full Text Available In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE. The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.
Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling

Science.gov (United States)

Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca

2015-01-01

In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples. PMID:26035837
The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases

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Dutartre Hélène

2005-10-01

Full Text Available Abstract Background The Flaviviridae virus family includes major human and animal pathogens. The RNA dependent RNA polymerase (RdRp plays a central role in the replication process, and thus is a validated target for antiviral drugs. Despite the increasing structural and enzymatic characterization of viral RdRps, detailed molecular replication mechanisms remain unclear. The hepatitis C virus (HCV is a major human pathogen difficult to study in cultured cells. The bovine viral diarrhea virus (BVDV is often used as a surrogate model to screen antiviral drugs against HCV. The structure of BVDV RdRp has been recently published. It presents several differences relative to HCV RdRp. These differences raise questions about the relevance of BVDV as a surrogate model, and cast novel interest on the "GB" virus C (GBV-C. Indeed, GBV-C is genetically closer to HCV than BVDV, and can lead to productive infection of cultured cells. There is no structural data for the GBV-C RdRp yet. Results We show in this study that the GBV-C RdRp is closest to the HCV RdRp. We report a 3D model of the GBV-C RdRp, developed using sequence-to-structure threading and comparative modeling based on the atomic coordinates of the HCV RdRp structure. Analysis of the predicted structural features in the phylogenetic context of the RNA polymerase family allows rationalizing most of the experimental data available. Both available structures and our model are explored to examine the catalytic cleft, allosteric and substrate binding sites. Conclusion Computational methods were used to infer evolutionary relationships and to predict the structure of a viral RNA polymerase. Docking a GTP molecule into the structure allows defining a GTP binding pocket in the GBV-C RdRp, such as that of BVDV. The resulting model suggests a new proposition for the mechanism of RNA synthesis, and may prove useful to design new experiments to implement our knowledge on the initiation mechanism of RNA

Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication.

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Herod, Morgan R; Ferrer-Orta, Cristina; Loundras, Eleni-Anna; Ward, Joseph C; Verdaguer, Nuria; Rowlands, David J; Stonehouse, Nicola J

2016-08-01

The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a coordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e., via expression from a separate RNA molecule), while others are required in cis (i.e., expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA polymerase (RdRp) 3D are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically active 3D molecules and those that build a replication complex. We report a novel nonenzymatic cis-acting function of 3D that is essential for viral-genome replication. Using an FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans acting. Immunofluorescence studies suggest that both cis- and trans-acting 3D molecules localize to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. This study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further. Foot-and-mouth disease virus (FMDV) is an important animal pathogen responsible for foot-and-mouth disease. The disease is endemic in many parts of the world with outbreaks within livestock resulting in major economic losses. Propagation of the viral genome occurs within
The Comparison of Hydrochloric Acid and Phosphoric Acid Treatments in the Preparation of Montmorillonite Catalysts for RNA Synthesis

Science.gov (United States)

Aldersley, Michael Frank; Joshi, Prakash C.; Huang, Yixing

2017-09-01

The treatment of clay minerals with a preliminary acid wash and titration to pH 7 has proven to generate catalysts for the most interesting of oligomerization reactions in which activated RNA-nucleotides generate oligomers up to 40-mers. Significantly, not all clay minerals become catalytic following this treatment and none are catalytic in the absence of such treatment. The washing procedure has been modified and explored further using phosphoric acid and the outcomes are compared to those obtained when clay samples are prepared following a hydrochloric acid wash.
Method of fabricating a catalytic structure

Science.gov (United States)

Rollins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

2009-09-22

A precursor to a catalytic structure comprising zinc oxide and copper oxide. The zinc oxide has a sheet-like morphology or a spherical morphology and the copper oxide comprises particles of copper oxide. The copper oxide is reduced to copper, producing the catalytic structure. The catalytic structure is fabricated by a hydrothermal process. A reaction mixture comprising a zinc salt, a copper salt, a hydroxyl ion source, and a structure-directing agent is formed. The reaction mixture is heated under confined volume conditions to produce the precursor. The copper oxide in the precursor is reduced to copper. A method of hydrogenating a carbon oxide using the catalytic structure is also disclosed, as is a system that includes the catalytic structure.
Secreted histidyl-tRNA synthetase splice variants elaborate major epitopes for autoantibodies in inflammatory myositis.

Science.gov (United States)

Zhou, Jie J; Wang, Feng; Xu, Zhiwen; Lo, Wing-Sze; Lau, Ching-Fun; Chiang, Kyle P; Nangle, Leslie A; Ashlock, Melissa A; Mendlein, John D; Yang, Xiang-Lei; Zhang, Mingjie; Schimmel, Paul

2014-07-11

Inflammatory and debilitating myositis and interstitial lung disease are commonly associated with autoantibodies (anti-Jo-1 antibodies) to cytoplasmic histidyl-tRNA synthetase (HisRS). Anti-Jo-1 antibodies from different disease-afflicted patients react mostly with spatially separated epitopes in the three-dimensional structure of human HisRS. We noted that two HisRS splice variants (SVs) include these spatially separated regions, but each SV lacks the HisRS catalytic domain. Despite the large deletions, the two SVs cross-react with a substantial population of anti-Jo-l antibodies from myositis patients. Moreover, expression of at least one of the SVs is up-regulated in dermatomyositis patients, and cell-based experiments show that both SVs and HisRS can be secreted. We suggest that, in patients with inflammatory myositis, anti-Jo-1 antibodies may have extracellular activity. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
PRMT1 methylates the single Argonaute of Toxoplasma gondii and is important for the recruitment of Tudor nuclease for target RNA cleavage by antisense guide RNA

Science.gov (United States)

Musiyenko, Alla; Majumdar, Tanmay; Andrews, Joel; Adams, Brian; Barik, Sailen

2013-01-01

Summary Argonaute (Ago) plays a central role in RNA interference in metazoans, but its status in lower organisms remains ill-defined. We report on the Ago complex of the unicellular protozoan, Toxoplasma gondii (Tg), an obligatory pathogen of mammalian hosts. The PIWI-like domain of TgAgo lacked the canonical DDE/H catalytic triad, explaining its weak target RNA cleavage activity. However, TgAgo associated with a stronger RNA slicer, a Tudor staphylococcal nuclease (TSN), and with a protein Arg methyl transferase, PRMT1. Mutational analysis suggested that the N-terminal RGG-repeat domain of TgAgo was methylated by PRMT1, correlating with the recruitment of TSN. The slicer activity of TgAgo was Mg2+-dependent and required perfect complementarity between the guide RNA and the target. In contrast, the TSN activity was Ca2+-dependent and required an imperfectly paired guide RNA. Ago knockout parasites showed essentially normal growth, but in contrast, the PRMT1 knockouts grew abnormally. Chemical inhibition of Arg-methylation also had an anti-parasitic effect. These results suggest that the parasitic PRMT1 plays multiple roles, and its loss affects the recruitment of a more potent second slicer to the parasitic RNA silencing complex, the exact mechanism of which remains to be determined. PMID:22309152
Effect of support on the catalytic activity of manganese oxide catalyts for toluene combustion

International Nuclear Information System (INIS)

Pozan, Gulin Selda

2012-01-01

Highlights: ► α-Al 2 O 3 , obtained from Bohmite, as a support for enhancing of the activity. ► The support material for catalytic oxidation. ► The manganese state and oxygen species effect on the catalytic combustion reaction. - Abstract: The aim of this work was to study combustion of toluene (1000 ppm) over MnO 2 modified with different supports. α-Al 2 O 3 and γ-Al 2 O 3 obtained from Boehmite, γ-Al 2 O 3 (commercial), SiO 2 , TiO 2 and ZrO 2 were used as commercial support materials. In view of potential interest of this process, the influence of support material on the catalytic performance was discussed. The deposition of 9.5MnO 2 was performed by impregnation over support. The catalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), temperature programmed reduction and oxidation (TPR/TPO) and thermogravimetric analysis (TGA). The catalytic tests were carried out at atmospheric pressure in a fixed-bed flow reactor. 9.5MnO 2 /α-Al 2 O 3 (B) (synthesized from Boehmite) catalyst exhibits the highest catalytic activity, over which the toluene conversion was up to 90% at a temperature of 289 °C. Considering all the characterization and reaction data reported in this study, it was concluded that the manganese state and oxygen species played an important role in the catalytic activity.
Comparative analysis among the small RNA populations of source, sink and conductive tissues in two different plant-virus pathosystems.

Science.gov (United States)

Herranz, Mari Carmen; Navarro, Jose Antonio; Sommen, Evelien; Pallas, Vicente

2015-02-22

In plants, RNA silencing plays a fundamental role as defence mechanism against viruses. During last years deep-sequencing technology has allowed to analyze the sRNA profile of a large variety of virus-infected tissues. Nevertheless, the majority of these studies have been restricted to a unique tissue and no comparative analysis between phloem and source/sink tissues has been conducted. In the present work, we compared the sRNA populations of source, sink and conductive (phloem) tissues in two different plant virus pathosystems. We chose two cucurbit species infected with two viruses very different in genome organization and replication strategy; Melon necrotic spot virus (MNSV) and Prunus necrotic ringspot virus (PNRSV). Our findings showed, in both systems, an increase of the 21-nt total sRNAs together with a decrease of those with a size of 24-nt in all the infected tissues, except for the phloem where the ratio of 21/24-nt sRNA species remained constant. Comparing the vsRNAs, both PNRSV- and MNSV-infected plants share the same vsRNA size distribution in all the analyzed tissues. Similar accumulation levels of sense and antisense vsRNAs were observed in both systems except for roots that showed a prevalence of (+) vsRNAs in both pathosystems. Additionally, the presence of overrepresented discrete sites along the viral genome, hot spots, were identified and validated by stem-loop RT-PCR. Despite that in PNRSV-infected plants the presence of vsRNAs was scarce both viruses modulated the host sRNA profile. We compare for the first time the sRNA profile of four different tissues, including source, sink and conductive (phloem) tissues, in two plant-virus pathosystems. Our results indicate that antiviral silencing machinery in melon and cucumber acts mainly through DCL4. Upon infection, the total sRNA pattern in phloem remains unchanged in contrast to the rest of the analyzed tissues indicating a certain tissue-tropism to this polulation. Independently of the
Monitoring of an RNA Multistep Folding Pathway by Isothermal Titration Calorimetry

OpenAIRE

Reymond, Cédric; Bisaillon, Martin; Perreault, Jean-Pierre

2009-01-01

Isothermal titration calorimetry was used to monitor the energetic landscape of a catalytic RNA, specifically that of the hepatitis delta virus ribozyme. Using mutants that isolated various tertiary interactions, the thermodynamic parameters of several ribozyme-substrate intermediates were determined. The results shed light on the impact of several tertiary interactions on the global structure of the ribozyme. In addition, the data indicate that the formation of the P1.1 pseudoknot is the lim...
Screening Yield of HIV Antigen/Antibody Combination and Pooled HIV RNA Testing for Acute HIV Infection in a High-Prevalence Population.

Science.gov (United States)

Peters, Philip J; Westheimer, Emily; Cohen, Stephanie; Hightow-Weidman, Lisa B; Moss, Nicholas; Tsoi, Benjamin; Hall, Laura; Fann, Charles; Daskalakis, Demetre C; Beagle, Steve; Patel, Pragna; Radix, Asa; Foust, Evelyn; Kohn, Robert P; Marmorino, Jenni; Pandori, Mark; Fu, Jie; Samandari, Taraz; Gay, Cynthia L

2016-02-16

established and acute HIV infections) by 10.4% (95% CI, 8.8%-12.2%) and pooled HIV RNA testing increased the relative HIV diagnostic yield by 12.4% (95% CI, 10.7%-14.3%). In a high-prevalence population, HIV screening using an HIV Ag/Ab combination assay following a negative rapid test detected 82% of acute HIV infections detectable by pooled HIV RNA testing, with a positive predictive value of 59%. Further research is needed to evaluate this strategy in lower-prevalence populations and in persons using preexposure prophylaxis for HIV prevention.
The Comparison of Hydrochloric Acid and Phosphoric Acid Treatments in the Preparation of Montmorillonite Catalysts for RNA Synthesis.

Science.gov (United States)

Aldersley, Michael Frank; Joshi, Prakash C; Huang, Yixing

2017-09-01

The treatment of clay minerals with a preliminary acid wash and titration to pH 7 has proven to generate catalysts for the most interesting of oligomerization reactions in which activated RNA-nucleotides generate oligomers up to 40-mers. Significantly, not all clay minerals become catalytic following this treatment and none are catalytic in the absence of such treatment. The washing procedure has been modified and explored further using phosphoric acid and the outcomes are compared to those obtained when clay samples are prepared following a hydrochloric acid wash.
Mutations in the catalytic core or the C-terminus of murine leukemia virus (MLV) integrase disrupt virion infectivity and exert diverse effects on reverse transcription

International Nuclear Information System (INIS)

Steinrigl, Adolf; Nosek, Dagmara; Ertl, Reinhard; Guenzburg, Walter H.; Salmons, Brian; Klein, Dieter

2007-01-01

Understanding of the structures and functions of the retroviral integrase (IN), a key enzyme in the viral replication cycle, is essential for developing antiretroviral treatments and facilitating the development of safer gene therapy vehicles. Thus, four MLV IN-mutants were constructed in the context of a retroviral vector system, harbouring either a substitution in the catalytic centre, deletions in the C-terminus, or combinations of both modifications. IN-mutants were tested for their performance in different stages of the viral replication cycle: RNA-packaging; RT-activity; transient and stable infection efficiency; dynamics of reverse transcription and nuclear entry. All mutant vectors packaged viral RNA with wild-type efficiencies and displayed only slight reductions in RT-activity. Deletion of either the IN C-terminus alone, or in addition to part of the catalytic domain exerted contrasting effects on intracellular viral DNA levels, implying that IN influences reverse transcription in more than one direction
Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

Science.gov (United States)

White, Neil A; Hoogstraten, Charles G

2017-09-01

The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.
Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

Science.gov (United States)

Strobel, Eric J; Watters, Kyle E; Nedialkov, Yuri; Artsimovitch, Irina; Lucks, Julius B

2017-07-07

RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

KAUST Repository

Ngugi, David; Stingl, Ulrich

2012-01-01

that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While
Redefining high-risk patients with stage II colon cancer by risk index and microRNA-21: results from a population-based cohort

DEFF Research Database (Denmark)

Hansen, T F; Kjær-Frifeldt, S; Christensen, R D

2014-01-01

Background:The aim of the present study was to analyse the prognostic value of microRNA-21 (miRNA-21) in patients with stage II colon cancer aiming at a risk index for this group of patients.Methods:A population-based cohort of 554 patients was included. MicroRNA-21 was analysed by qPCR based...... on tumour tissue. An index was created using the coefficients obtained from a collective multiple Cox regression. The entire procedure was cross-validated (10-fold). The performance of the index was quantified by time-dependent receiver operating characteristics curves.Results:High miRNA-21 expression...... was associated with an unfavourable recurrence-free cancer-specific survival (RF-CSS), hazard ratio 1.35 (95% confidence interval, 1.03-1.76) (P=0.028). The generated RF-CSS index divided the traditional high-risk patients into subgroups with 5-year RF-CSS rates of 87% and 73%, respectively (P...
A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii.

Directory of Open Access Journals (Sweden)

Laurence Braun

2010-05-01

Full Text Available In RNA silencing, small RNAs produced by the RNase-III Dicer guide Argonaute-like proteins as part of RNA-induced silencing complexes (RISC to regulate gene expression transcriptionally or post-transcriptionally. Here, we have characterized the RNA silencing machinery and exhaustive small RNAome of Toxoplasma gondii, member of the Apicomplexa, a phylum of animal- and human-infecting parasites that cause extensive health and economic damages to human populations worldwide. Remarkably, the small RNA-generating machinery of Toxoplasma is phylogenetically and functionally related to that of plants and fungi, and accounts for an exceptionally diverse array of small RNAs. This array includes conspicuous populations of repeat-associated small interfering RNA (siRNA, which, as in plants, likely generate and maintain heterochromatin at DNA repeats and satellites. Toxoplasma small RNAs also include many microRNAs with clear metazoan-like features whose accumulation is sometimes extremely high and dynamic, an unexpected finding given that Toxoplasma is a unicellular protist. Both plant-like heterochromatic small RNAs and metazoan-like microRNAs bind to a single Argonaute protein, Tg-AGO. Toxoplasma miRNAs co-sediment with polyribosomes, and thus, are likely to act as translational regulators, consistent with the lack of catalytic residues in Tg-AGO. Mass spectrometric analyses of the Tg-AGO protein complex revealed a common set of virtually all known RISC components so far characterized in human and Drosophila, as well as novel proteins involved in RNA metabolism. In agreement with its loading with heterochromatic small RNAs, Tg-AGO also associates substoichiometrically with components of known chromatin-repressing complexes. Thus, a puzzling patchwork of silencing processor and effector proteins from plant, fungal and metazoan origin accounts for the production and action of an unsuspected variety of small RNAs in the single-cell parasite Toxoplasma and
Reconstruction and analysis of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in rheumatoid arthritis.

Science.gov (United States)

Jiang, Hui; Ma, Rong; Zou, Shubiao; Wang, Yongzhong; Li, Zhuqing; Li, Weiping

2017-06-01

Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper. Meanwhile, Gene Ontology (GO) and pathway analysis were performed using Cytoscape plug-in BinGO and Database for Annotation, Visualization, and Integration Discovery (DAVID), respectively. We found that the lncRNA-miRNA-mRNA network was composed of 7 lncRNA nodes, 90 mRNA nodes, 24 miRNA nodes, and 301 edges. The functional assay showed that 147 GO terms and 23 pathways were enriched. In addition, three lncRNAs (S5645.1, XR_006437.1, J01878) were highly related to RA, and therefore, were selected as key lncRNAs. This study suggests that specific lncRNAs are associated with the development of RA, and three lncRNAs (S5645.1, XR_006437.1, J01878) could be used as potential diagnostic biomarkers and therapeutic targets.
Heterogeneous catalytic materials solid state chemistry, surface chemistry and catalytic behaviour

CERN Document Server

Busca, Guido

2014-01-01

Heterogeneous Catalytic Materials discusses experimental methods and the latest developments in three areas of research: heterogeneous catalysis; surface chemistry; and the chemistry of catalysts. Catalytic materials are those solids that allow the chemical reaction to occur efficiently and cost-effectively. This book provides you with all necessary information to synthesize, characterize, and relate the properties of a catalyst to its behavior, enabling you to select the appropriate catalyst for the process and reactor system. Oxides (used both as catalysts and as supports for cata
The RNA World as a Model System to Study the Origin of Life.

Science.gov (United States)

Pressman, Abe; Blanco, Celia; Chen, Irene A

2015-10-05

Understanding how life arose is a fundamental problem of biology. Much progress has been made by adopting a synthetic and mechanistic perspective on originating life. We present a current view of the biochemistry of the origin of life, focusing on issues surrounding the emergence of an RNA World in which RNA dominated informational and functional roles. There is cause for optimism on this difficult problem: the prebiotic chemical inventory may not have been as nightmarishly complex as previously thought; the catalytic repertoire of ribozymes continues to expand, approaching the goal of self-replicating RNA; encapsulation in protocells provides evolutionary and biophysical advantages. Nevertheless, major issues remain unsolved, such as the origin of a genetic code. Attention to this field is particularly timely given the accelerating discovery and characterization of exoplanets. Copyright © 2015 Elsevier Ltd. All rights reserved.
Kinetic and catalytic performance of a BI-porous composite material in catalytic cracking and isomerisation reactions

KAUST Repository

Al-Khattaf, S.

2012-01-10

Catalytic behaviour of pure zeolite ZSM-5 and a bi-porous composite material (BCM) were investigated in transformation of m-xylene, while zeolite HY and the bi-porous composite were used in the cracking of 1,3,5-triisopropylbenzene (TIPB). The micro/mesoporous material was used to understand the effect of the presence of mesopores on these reactions. Various characterisation techniques, that is, XRD, SEM, TGA, FT-IR and nitrogen sorption measurements were applied for complete characterisation of the catalysts. Catalytic tests using CREC riser simulator showed that the micro/mesoporous composite catalyst exhibited higher catalytic activity as compared with the conventional microporous ZSM-5 and HY zeolite for transformation of m-xylene and for the catalytic cracking of TIPB, respectively. The outstanding catalytic reactivity of m-xylene and TIPB molecules were mainly attributed to the easier access of active sites provided by the mesopores. Apparent activation energies for the disappearance of m-xylene and TIPB over all catalysts were found to decrease in the order: EBCM>EZSM-5 and EBCM>EHY, respectively. © 2012 Canadian Society for Chemical Engineering.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Science.gov (United States)

2018-01-01

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679
The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes.

Science.gov (United States)

Hayden, Eric J; Bratulic, Sinisa; Koenig, Iwo; Ferrada, Evandro; Wagner, Andreas

2014-02-01

The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a population's response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged.
The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during MicroRNA biogenesis

KAUST Repository

Liu, Chenggang

2012-04-03

Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 mutants accumulate low levels of miRNAs and display pleiotropic developmental phenotypes. We report the identification of five new hyl1 suppressor mutants, all of which are alleles of DCL1. These new alleles affect either the helicase or the RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. Biochemical analysis of the DCL1 suppressor variants reveals that they process the primary transcript (pri-miRNA) more efficiently than wild-type DCL1, with both higher Kcat and lower Km values. The DCL1 variants largely rescue wild-type miRNA accumulation levels in vivo, but do not rescue the MIRNA processing precision defects of the hyl1 mutant. In vitro, the helicase domain confers ATP dependence on DCL1-catalyzed MIRNA processing, attenuates DCL1 cleavage activity, and is required for precise MIRNA processing of some substrates. © 2012 American Society of Plant Biologists.
Catalytic modification of cellulose and hemicellulose - Sugarefine

Energy Technology Data Exchange (ETDEWEB)

Repo, T. [Helsinki Univ. (Finland),Laboratory of Inorganic Chemistry], email: timo.repo@helsinki.fi

2012-07-01

The main goal of the project is to develop catalytic methods for the modification of lignocellulose-based saccharides in the biorefineries. The products of these reactions could be used for example as biofuel components, raw materials for the chemical industry, solvents and precursors for biopolymers. The catalyst development aims at creating efficient, selective and green catalytic methods for profitable use in biorefineries. The project is divided in three work packages: In WP1 (Catalytic dehydration of cellulose) the aim is at developing non-toxic, efficient methods for the catalytic dehydration of cellulose the target molecule being here 5-hydroxymethylfurfural (5-HMF). 5-HMF is an interesting platform chemical for the production of fuel additives, solvents and polymers. In WP2 (Catalytic reduction), the objective of the catalytic reduction studies is to produce commercially interesting monofunctional chemicals, such as 1-butanol or 2-methyltetrahydrofuran (2-MeTHF). In WP3 (Catalytic oxidation), the research focuses on developing a green and efficient oxidation method for producing acids. Whereas acetic and formic acids are bulk chemicals, diacids such as glucaric and xylaric acids are valuable specialty chemicals for detergent, polymer and food production.
Efficient recovery of whole blood RNA - a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species

Directory of Open Access Journals (Sweden)

Schwochow Doreen

2012-06-01

Full Text Available Abstract Background Since the emergence of next generation sequencing platforms, unprecedented opportunities have arisen in the study of natural vertebrate populations. In particular, insights into the genetic and epigenetic mechanisms of adaptation can be revealed through study of the expression profiles of genes. However, as a pre-requisite to expression profiling, care must be taken in RNA preparation as factors like DNA contamination, RNA integrity or transcript abundance can affect downstream applications. Here, we evaluated five commonly used RNA extraction methods using whole blood sampled under varying conditions from 20 wild carnivores. Results Despite the use of minute starting volumes, all methods produced quantifiable RNA extracts (1.4 – 18.4 μg with varying integrity (RIN 4.6 - 7.7, the latter being significantly affected by the storage and extraction method used. We observed a significant overall effect of the extraction method on DNA contamination. One particular extraction method, the LeukoLOCK™ filter system, yielded high RNA integrity along with low DNA contamination and efficient depletion of hemoglobin transcripts highly abundant in whole blood. In a proof of concept sequencing experiment, we found globin RNA transcripts to occupy up to ¼ of all sequencing reads if libraries were not depleted of hemoglobin prior to sequencing. Conclusion By carefully choosing the appropriate RNA extraction method, whole blood can become a valuable source for high-throughput applications like expression arrays or transcriptome sequencing from natural populations. Additionally, candidate genes showing signs of selection could subsequently be genotyped in large population samples using whole blood as a source for RNA without harming individuals from rare or endangered species.
Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA-protein interactions.

Science.gov (United States)

Khanova, Elena; Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2012-04-01

Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA-protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes.
miRNA as potential biomarkers of breast cancer in the Lebanese population and in young women: a pilot study.

Directory of Open Access Journals (Sweden)

Farah J Nassar

Full Text Available Relative to western populations, the percentage of women diagnosed with breast cancer at a young age in Lebanon is high. While the younger age of the Lebanese population compared to the West certainly contributes to this difference, potential genetic, reproductive and/or biological factors likely play an important role. The objective of this study is to investigate the contribution of miRNAs in this setting through the analysis of the expression of five reported dysregulated miRNAs, miR-148b, miR-10b, miR-21, miR-221, and miR-155 in 20 normal and 57 cancerous breast tissues from Lebanese breast cancer patients. After finding their relative expression by quantitative reverse transcription real time PCR, the results were analyzed with respect to the patients' clinical and histopathology presentations. Compared to normal breast tissues, significant upregulation of miR-155, miR-21 and miR-148b, notable downregulation of miR-10b and non-significant expression of miR-221 were observed in tumor tissues. Moreover, miR-10b was significantly underexpressed in estrogen/progesterone receptor (ER/PR negative tumors relative to ER/PR positive tumor tissues. miR-155 was also significantly overexpressed in postmenopausal patients and in those of age at diagnosis greater than 40 years old as well as in PR negative or in human epidermal growth factor 2 (Her2 positive tissues. This study is the first one to report miRNA expression patterns in Lebanese breast cancer patients. We found that differential miRNA expression in breast cancer could be variable between Lebanese and Western populations. miR-10b was positively correlated with the ER and PR status and miR-155 could be a noteworthy biomarker for the menopausal state, age at diagnosis, PR and Her2 status. Hence, miRNA can be used as biomarkers for early breast cancer detection.
Engineering reactors for catalytic reactions

Indian Academy of Sciences (India)

Extensive studies have been conducted to establish sound basis for design and engineering of reactors for practising such catalytic reactions and for realizing improvements in reactor performance. In this article, application of recent (and not so recent) developments in engineering reactors for catalytic reactions is ...
Kin Selection in the RNA World.

Science.gov (United States)

Levin, Samuel R; West, Stuart A

2017-12-05

Various steps in the RNA world required cooperation. Why did life's first inhabitants, from polymerases to synthetases, cooperate? We develop kin selection models of the RNA world to answer these questions. We develop a very simple model of RNA cooperation and then elaborate it to model three relevant issues in RNA biology: (1) whether cooperative RNAs receive the benefits of cooperation; (2) the scale of competition in RNA populations; and (3) explicit replicator diffusion and survival. We show: (1) that RNAs are likely to express partial cooperation; (2) that RNAs will need mechanisms for overcoming local competition; and (3) in a specific example of RNA cooperation, persistence after replication and offspring diffusion allow for cooperation to overcome competition. More generally, we show how kin selection can unify previously disparate answers to the question of RNA world cooperation.
tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

Science.gov (United States)

Carter, Charles W.; Wolfenden, Richard

2016-01-01

abstract The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyl-tRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology. PMID:26595350
The decapping activator Edc3 and the Q/N-rich domain of Lsm4 function together to enhance mRNA stability and alter mRNA decay pathway dependence in Saccharomyces cerevisiae

Directory of Open Access Journals (Sweden)

Susanne Huch

2016-10-01

Full Text Available The rate and regulation of mRNA decay are major elements in the proper control of gene expression. Edc3 and Lsm4 are two decapping activator proteins that have previously been shown to function in the assembly of RNA granules termed P bodies. Here, we show that deletion of edc3, when combined with a removal of the glutamine/asparagine rich region of Lsm4 (edc3Δ lsm4ΔC reduces mRNA stability and alters pathways of mRNA degradation. Multiple tested mRNAs exhibited reduced stability in the edc3Δ lsm4ΔC mutant. The destabilization was linked to an increased dependence on Ccr4-mediated deadenylation and mRNA decapping. Unlike characterized mutations in decapping factors that either are neutral or are able to stabilize mRNA, the combined edc3Δ lsm4ΔC mutant reduced mRNA stability. We characterized the growth and activity of the major mRNA decay systems and translation in double mutant and wild-type yeast. In the edc3Δ lsm4ΔC mutant, we observed alterations in the levels of specific mRNA decay factors as well as nuclear accumulation of the catalytic subunit of the decapping enzyme Dcp2. Hence, we suggest that the effects on mRNA stability in the edc3Δ lsm4ΔC mutant may originate from mRNA decay protein abundance or changes in mRNPs, or alternatively may imply a role for P bodies in mRNA stabilization.
Larval application of sodium channel homologous dsRNA restores pyrethroid insecticide susceptibility in a resistant adult mosquito population.

Science.gov (United States)

Bona, Ana Caroline Dalla; Chitolina, Rodrigo Faitta; Fermino, Marise Lopes; de Castro Poncio, Lisiane; Weiss, Avital; Lima, José Bento Pereira; Paldi, Nitzan; Bernardes, Emerson Soares; Henen, Jonathan; Maori, Eyal

2016-07-14

Mosquitoes host and pass on to humans a variety of disease-causing pathogens such as infectious viruses and other parasitic microorganisms. The emergence and spread of insecticide resistance is threatening the effectiveness of current control measures for common mosquito vector borne diseases, such as malaria, dengue and Zika. Therefore, the emerging resistance to the widely used pyrethroid insecticides is an alarming problem for public health. Herein we demonstrated the use of RNA interference (RNAi) to increase susceptibility of adult mosquitoes to a widely used pyrethroid insecticide. Experiments were performed on a field-collected pyrethroid resistant strain of Ae. aegypti (Rio de Janeiro; RJ). Larvae from the resistant Ae. aegypti population were soaked with double-stranded RNAs (dsRNAs) that correspond either to voltage-gate sodium channel (VGSC), P-glycoprotein, or P450 detoxification genes and reared to adulthood. Adult mortality rates in the presence of various Deltamethrin pyrethroid concentrations were used to assess mosquito insecticide susceptibility. We characterized the RJ Ae. aegypti strain with regard to its level of resistance to a pyrethroid insecticide and found that it was approximately 6 times more resistant to Deltamethrin compared to the laboratory Rockefeller strain. The RJ strain displayed a higher frequency of Val1016Ile and Phe1534Cys substitutions of the VGSC gene. The resistant strain also displayed a higher basal expression level of VGSC compared to the Rockefeller strain. When dsRNA-treated mosquitoes were subjected to a standard pyrethroid contact bioassay, only dsRNA targeting VGSC increased the adult mortality of the pyrethroid resistant strain. The dsRNA treatment proved effective in increasing adult mosquito susceptibility over a range of pyrethroid concentrations and these results were associated with dsRNA-specific small interfering RNAs in treated adults, and the corresponding specific down regulation of VGSC gene expression
Alterations in Lipoxygenase and Cyclooxygenase-2 Catalytic Activity and mRNA Expression in Prostate Carcinoma

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Scott B. Shappell

2001-01-01

Full Text Available Recent studies in prostate tissues and especially cell lines have suggested roles for arachidonic acid (AA metabolizing enzymes in prostate adenocarcinoma (Pca development or progression. The goal of this study was to more fully characterize lipoxygenase (LOX and cyclooxygenase-2 (COX-2 gene expression and AA metabolism in benign and malignant prostate using snap-frozen tissues obtained intraoperatively and mRNA analyses and enzyme assays. Formation of 15-hydroxyeicosatetraenoic acid (15-HETE was detected in 23/29 benign samples and 15-LOX-2 mRNA was detected in 21/25 benign samples. In pairs of pure benign and Pca from the same patients, 15-HETE production and 15-LOX-2 mRNA were reduced in Pca versus benign in 9/14 (P=.04 and 14/17 (P=.002, respectively. Under the same conditions, neither 5HETE nor 12-HETE formation was detectable in 29 benign and 24 tumor samples; with a more sensitive assay, traces were detected in some samples, but there was no clear association with tumor tissue. COX-2 mRNA was detected by nuclease protection assay in 7/16 benign samples and 5/16 tumors. In benign and tumor pairs from 10 patients, COX-2 was higher in tumor versus benign in only 2, with similar results by in situ hybridization. Paraffin immunoperoxidase for COX2 was performed in whole mount sections from 87 additional radical prostatectomy specimens, with strong expression in ejaculatory duct as a positive control and corroboration with in situ hybridization. No immunostaining was detected in benign prostate or tumor in 45% of cases. Greater immunostaining in tumor versus benign was present in only 17% of cases, and correlated with high tumor grade (Gleason score 8 and 9 vs. 5 to 7. In conclusion, reduced 15-LOX-2 expression and 15-HETE formation is the most characteristic alteration of AA metabolism in Pca. Increased 12-HETE and 5-HETE formation in Pca were not discernible. Increased COX-2 expression is not a typical abnormality in Pca in general, but
Synthesis, spectroscopic characterization and catalytic oxidation ...

Indian Academy of Sciences (India)

were characterized by infrared, electronic, electron paramagnetic resonance ... The catalytic oxidation property of ruthenium(III) complexes were also ... cies at room temperature. ..... aldehyde part of Schiff base ligands, catalytic activ- ity of new ...
Catalytic exhaust control

Energy Technology Data Exchange (ETDEWEB)

Heinemann, H

1973-09-01

Recent achievements and problems in the development of exhaust control devices in the USA are reviewed. To meet the 1976 emission standards, catalytic systems for the oxidation of carbon monoxide and hydrocarbons and for the reduction of nitrogen oxides to nitrogen and water are needed. While oxidizing catalysts using platinum, palladium, copper, vanadium, and chromium appplied on alumina or ceramic materials are more or less effective in emission control, there are no catalytic devices for the reduction of nitrogen oxides with the required useful life of 25,000 to 50,000 miles as yet available. In the case of platinum catalysts on monolithic supports, the operating temperature of 650 to 750/sup 0/C as required for the oxidation process may cause inactivation of the catalysts and fusion of the support material. The oxidation of CO and hydrocarbons is inhibited by high concentrations of CO, nitric oxide, and hydrocarbons. The use of catalytic converters requires the use of lead-free or low-lead gasoline. The nitrogen oxides conversion efficiency is considerably influenced by the oxygen-to-CO ratio of the exhaust gas, which makes limitation of this ratio necessary.
Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications

Science.gov (United States)

Nam, Seungyoon; Ryu, Hyojung; Son, Won-joon; Kim, Yon Hui; Kim, Kyung Tae; Balch, Curt; Nephew, Kenneth P.; Lee, Jinhyuk

2014-01-01

RNA interference (RNAi), mediated by small non-coding RNAs (e.g., miRNAs, siRNAs), influences diverse cellular functions. Highly complementary miRNA-target RNA (or siRNA-target RNA) duplexes are recognized by an Argonaute family protein (Ago2), and recent observations indicate that the concentration of Mg2+ ions influences miRNA targeting of specific mRNAs, thereby modulating miRNA-mRNA networks. In the present report, we studied the thermodynamic effects of differential [Mg2+] on slicing (RNA silencing cycle) through molecular dynamics simulation analysis, and its subsequent statistical analysis. Those analyses revealed different structural conformations of the RNA duplex in Ago2, depending on Mg2+ concentration. We also demonstrate that cation effects on Ago2 structural flexibility are critical to its catalytic/functional activity, with low [Mg2+] favoring greater Ago2 flexibility (e.g., greater entropy) and less miRNA/mRNA duplex stability, thus favoring slicing. The latter finding was supported by a negative correlation between expression of an Mg2+ influx channel, TRPM7, and one miRNA’s (miR-378) ability to downregulate its mRNA target, TMEM245. These results imply that thermodynamics could be applied to siRNA-based therapeutic strategies, using highly complementary binding targets, because Ago2 is also involved in RNAi slicing by exogenous siRNAs. However, the efficacy of a siRNA-based approach will differ, to some extent, based on the Mg2+ concentration even within the same disease type; therefore, different siRNA-based approaches might be considered for patient-to-patient needs. PMID:25330448
The Associations between RNA Splicing Complex Gene SF3A1 Polymorphisms and Colorectal Cancer Risk in a Chinese Population.

Directory of Open Access Journals (Sweden)

Xiaohua Chen

Full Text Available Aberrant alternative splicing included alterations in components of the mRNA splicing machinery often occurred in colon cancer. However, the role of SF3A1, one key component of the mRNA splicing machinery, on colorectal cancer (CRC risk was still not elucidated.We performed a hospital-based case-control study containing 801 CRC patients and 817 cancer-free controls to examine the association between SF3A1 polymorphisms and CRC risk in a Chinese population. Four candidate SNPs (rs10376, rs5753073, rs2839998 and rs2074733 were selected based on bioinformatics analysis and previous findings. The results showed no significant associations between these SNPs and CRC risk (P > 0.05. Besides, the stratified analysis based on the smoking and alcohol use status obtained no statistically significant results.Our study was the first one to investigate the association between SF3A1 polymorphisms and CRC risk. The results suggested these four SNPs in SF3A1 were not associated with CRC risk in a Chinese population, however, further more studies are needed to confirm our findings.
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

Science.gov (United States)

Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

2013-04-02

A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.
Identifying and characterizing Hfq-RNA interactions.

Science.gov (United States)

Faner, M A; Feig, A L

2013-09-15

To regulate stress responses and virulence, bacteria use small regulatory RNAs (sRNAs). These RNAs can up or down regulate target mRNAs through base pairing by influencing ribosomal access and RNA decay. A large class of these sRNAs, called trans-encoded sRNAs, requires the RNA binding protein Hfq to facilitate base pairing between the regulatory RNA and its target mRNA. The resulting network of regulation is best characterized in Escherichia coli and Salmonella typhimurium, but the importance of Hfq dependent sRNA regulation is recognized in a diverse population of bacteria. In this review we present the approaches and methods used to discover Hfq binding RNAs, characterize their interactions and elucidate their functions. Copyright © 2013 Elsevier Inc. All rights reserved.
Catalytic Wittig and aza-Wittig reactions

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Zhiqi Lao

2016-11-01

Full Text Available This review surveys the literature regarding the development of catalytic versions of the Wittig and aza-Wittig reactions. The first section summarizes how arsenic and tellurium-based catalytic Wittig-type reaction systems were developed first due to the relatively easy reduction of the oxides involved. This is followed by a presentation of the current state of the art regarding phosphine-catalyzed Wittig reactions. The second section covers the field of related catalytic aza-Wittig reactions that are catalyzed by both phosphine oxides and phosphines.

Efficient catalytic combustion in integrated micropellistors

International Nuclear Information System (INIS)

Bársony, I; Ádám, M; Fürjes, P; Dücső, Cs; Lucklum, R; Hirschfelder, M; Kulinyi, S

2009-01-01

This paper analyses two of the key issues of the development of catalytic combustion-type sensors: the selection and production of active catalytic particles on the micropellistor surface as well as the realization of a reliable thermal conduction between heater element and catalytic surface, for the sensing of temperature increase produced by the combustion. The report also demonstrates that chemical sensor product development by a MEMS process is a continuous struggle for elimination of all uncertainties influencing reliability and sensitivity of the final product
Adsorbent catalytic nanoparticles and methods of using the same

Energy Technology Data Exchange (ETDEWEB)

Slowing, Igor Ivan; Kandel, Kapil

2017-01-31

The present invention provides an adsorbent catalytic nanoparticle including a mesoporous silica nanoparticle having at least one adsorbent functional group bound thereto. The adsorbent catalytic nanoparticle also includes at least one catalytic material. In various embodiments, the present invention provides methods of using and making the adsorbent catalytic nanoparticles. In some examples, the adsorbent catalytic nanoparticles can be used to selectively remove fatty acids from feedstocks for biodiesel, and to hydrotreat the separated fatty acids.
Catalytic pyrolysis of hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Vail' eva, N A; Buyanov, R A

1979-01-01

Catalytic pyrolysis of petroleum fractions (undecane) was performed with the object of clarifying such questions as the mechanism of action of the catalyst, the concepts of activity and selectivity of the catalyst, the role of transport processes, the temperature ranges and limitations of the catalytic process, the effect of the catalyst on secondary processes, and others. Catalysts such as quartz, MgO, Al/sub 2/O/sub 3/, were used. Analysis of the experimental findings and the fact that the distribution of products is independent of the nature of the surface, demonstrate that the pyrolysis of hydrocarbons in the presence of catalysts is based on the heterogeneous-homogeneous radical-chain mechanism of action, and that the role of the catalysts reduces to increasing the concentration of free radicals. The concept of selectivity cannot be applied to catalysts here, since they do not affect the mechanism of the unfolding of the process of pyrolysis and their role consists solely in initiating the process. In catalytic pyrolysis the concepts of kinetic and diffusive domains of unfolding of the catalytic reaction do not apply, and only the outer surface of the catalyst is engaged, whereas the inner surface merely promotes deletorious secondary processes reducing the selectivity of the process and the activity of the catalyst. 6 references, 2 figures.
Organization and alternative splicing of the Caenorhabditis elegans cAMP-dependent protein kinase catalytic-subunit gene (kin-1).

Science.gov (United States)

Tabish, M; Clegg, R A; Rees, H H; Fisher, M J

1999-04-01

The cAMP-dependent protein kinase (protein kinase A, PK-A) is multifunctional in nature, with key roles in the control of diverse aspects of eukaryotic cellular activity. In the case of the free-living nematode, Caenorhabditis elegans, a gene encoding the PK-A catalytic subunit has been identified and two isoforms of this subunit, arising from a C-terminal alternative-splicing event, have been characterized [Gross, Bagchi, Lu and Rubin (1990) J. Biol. Chem. 265, 6896-6907]. Here we report the occurrence of N-terminal alternative-splicing events that, in addition to generating a multiplicity of non-myristoylatable isoforms, also generate the myristoylated variant(s) of the catalytic subunit that we have recently characterized [Aspbury, Fisher, Rees and Clegg (1997) Biochem. Biophys. Res. Commun. 238, 523-527]. The gene spans more than 36 kb and is divided into a total of 13 exons. Each of the mature transcripts contains only 7 exons. In addition to the already characterized exon 1, the 5'-untranslated region and first intron actually contain 5 other exons, any one of which may be alternatively spliced on to exon 2 at the 5' end of the pre-mRNA. This N-terminal alternative splicing occurs in combination with either of the already characterized C-terminal alternative exons. Thus, C. elegans expresses at least 12 different isoforms of the catalytic subunit of PK-A. The significance of this unprecedented structural diversity in the family of PK-A catalytic subunits is discussed.
Structural Analysis of Monomeric RNA-Dependent Polymerases: Evolutionary and Therapeutic Implications.

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Rodrigo Jácome

Full Text Available The crystal structures of monomeric RNA-dependent RNA polymerases and reverse transcriptases of more than 20 different viruses are available in the Protein Data Bank. They all share the characteristic right-hand shape of DNA- and RNA polymerases formed by the fingers, palm and thumb subdomains, and, in many cases, "fingertips" that extend from the fingers towards the thumb subdomain, giving the viral enzyme a closed right-hand appearance. Six conserved structural motifs that contain key residues for the proper functioning of the enzyme have been identified in all these RNA-dependent polymerases. These enzymes share a two divalent metal-ion mechanism of polymerization in which two conserved aspartate residues coordinate the interactions with the metal ions to catalyze the nucleotidyl transfer reaction. The recent availability of crystal structures of polymerases of the Orthomyxoviridae and Bunyaviridae families allowed us to make pairwise comparisons of the tertiary structures of polymerases belonging to the four main RNA viral groups, which has led to a phylogenetic tree in which single-stranded negative RNA viral polymerases have been included for the first time. This has also allowed us to use a homology-based structural prediction approach to develop a general three-dimensional model of the Ebola virus RNA-dependent RNA polymerase. Our model includes several of the conserved structural motifs and residues described in other viral RNA-dependent RNA polymerases that define the catalytic and highly conserved palm subdomain, as well as portions of the fingers and thumb subdomains. The results presented here help to understand the current use and apparent success of antivirals, i.e. Brincidofovir, Lamivudine and Favipiravir, originally aimed at other types of polymerases, to counteract the Ebola virus infection.
Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis.

Directory of Open Access Journals (Sweden)

Yonghua Wang

Full Text Available MicroRNAs (miRNAs are endogenously produced approximately 21-nt riboregulators that associate with Argonaute (Ago proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1 three important (PAZ, Mid and PIWI domains exist in Argonaute which define the global dynamics of the protein; 2 the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3 it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5'-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg(2+ plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA. Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago.
Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis.

Science.gov (United States)

Wang, Yonghua; Li, Yan; Ma, Zhi; Yang, Wei; Ai, Chunzhi

2010-07-29

MicroRNAs (miRNAs) are endogenously produced approximately 21-nt riboregulators that associate with Argonaute (Ago) proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target) and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1) three important (PAZ, Mid and PIWI) domains exist in Argonaute which define the global dynamics of the protein; 2) the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3) it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5'-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg(2+)) plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA). Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago.
Catalytic cracking models developed for predictive control purposes

Directory of Open Access Journals (Sweden)

Dag Ljungqvist

1993-04-01

Full Text Available The paper deals with state-space modeling issues in the context of model-predictive control, with application to catalytic cracking. Emphasis is placed on model establishment, verification and online adjustment. Both the Fluid Catalytic Cracking (FCC and the Residual Catalytic Cracking (RCC units are discussed. Catalytic cracking units involve complex interactive processes which are difficult to operate and control in an economically optimal way. The strong nonlinearities of the FCC process mean that the control calculation should be based on a nonlinear model with the relevant constraints included. However, the model can be simple compared to the complexity of the catalytic cracking plant. Model validity is ensured by a robust online model adjustment strategy. Model-predictive control schemes based on linear convolution models have been successfully applied to the supervisory dynamic control of catalytic cracking units, and the control can be further improved by the SSPC scheme.
Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

Science.gov (United States)

Coari, Kristin M.; Martin, Rebecca C.; Jain, Kopal; McGown, Linda B.

2017-09-01

In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.
Nucleotide Selectivity in Abiotic RNA Polymerization Reactions.

Science.gov (United States)

Coari, Kristin M; Martin, Rebecca C; Jain, Kopal; McGown, Linda B

2017-09-01

In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.
Effect of inlet cone pipe angle in catalytic converter

Science.gov (United States)

Amira Zainal, Nurul; Farhain Azmi, Ezzatul; Arifin Samad, Mohd

2018-03-01

The catalytic converter shows significant consequence to improve the performance of the vehicle start from it launched into production. Nowadays, the geometric design of the catalytic converter has become critical to avoid the behavior of backpressure in the exhaust system. The backpressure essentially reduced the performance of vehicles and increased the fuel consumption gradually. Consequently, this study aims to design various models of catalytic converter and optimize the volume of fluid flow inside the catalytic converter by changing the inlet cone pipe angles. Three different geometry angles of the inlet cone pipe of the catalytic converter were assessed. The model is simulated in Solidworks software to determine the optimum geometric design of the catalytic converter. The result showed that by decreasing the divergence angle of inlet cone pipe will upsurge the performance of the catalytic converter.
CORSEN, a new software dedicated to microscope-based 3D distance measurements: mRNA-mitochondria distance, from single-cell to population analyses.

Science.gov (United States)

Jourdren, Laurent; Delaveau, Thierry; Marquenet, Emelie; Jacq, Claude; Garcia, Mathilde

2010-07-01

Recent improvements in microscopy technology allow detection of single molecules of RNA, but tools for large-scale automatic analyses of particle distributions are lacking. An increasing number of imaging studies emphasize the importance of mRNA localization in the definition of cell territory or the biogenesis of cell compartments. CORSEN is a new tool dedicated to three-dimensional (3D) distance measurements from imaging experiments especially developed to access the minimal distance between RNA molecules and cellular compartment markers. CORSEN includes a 3D segmentation algorithm allowing the extraction and the characterization of the cellular objects to be processed--surface determination, aggregate decomposition--for minimal distance calculations. CORSEN's main contribution lies in exploratory statistical analysis, cell population characterization, and high-throughput assays that are made possible by the implementation of a batch process analysis. We highlighted CORSEN's utility for the study of relative positions of mRNA molecules and mitochondria: CORSEN clearly discriminates mRNA localized to the vicinity of mitochondria from those that are translated on free cytoplasmic polysomes. Moreover, it quantifies the cell-to-cell variations of mRNA localization and emphasizes the necessity for statistical approaches. This method can be extended to assess the evolution of the distance between specific mRNAs and other cellular structures in different cellular contexts. CORSEN was designed for the biologist community with the concern to provide an easy-to-use and highly flexible tool that can be applied for diverse distance quantification issues.
Catalytic burners in larger boiler appliances

Energy Technology Data Exchange (ETDEWEB)

Silversand, Fredrik; Persson, Mikael (Catator AB, Lund (Sweden))

2009-02-15

This project focuses on the scale up of a Catator's catalytic burner technology to enable retrofit installation in existing boilers and the design of new innovative combinations of catalytic burners and boilers. Different design approaches are discussed and evaluated in the report and suggestions are made concerning scale-up. Preliminary test data, extracted from a large boiler installation are discussed together with an accurate analysis of technical possibilities following an optimization of the boiler design to benefit from the advantages of catalytic combustion. The experimental work was conducted in close collaboration with ICI Caldaie (ICI), located in Verona, Italy. ICI is a leading European boiler manufacturer in the effect segment ranging from about 20 kWt to several MWt. The study shows that it is possibly to scale up the burner technology and to maintain low emissions. The boilers used in the study were designed around conventional combustion and were consequently not optimized for implementation of catalytic burners. From previous experiences it stands clear that the furnace volume can be dramatically decreased when applying catalytic combustion. In flame combustion, this volume is normally dimensioned to avoid flame impingement on cold surfaces and to facilitate completion of the gas-phase reactions. The emissions of nitrogen oxides can be reduced by decreasing the residence time in the furnace. Even with the over-dimensioned furnace used in this study, we easily reached emission values close to 35 mg/kWh. The emissions of carbon monoxide and unburned hydrocarbons were negligible (less than 5 ppmv). It is possible to decrease the emissions of nitrogen oxides further by designing the furnace/boiler around the catalytic burner, as suggested in the report. Simultaneously, the size of the boiler installation can be reduced greatly, which also will result in material savings, i.e. the production cost can be reduced. It is suggested to optimize the
MicroRNA Expression Profiles in Cultured Human Fibroblasts in Space

Science.gov (United States)

Wu, Honglu; Lu, Tao; Jeevarajan, John; Rohde, Larry; Zhang, Ye

2014-01-01

Microgravity, or an altered gravity environment from the static 1g, has been shown to influence global gene expression patterns and protein levels in living organisms. However, it is unclear how these changes in gene and protein expressions are related to each other or are related to other factors regulating such changes. A different class of RNA, the small non-coding microRNA (miRNA), can have a broad effect on gene expression networks by mainly inhibiting the translation process. Previously, we investigated changes in the expression of miRNA and related genes under simulated microgravity conditions on the ground using the NASA invented bioreactor. In comparison to static 1 g, simulated microgravity altered a number of miRNAs in human lymphoblastoid cells. Pathway analysis with the altered miRNAs and RNA expressions revealed differential involvement of cell communication and catalytic activity, as well as immune response signaling and NGF activation of NF-kB pathways under simulated microgravity condition. The network analysis also identified several projected networks with c- Rel, ETS1 and Ubiquitin C as key factors. In a flight experiment on the International Space Station (ISS), we will investigate the effects of actual spaceflight on miRNA expressions in nondividing human fibroblast cells in mostly G1 phase of the cell cycle. A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework for tissues, and plays a critical role in wound healing and other functions. In addition to miRNA expressions, we will investigate the effects of spaceflight on the cellular response to DNA damages from bleomycin treatment.
Mapping the active site of vaccinia virus RNA triphosphatase

International Nuclear Information System (INIS)

Gong Chunling; Shuman, Stewart

2003-01-01

The RNA triphosphatase component of vaccinia virus mRNA capping enzyme (the product of the viral D1 gene) belongs to a family of metal-dependent phosphohydrolases that includes the RNA triphosphatases of fungi, protozoa, Chlorella virus, and baculoviruses. The family is defined by two glutamate-containing motifs (A and C) that form the metal-binding site. Most of the family members resemble the fungal and Chlorella virus enzymes, which have a complex active site located within the hydrophilic interior of a topologically closed eight-stranded β barrel (the so-called ''triphosphate tunnel''). Here we queried whether vaccinia virus capping enzyme is a member of the tunnel subfamily, via mutational mapping of amino acids required for vaccinia triphosphatase activity. We identified four new essential side chains in vaccinia D1 via alanine scanning and illuminated structure-activity relationships by conservative substitutions. Our results, together with previous mutational data, highlight a constellation of six acidic and three basic amino acids that likely compose the vaccinia triphosphatase active site (Glu37, Glu39, Arg77, Lys107, Glu126, Asp159, Lys161, Glu192, and Glu194). These nine essential residues are conserved in all vertebrate and invertebrate poxvirus RNA capping enzymes. We discerned no pattern of clustering of the catalytic residues of the poxvirus triphosphatase that would suggest structural similarity to the tunnel proteins (exclusive of motifs A and C). We infer that the poxvirus triphosphatases are a distinct lineage within the metal-dependent RNA triphosphatase family. Their unique active site, which is completely different from that of the host cell's capping enzyme, recommends the poxvirus RNA triphosphatase as a molecular target for antipoxviral drug discovery
Concentric catalytic combustor

Science.gov (United States)

Bruck, Gerald J [Oviedo, FL; Laster, Walter R [Oviedo, FL

2009-03-24

A catalytic combustor (28) includes a tubular pressure boundary element (90) having a longitudinal flow axis (e.g., 56) separating a first portion (94) of a first fluid flow (e.g., 24) from a second portion (95) of the first fluid flow. The pressure boundary element includes a wall (96) having a plurality of separate longitudinally oriented flow paths (98) annularly disposed within the wall and conducting respective portions (100, 101) of a second fluid flow (e.g., 26) therethrough. A catalytic material (32) is disposed on a surface (e.g., 102, 103) of the pressure boundary element exposed to at least one of the first and second portions of the first fluid flow.
Effect of support on the catalytic activity of manganese oxide catalyts for toluene combustion.

Science.gov (United States)

Pozan, Gulin Selda

2012-06-30

The aim of this work was to study combustion of toluene (1000ppm) over MnO(2) modified with different supports. α-Al(2)O(3) and γ-Al(2)O(3) obtained from Boehmite, γ-Al(2)O(3) (commercial), SiO(2), TiO(2) and ZrO(2) were used as commercial support materials. In view of potential interest of this process, the influence of support material on the catalytic performance was discussed. The deposition of 9.5MnO(2) was performed by impregnation over support. The catalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), temperature programmed reduction and oxidation (TPR/TPO) and thermogravimetric analysis (TGA). The catalytic tests were carried out at atmospheric pressure in a fixed-bed flow reactor. 9.5MnO(2)/α-Al(2)O(3)(B) (synthesized from Boehmite) catalyst exhibits the highest catalytic activity, over which the toluene conversion was up to 90% at a temperature of 289°C. Considering all the characterization and reaction data reported in this study, it was concluded that the manganese state and oxygen species played an important role in the catalytic activity. Copyright © 2012 Elsevier B.V. All rights reserved.
RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star.

Directory of Open Access Journals (Sweden)

Sabah Kadri

Full Text Available microRNAs (miRNAs are small (20-23 nt, non-coding single stranded RNA molecules that act as post-transcriptional regulators of mRNA gene expression. They have been implicated in regulation of developmental processes in diverse organisms. The echinoderms, Strongylocentrotus purpuratus (sea urchin and Patiria miniata (sea star are excellent model organisms for studying development with well-characterized transcriptional networks. However, to date, nothing is known about the role of miRNAs during development in these organisms, except that the genes that are involved in the miRNA biogenesis pathway are expressed during their developmental stages. In this paper, we used Illumina Genome Analyzer (Illumina, Inc. to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of sea urchin and sea star (total of 22,670,000 reads. Analysis of these data revealed the miRNA populations in these two species. We found that 47 and 38 known miRNAs are expressed in sea urchin and sea star, respectively, during early development (32 in common. We also found 13 potentially novel miRNAs in the sea urchin embryonic library. miRNA expression is generally conserved between the two species during development, but 7 miRNAs are highly expressed in only one species. We expect that our two datasets will be a valuable resource for everyone working in the field of developmental biology and the regulatory networks that affect it. The computational pipeline to analyze Illumina reads is available at http://www.benoslab.pitt.edu/services.html.
RNA Deep Sequencing Reveals Differential MicroRNA Expression during Development of Sea Urchin and Sea Star

Science.gov (United States)

Kadri, Sabah; Hinman, Veronica F.; Benos, Panayiotis V.

2011-01-01

microRNAs (miRNAs) are small (20–23 nt), non-coding single stranded RNA molecules that act as post-transcriptional regulators of mRNA gene expression. They have been implicated in regulation of developmental processes in diverse organisms. The echinoderms, Strongylocentrotus purpuratus (sea urchin) and Patiria miniata (sea star) are excellent model organisms for studying development with well-characterized transcriptional networks. However, to date, nothing is known about the role of miRNAs during development in these organisms, except that the genes that are involved in the miRNA biogenesis pathway are expressed during their developmental stages. In this paper, we used Illumina Genome Analyzer (Illumina, Inc.) to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of sea urchin and sea star (total of 22,670,000 reads). Analysis of these data revealed the miRNA populations in these two species. We found that 47 and 38 known miRNAs are expressed in sea urchin and sea star, respectively, during early development (32 in common). We also found 13 potentially novel miRNAs in the sea urchin embryonic library. miRNA expression is generally conserved between the two species during development, but 7 miRNAs are highly expressed in only one species. We expect that our two datasets will be a valuable resource for everyone working in the field of developmental biology and the regulatory networks that affect it. The computational pipeline to analyze Illumina reads is available at http://www.benoslab.pitt.edu/services.html. PMID:22216218
A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics.

Science.gov (United States)

Feng, Lihui; Rutherford, Steven T; Papenfort, Kai; Bagert, John D; van Kessel, Julia C; Tirrell, David A; Wingreen, Ned S; Bassler, Bonnie L

2015-01-15

Quorum sensing is a cell-cell communication process that bacteria use to transition between individual and social lifestyles. In vibrios, homologous small RNAs called the Qrr sRNAs function at the center of quorum-sensing pathways. The Qrr sRNAs regulate multiple mRNA targets including those encoding the quorum-sensing regulatory components luxR, luxO, luxM, and aphA. We show that a representative Qrr, Qrr3, uses four distinct mechanisms to control its particular targets: the Qrr3 sRNA represses luxR through catalytic degradation, represses luxM through coupled degradation, represses luxO through sequestration, and activates aphA by revealing the ribosome binding site while the sRNA itself is degraded. Qrr3 forms different base-pairing interactions with each mRNA target, and the particular pairing strategy determines which regulatory mechanism occurs. Combined mathematical modeling and experiments show that the specific Qrr regulatory mechanism employed governs the potency, dynamics, and competition of target mRNA regulation, which in turn, defines the overall quorum-sensing response. Copyright © 2015 Elsevier Inc. All rights reserved.

Competing to destroy: a fight between two RNA-degradation systems

DEFF Research Database (Denmark)

Thon, Genevieve

2008-01-01

The Argonaute-1 (Ago1) protein bound to small interfering RNAs (siRNAs) directs heterochromatin formation in fission yeast. A high-throughput sequencing approach reveals that the composition of the Ago1-bound siRNA population is sensitive to the noncanonical poly(A) polymerase Cid14, indicating t...... that the RNA-interference and Cid14-TRAMP RNA-degradation pathways compete for substrates in fission yeast.......The Argonaute-1 (Ago1) protein bound to small interfering RNAs (siRNAs) directs heterochromatin formation in fission yeast. A high-throughput sequencing approach reveals that the composition of the Ago1-bound siRNA population is sensitive to the noncanonical poly(A) polymerase Cid14, indicating...
Catalytic models developed through social work

DEFF Research Database (Denmark)

Jensen, Mogens

2015-01-01

of adolescents placed in out-of-home care and is characterised using three situated cases as empirical data. Afterwards the concept of catalytic processes is briefly presented and then applied in an analysis of pedagogical treatment in the three cases. The result is a different conceptualisation of the social......The article develops the concept of catalytic processes in relation to social work with adolescents in an attempt to both reach a more nuanced understanding of social work and at the same time to develop the concept of catalytic processes in psychology. The social work is pedagogical treatment...
How to Tackle the Challenge of siRNA Delivery with Sequence-Defined Oligoamino Amides.

Science.gov (United States)

Reinhard, Sören; Wagner, Ernst

2017-01-01

RNA interference (RNAi) as a mechanism of gene regulation provides exciting opportunities for medical applications. Synthetic small interfering RNA (siRNA) triggers the knockdown of complementary mRNA sequences in a catalytic fashion and has to be delivered into the cytosol of the targeted cells. The design of adequate carrier systems to overcome multiple extracellular and intracellular roadblocks within the delivery process has utmost importance. Cationic polymers form polyplexes through electrostatic interaction with negatively charged nucleic acids and present a promising class of carriers. Issues of polycations regarding toxicity, heterogeneity, and polydispersity can be overcome by solid-phase-assisted synthesis of sequence-defined cationic oligomers. These medium-sized highly versatile nucleic acid carriers display low cytotoxicity and can be modified and tailored in multiple ways to meet specific requirements of nucleic acid binding, polyplex size, shielding, targeting, and intracellular release of the cargo. In this way, sequence-defined cationic oligomers can mimic the dynamic and bioresponsive behavior of viruses. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana

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Hafidh Said

2009-12-01

Full Text Available Abstract Background New generation sequencing technology has allowed investigation of the small RNA populations of flowering plants at great depth. However, little is known about small RNAs in their reproductive cells, especially in post-meiotic cells of the gametophyte generation. Pollen - the male gametophyte - is the specialised haploid structure that generates and delivers the sperm cells to the female gametes at fertilisation. Whether development and differentiation of the male gametophyte depends on the action of microRNAs and trans-acting siRNAs guiding changes in gene expression is largely unknown. Here we have used 454 sequencing to survey the various small RNA populations present in mature pollen of Arabidopsis thaliana. Results In this study we detected the presence of 33 different microRNA families in mature pollen and validated the expression levels of 17 selected miRNAs by Q-RT-PCR. The majority of the selected miRNAs showed pollen-enriched expression compared with leaves. Furthermore, we report for the first time the presence of trans-acting siRNAs in pollen. In addition to describing new patterns of expression for known small RNAs in each of these classes, we identified 7 putative novel microRNAs. One of these, ath-MIR2939, targets a pollen-specific F-box transcript and we demonstrate cleavage of its target mRNA in mature pollen. Conclusions Despite the apparent simplicity of the male gametophyte, comprising just two different cell types, pollen not only utilises many miRNAs and trans-acting siRNAs expressed in the somatic tissues but also expresses novel miRNAs.
Triose phosphate isomerase deficiency is caused by altered dimerization--not catalytic inactivity--of the mutant enzymes.

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Markus Ralser

Full Text Available Triosephosphate isomerase (TPI deficiency is an autosomal recessive disorder caused by various mutations in the gene encoding the key glycolytic enzyme TPI. A drastic decrease in TPI activity and an increased level of its substrate, dihydroxyacetone phosphate, have been measured in unpurified cell extracts of affected individuals. These observations allowed concluding that the different mutations in the TPI alleles result in catalytically inactive enzymes. However, despite a high occurrence of TPI null alleles within several human populations, the frequency of this disorder is exceptionally rare. In order to address this apparent discrepancy, we generated a yeast model allowing us to perform comparative in vivo analyses of the enzymatic and functional properties of the different enzyme variants. We discovered that the majority of these variants exhibit no reduced catalytic activity per se. Instead, we observed, the dimerization behavior of TPI is influenced by the particular mutations investigated, and by the use of a potential alternative translation initiation site in the TPI gene. Additionally, we demonstrated that the overexpression of the most frequent TPI variant, Glu104Asp, which displays altered dimerization features, results in diminished endogenous TPI levels in mammalian cells. Thus, our results reveal that enzyme deregulation attributable to aberrant dimerization of TPI, rather than direct catalytic inactivation of the enzyme, underlies the pathogenesis of TPI deficiency. Finally, we discovered that yeast cells expressing a TPI variant exhibiting reduced catalytic activity are more resistant against oxidative stress caused by the thiol-oxidizing reagent diamide. This observed advantage might serve to explain the high allelic frequency of TPI null alleles detected among human populations.
Catalytically favorable surface patterns in Pt-Au nanoclusters

KAUST Repository

Mokkath, Junais Habeeb

2013-01-01

Motivated by recent experimental demonstrations of novel PtAu nanoparticles with highly enhanced catalytic properties, we present a systematic theoretical study that explores principal catalytic indicators as a function of the particle size and composition. We find that Pt electronic states in the vicinity of the Fermi level combined with a modified electron distribution in the nanoparticle due to Pt-to-Au charge transfer are the origin of the outstanding catalytic properties. From our model we deduce the catalytically favorable surface patterns that induce ensemble and ligand effects. © The Royal Society of Chemistry 2013.
The Transcription Bubble of the RNA Polymerase-Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics : Implications for Transcription Start-Site Selection

NARCIS (Netherlands)

Robb, Nicole C.; Cordes, Thorben; Hwang, Ling Chin; Gryte, Kristofer; Duchi, Diego; Craggs, Timothy D.; Santoso, Yusdi; Weiss, Shimon; Ebright, Richard H.; Kapanidis, Achillefs N.

2013-01-01

Bacterial transcription is initiated after RNA polymerase (RNAP) binds to promoter DNA, melts similar to 14 bp around the transcription start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP-DNA open complex (RPo). There is significant flexibility in the
Turning goals into results: the power of catalytic mechanisms.

Science.gov (United States)

Collins, J

1999-01-01

Most executives have a big, hairy, audacious goal. They write vision statements, formalize procedures, and develop complicated incentive programs--all in pursuit of that goal. In other words, with the best of intentions, they install layers of stultifying bureaucracy. But it doesn't have to be that way. In this article, Jim Collins introduces the catalytic mechanism, a simple yet powerful managerial tool that helps translate lofty aspirations into concrete reality. Catalytic mechanisms are the crucial link between objectives and performance; they are a galvanizing, nonbureaucratic means to turn one into the other. What's the difference between catalytic mechanisms and most traditional managerial controls? Catalytic mechanisms share five characteristics. First, they produce desired results in unpredictable ways. Second, they distribute power for the benefit of the overall system, often to the discomfort of those who traditionally hold power. Third, catalytic mechanisms have teeth. Fourth, they eject "viruses"--those people who don't share the company's core values. Finally, they produce an ongoing effect. Catalytic mechanisms are just as effective for reaching individual goals as they are for corporate ones. To illustrate how catalytic mechanisms work, the author draws on examples of individuals and organizations that have relied on such mechanisms to achieve their goals. The same catalytic mechanism that works in one organization, however, will not necessarily work in another. Catalytic mechanisms must be tailored to specific goals and situations. To help readers get started, the author offers some general principles that support the process of building catalytic mechanisms effectively.
Atomically Precise Metal Nanoclusters for Catalytic Application

Energy Technology Data Exchange (ETDEWEB)

Jin, Rongchao [Carnegie Mellon Univ., Pittsburgh, PA (United States)

2016-11-18

The central goal of this project is to explore the catalytic application of atomically precise gold nanoclusters. By solving the total structures of ligand-protected nanoclusters, we aim to correlate the catalytic properties of metal nanoclusters with their atomic/electronic structures. Such correlation unravel some fundamental aspects of nanocatalysis, such as the nature of particle size effect, origin of catalytic selectivity, particle-support interactions, the identification of catalytically active centers, etc. The well-defined nanocluster catalysts mediate the knowledge gap between single crystal model catalysts and real-world conventional nanocatalysts. These nanoclusters also hold great promise in catalyzing certain types of reactions with extraordinarily high selectivity. These aims are in line with the overall goals of the catalytic science and technology of DOE and advance the BES mission “to support fundamental research to understand, predict, and ultimately control matter and energy at the level of electrons, atoms, and molecules”. Our group has successfully prepared different sized, robust gold nanoclusters protected by thiolates, such as Au₂₅(SR)₁₈, Au₂₈(SR)₂₀, Au₃₈(SR)₂₄, Au₉₉(SR)₄₂, Au₁₄₄(SR)₆₀, etc. Some of these nanoclusters have been crystallographically characterized through X-ray crystallography. These ultrasmall nanoclusters (< 2 nm diameter) exhibit discrete electronic structures due to quantum size effect, as opposed to quasicontinuous band structure of conventional metal nanoparticles or bulk metals. The available atomic structures (metal core plus surface ligands) of nanoclusters serve as the basis for structure-property correlations. We have investigated the unique catalytic properties of nanoclusters (i.e. not observed in conventional nanogold catalysts) and revealed the structure-selectivity relationships. Highlights of our
Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.

Science.gov (United States)

Yip, Shun H; Sham, Pak Chung; Wang, Junwen

2018-02-21

Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.
The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster.

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Yuh Chwen G Lee

2015-06-01

Full Text Available The piwi-interacting RNAs (piRNA are small RNAs that target selfish transposable elements (TEs in many animal genomes. Until now, piRNAs' role in TE population dynamics has only been discussed in the context of their suppression of TE transposition, which alone is not sufficient to account for the skewed frequency spectrum and stable containment of TEs. On the other hand, euchromatic TEs can be epigenetically silenced via piRNA-dependent heterochromatin formation and, similar to the widely known "Position-effect variegation", heterochromatin induced by TEs can "spread" into nearby genes. We hypothesized that the piRNA-mediated spread of heterochromatin from TEs into adjacent genes has deleterious functional effects and leads to selection against individual TEs. Unlike previously identified deleterious effects of TEs due to the physical disruption of DNA, the functional effect we investigated here is mediated through the epigenetic influences of TEs. We found that the repressive chromatin mark, H3K9me, is elevated in sequences adjacent to euchromatic TEs at multiple developmental stages in Drosophila melanogaster. Furthermore, the heterochromatic states of genes depend not only on the number of and distance from adjacent TEs, but also on the likelihood that their nearest TEs are targeted by piRNAs. These variations in chromatin status probably have functional consequences, causing genes near TEs to have lower expression. Importantly, we found stronger selection against TEs that lead to higher H3K9me enrichment of adjacent genes, demonstrating the pervasive evolutionary consequences of TE-induced epigenetic silencing. Because of the intrinsic biological mechanism of piRNA amplification, spread of TE heterochromatin could result in the theoretically required synergistic deleterious effects of TE insertions for stable containment of TE copy number. The indirect deleterious impact of piRNA-mediated epigenetic silencing of TEs is a previously
Kinetic Parameters of Non-Isothermal Thermogravimetric Non-Catalytic and Catalytic Pyrolysis of Empty Fruit Bunch with Alumina by Kissinger and Ozawa Methods

Science.gov (United States)

Rahayu Mohamed, Alina; Li, Nurfahani; Sohaimi, Khairunissa Syairah Ahmad; Izzati Iberahim, Nur; Munirah Rohaizad, Nor; Hamzah, Rosniza

2018-03-01

The non-isothermal thermogravimetric non-catalytic and catalytic empty fruit bunch (EFB) pyrolysis with alumina were performed at different heating rates of 10, 15, 20, 25, 30 and 40 K/min under nitrogen atmosphere at a flow rate of 100 ml/min under dynamic conditions from 301 K to 1273 K. The activation energy were calculated based on Kissinger and Ozawa methods. Both reactions followed first order reactions. By Kissinger method, the activation energy and Ln A values for non-catalytic and catalytic EFB pyrolysis with alumina were 188.69 kJ mol-1 and 201.67 kJ/mol respectively. By Ozawa method, the activation energy values for non-catalytic and catalytic EFB pyrolysis with alumina were 189.13 kJ/mol and 201.44 kJ/mol respectively. The presence of catalyst increased the activation energy values for EFB pyrolysis as calculated by Kissinger and Ozawa methods.
Analysis of hepatic deiodinase 2 mRNA levels in natural fish lake populations exposed to different levels of putative thyroid disrupters

International Nuclear Information System (INIS)

Jarque, Sergio; Bosch, Carme; Casado, Marta; Grimalt, Joan O.; Raldúa, Demetrio; Piña, Benjamin

2014-01-01

Hepatic mRNA levels of the dio2 gene (deiodinase 2), implicated in thyroid hormone homeostasis, were analyzed in trout from six remote lakes in the Pyrenees (Spain) and the Tatra Mountains (Slovakia). Highest levels corresponded to fish from the two coldest lakes in Pyrenees, whereas relatively low levels were found in the Tatra lakes. These values correlated with the presence of highly-brominated polybrominated diphenyl ethers (PBDE) congeners in the muscle of the same animals, reflecting the distribution of these compounds across European mountain ranges. In contrast, cyp1a expression levels, diagnostic for the presence of dioxin-like pollutants, mirrored the distribution of semi-volatile organochlorine compounds, indicating the specificity of the two types of biological responses. Exposure to PDBEs is known to increase transcription of dio2 and other thyroid-related genes in laboratory experiments; we propose that our data reflects the same phenomenon in natural populations, driven by anthropogenic pollutants at the environmental concentrations. - Highlights: • Hepatic deiodinase 2 (dio2) mRNA levels vary among mountain lake trout populations. • High dio2 expression correlated with elevated levels of PBDE 153 and 154 in muscle. • Expression patterns of dio2 and cyp1a diverge among the same fish populations. • Elevated biological responses associated to high loads of specific pollutants. • These data indicate that thyroid disruption may occur in remote ecosystems. - Deionidase dio2 expression as a marker for exposure to putative thyroid disruptors in mountain lake trout
Catalytic Stereoinversion of L-Alanine to Deuterated D-Alanine.

Science.gov (United States)

Moozeh, Kimia; So, Soon Mog; Chin, Jik

2015-08-03

A combination of an achiral pyridoxal analogue and a chiral base has been developed for catalytic deuteration of L-alanine with inversion of stereochemistry to give deuterated D-alanine under mild conditions (neutral pD and 25 °C) without the use of any protecting groups. This system can also be used for catalytic deuteration of D-alanine with retention of stereochemistry to give deuterated D-alanine. Thus a racemic mixture of alanine can be catalytically deuterated to give an enantiomeric excess of deuterated D-alanine. While catalytic deracemization of alanine is forbidden by the second law of thermodynamics, this system can be used for catalytic deracemization of alanine with deuteration. Such green and biomimetic approach to catalytic stereocontrol provides insights into efficient amino acid transformations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
A Review on Catalytic Membranes Production and Applications

Directory of Open Access Journals (Sweden)

Heba Abdallah

2017-05-01

Full Text Available The development of the chemical industry regarding reducing the production cost and obtaining a high-quality product with low environmental impact became the essential requirements of the world in these days. The catalytic membrane is considered as one of the new alternative solutions of catalysts problems in the industries, where the reaction and separation can be amalgamated in one unit. The catalytic membrane has numerous advantages such as breaking the thermodynamic equilibrium limitation, increasing conversion rate, reducing the recycle and separation costs. But the limitation or most disadvantages of catalytic membranes related to the high capital costs for fabrication or the fact that manufacturing process is still under development. This review article summarizes the most recent advances and research activities related to preparation, characterization, and applications of catalytic membranes. In this article, various types of catalytic membranes are displayed with different applications and explained the positive impacts of using catalytic membranes in various reactions. Copyright © 2017 BCREC Group. All rights reserved. Received: 1st April 2016; Revised: 14th February 2017; Accepted: 22nd February 2017 How to Cite: Abdallah, H. (2017. A Review on Catalytic Membranes Production and Applications. Bulletin of Chemical Reaction Engineering & Catalysis, 12 (2: 136-156 (doi:10.9767/bcrec.12.2.462.136-156 Permalink/DOI: http://dx.doi.org/10.9767/bcrec.12.2.462.136-156
Phosphorolytic activity of Escherichia coli glycyl-tRNA synthetase towards its cognate aminoacyl adenylate detected by 31P-NMR spectroscopy and thin-layer chromatography

DEFF Research Database (Denmark)

Led, Jens Jørgen; Switon, Werner K.; Jensen, Kaj Frank

1983-01-01

The catalytic activity of highly purified Escherichia coli glycyl-tRNA synthetase has been studied by 31P-NMR spectroscopy and thin-layer chromatography on poly(ethyleneimine)-cellulose. It was found that this synthetase, besides the activation of its cognate amino acid and the syntheses...
On the Structural Context and Identification of Enzyme Catalytic Residues

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Yu-Tung Chien

2013-01-01

Full Text Available Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.
Catalytic activity of Au nanoparticles

DEFF Research Database (Denmark)

Larsen, Britt Hvolbæk; Janssens, Ton V.W.; Clausen, Bjerne

2007-01-01

Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change with par......Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change...... with particle size. We find that the fraction of low-coordinated Au atoms scales approximately with the catalytic activity, suggesting that atoms on the corners and edges of Au nanoparticles are the active sites. This effect is explained using density functional calculations....
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.
A Hypothesis: Life Initiated from Two Genes, as Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems

Directory of Open Access Journals (Sweden)

Kunio Kawamura

2016-08-01

Full Text Available RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life. For instance, an RNA-based life-like system should possess enough stability to resist environmental perturbations, by developing a cell-like compartment, for instance. Here, a conceptual viewpoint is summarized to provide a realistic life-like system that is compatible with the primitive Earth environment and the capabilities of RNA molecules. According to the empirical and conceptual analysis, I propose the hypothesis that the first life-like system could have initiated from only two genes.

Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA–microRNA regulatory network in nasopharyngeal carcinoma model systems

Directory of Open Access Journals (Sweden)

Carol Ying-Ying Szeto

2014-01-01

Full Text Available Nasopharyngeal carcinoma (NPC is a prevalent malignancy in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein–Barr virus (EBV-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 were sequenced by Solexa technology. We found 2812 genes and 149 miRNAs (human and EBV to be differentially expressed in NP460, HK1, C666 and X666 with RNASeq; 533 miRNA–mRNA target pairs were inversely regulated in the three NPC cell lines compared to NP460. Integrated mRNA/miRNA expression profiling and pathway analysis show extracellular matrix organization, Beta-1 integrin cell surface interactions, and the PI3K/AKT, EGFR, ErbB, and Wnt pathways were potentially deregulated in NPC. Real-time quantitative PCR was performed on selected mRNA/miRNAs in order to validate their expression. Transcript sequence variants such as short insertions and deletions (INDEL, single nucleotide variant (SNV, and isomiRs were characterized in the NPC model systems. A novel TP53 transcript variant was identified in NP460, HK1, and C666. Detection of three previously reported novel EBV-encoded BART miRNAs and their isomiRs were also observed. Meta-analysis of a model system to a clinical system aids the choice of different cell lines in NPC studies. This comprehensive characterization of mRNA and miRNA transcriptomes in NPC cell lines and the xenograft provides insights on miRNA regulation of mRNA and valuable resources on transcript variation and regulation in NPC, which are potentially useful for mechanistic and preclinical studies.
Engineering Metallic Nanoparticles for Enhancing and Probing Catalytic Reactions.

Science.gov (United States)

Collins, Gillian; Holmes, Justin D

2016-07-01

Recent developments in tailoring the structural and chemical properties of colloidal metal nanoparticles (NPs) have led to significant enhancements in catalyst performance. Controllable colloidal synthesis has also allowed tailor-made NPs to serve as mechanistic probes for catalytic processes. The innovative use of colloidal NPs to gain fundamental insights into catalytic function will be highlighted across a variety of catalytic and electrocatalytic applications. The engineering of future heterogenous catalysts is also moving beyond size, shape and composition considerations. Advancements in understanding structure-property relationships have enabled incorporation of complex features such as tuning surface strain to influence the behavior of catalytic NPs. Exploiting plasmonic properties and altering colloidal surface chemistry through functionalization are also emerging as important areas for rational design of catalytic NPs. This news article will highlight the key developments and challenges to the future design of catalytic NPs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
The simple fool's guide to population genomics via RNA-Seq: An introduction to high-throughput sequencing data analysis

DEFF Research Database (Denmark)

De Wit, P.; Pespeni, M.H.; Ladner, J.T.

2012-01-01

to Population Genomics via RNA-seq' (SFG), a document intended to serve as an easy-to-follow protocol, walking a user through one example of high-throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods...... used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http://sfg.......stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom-made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal components...
Hydrocarbon conversion with an attenuated superactive multimetallic catalytic composite

International Nuclear Information System (INIS)

Antos, G.J.

1981-01-01

Hydrocarbons are converted by contacting them at hydrocarbon conversion conditions with a novel attenuated superactive multimetallic catalytic composite comprising a combination of a catalytically effective amount of a pyrolyzed rhenium carbonyl component with a porous carrier material containing a uniform dispersion of catalytically effective amounts of a platinum group component, which is maintained in the elemental metallic state during the incorporation and pyrolysis of the rhenium carbonyl component, and of an iron component. In a highly preferred embodiment, this novel catalytic composite also contains a catalytically effective amount of a halogen component. The platinum group component, pyrolyzed rhenium carbonyl component, iron component and optional halogen component are preferably present in the multimetallic catalytic composite in amounts, calculated on an elemental basis, corresponding to about 0.01 to about 2 wt. % platinum group metal, about 0.01 to about 5 wt. % rhenium, about 0.005 to about 4 wt. % iron and about 0.1 to about 5 wt. % halogen. A key feature associated with the preparation of the subject catalytic composite is reaction of a rhenium carbonyl complex with a porous carrier material containing a uniform dispersion of an iron component and of a platinum group component maintained in the elemental state, whereby the interaction of the rhenium moiety with the platinum group moiety is maximized due to the platinophilic (i.e., platinum-seeking) propensities of the carbon monoxide ligands associated with the rhenium reagent. A specific example of the type of hydrocarbon conversion process disclosed herein is a process for the catalytic reforming of a low octane gasoline fraction wherein the gasoline fraction and a hydrogen stream are contacted with the attenuated superactive multimetallic catalytic composite at reforming conditions
[Analysis of mitochondrial 12S rRNA and tRNA(Ser(UCN)) genes in patients with nonsyndromic sensorineural hearing loss from various regions of Russia].

Science.gov (United States)

Dzhemileva, L U; Posukh, O L; Tazetdinov, A M; Barashkov, N A; Zhuravskiĭ, S G; Ponidelko, S N; Markova, T G; Tadinova, V N; Fedorova, S A; Maksimova, N R; Khusnutdinova, E K

2009-07-01

Mitochondrial DNA (mtDNA) mutations play an important role in etiology of hereditary hearing loss. In various regions of the world, patients suffer from nonsyndromic sensorineural hearing loss initiated by aminoglycoside antibiotics. Mutations that had been shown as pathogenetically important for hearing function disturbance were identified in mitochondrial 12S rRNA and tRNA(Ser(UCN)) genes while pathogenic role of several DNA sequences requires additional studies. This work presents the results of studying the spectrum of mutations and polymorphic variations in mtDNA genes 12S rRNA and tRNA(Ser(UGN)) in 410 patients with nonsyndromal sensoneural hearing impairment/loss from the Volga Ural region, St Petersburg, Yakutia, and Altai and in 520 individuals with normal hearing, which represent several ethnic groups (Russians, Tatars, Bashkirs, Yakuts, Altaians) residing in the Russian Federation. Pathogenetically significant mutation A1555G (12S rRNA) was found in two families (from Yakutia and St Peresburg) with hearing loss, probably caused by treatment with aminoglucosides, and in the population sample of Yakuts with a frequency of 0.83%. Further research is needed to confirm the role in hearing impairment of mutations 961insC, 961insC(n), 961delTinsC(n), T961G, T1095C (12S rRNA) and G7444A, A7445C (tRNA(Ser(UGN revealed in the patients. In addition, in the patients and the population groups, polymorphic mt DNA variants were detected, which are characteristic also of other Eurasian populations both in spectrum and frequency.
Catalytic treatment

Energy Technology Data Exchange (ETDEWEB)

Bindley, W T.R.

1931-04-18

An apparatus is described for the catalytic treatment of liquids, semi-liquids, and gases comprising a vessel into which the liquid, semi-liquid, or gas to be treated is introduced through a common inlet to a chamber within the vessel whence it passes to contact with a catalyst through radially arranged channels or passages to a common outlet chamber.
Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains.

Science.gov (United States)

Keren, Ido; Klipcan, Liron; Bezawork-Geleta, Ayenachew; Kolton, Max; Shaya, Felix; Ostersetzer-Biran, Oren

2008-08-22

CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.
Catalytic cleavage activities of 10–23 DNAzyme analogs functionalized with an amino group in its catalytic core

Directory of Open Access Journals (Sweden)

Qi Wang

2012-02-01

Full Text Available Functionalization of the catalytic loop of 10–23 DNAzyme with an amino group was performed by incorporation of 7-(3-aminopropyl-8-aza-7-deaza-2′-deoxyadenosine in different single positions. Among the nine modified positions in the catalytic loop, A9 is the unique position with positive contribution by such modification. These results indicated that more efficient deoxyribozymes remain to be explored by introduction of exogenous functional groups in an appropriate position in the catalytic loop of 10–23 DNAzyme, such as the combination of 7-functional group substituted 8-aza-7-deaza-2′-deoxyadenosine analogs and A9 position.
A survey of small RNA population during FR-induced apical hook opening

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Ying eLi

2014-04-01

Full Text Available Photomorphogenesis is a mechanism employed by plants to regulate their architecture and developmental program in response to light conditions. As they emerge into light for the first time, dark-grown seedlings employ a rapid and finely-controlled photomorphogenic signaling network. Small RNAs have increasingly been revealed to play an important role in regulating multiple aspects of plant development, by modulating the stability of mRNAs. The rapid alteration of the mRNA transcriptome is a known hallmark of the de-etiolation response, thus we investigated the small RNA transcriptome during this process in specific seedling tissues. Here we describe a survey of the small RNA expression profile in four tissues of etiolated soybean seedlings, the cotyledons, hypocotyl and the convex and concave sides of the apical hook. We also investigate how this profile responds to a one-hour far-red light treatment. Our data suggests that miRNAs show a different global profile between these tissues and treatments, suggesting a possible role for tissue- and treatment-specific expression in the differential morphology of the seedling on de-etiolation. Further evidence for the role of miRNA in light-regulated development is given by the de-etiolation responses of a hypomorphic ago1 mutant, which displays reduced and delayed photomorphogenic responses in apical hook and cotyledon angle to far-red light.
Production of high quality brain-derived neurotrophic factor (BDNF) and tropomyosin receptor kinase B (TrkB) RNA from isolated populations of rat spinal cord motor neurons obtained by Laser Capture Microdissection (LCM).

Science.gov (United States)

Mehta, Prachi; Premkumar, Brian; Morris, Renée

2016-08-03

The mammalian central nervous system (CNS) is composed of multiple cellular elements, making it challenging to segregate one particular cell type to study their gene expression profile. For instance, as motor neurons represent only 5-10% of the total cell population of the spinal cord, meaningful transcriptional analysis on these neurons is almost impossible to achieve from homogenized spinal cord tissue. A major challenge faced by scientists is to obtain good quality RNA from small amounts of starting material. In this paper, we used Laser Capture Microdissection (LCM) techniques to identify and isolate spinal cord motor neurons. The present analysis revealed that perfusion with paraformaldehyde (PFA) does not alter RNA quality. RNA integrity numbers (RINs) of tissue samples from rubrospinal tract (RST)-transected, intact spinal cord or from whole spinal cord homogenate were all above 8, which indicates intact, high-quality RNA. Levels of mRNA for brain-derived neurotrophic factor (BDNF) or for its tropomyosin receptor kinase B (TrkB) were not affected by rubrospinal tract (RST) transection, a surgical procedure that deprive motor neurons from one of their main supraspinal input. The isolation of pure populations of neurons with LCM techniques allows for robust transcriptional characterization that cannot be achieved with spinal cord homogenates. Such preparations of pure population of motor neurons will provide valuable tools to advance our understanding of the molecular mechanisms underlying spinal cord injury and neuromuscular diseases. In the near future, LCM techniques might be instrumental to the success of gene therapy for these debilitating conditions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop.

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Chenxi Qiu

2016-11-01

Full Text Available The active sites of multisubunit RNA polymerases have a "trigger loop" (TL that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis. Furthermore, allele-specific genetic interactions among TL and TL-proximal domain residues support the contribution of the funnel and bridge helices (BH to TL dynamics. Our structural genetics approach incorporates structural and phenotypic data for high-resolution dissection of transcription mechanisms and their evolution, and is readily applicable to other essential yeast proteins.
Progress in catalytic naphtha reforming process: A review

International Nuclear Information System (INIS)

Rahimpour, Mohammad Reza; Jafari, Mitra; Iranshahi, Davood

2013-01-01

Catalytic naphtha reforming process is a vital process for refineries due to the production of high-octane components, which is intensely demanded in our modern life. The significance of this industrial process induced researchers to investigate different aspects of catalytic naphtha reforming process intensively. Some of the investigators try to improve this process by representing more effective catalysts, while others try to elucidate its kinetic and deactivation mechanisms and design more efficient reactor setups. The amount of these established papers is so much that may confuse some of the researchers who want to find collective information about catalytic naphtha reforming process. In the present paper, the published studies from 1949 until now are categorized into three main groups including finding suitable catalyst, revealing appropriate kinetic and deactivation model, and suggesting efficient reactor configuration and mode of operation. These studies are reviewed separately, and a suitable reference is provided for those who want to have access to generalized information about catalytic naphtha reforming process. Finally, various suggestions for revamping the catalytic naphtha reforming process have been proposed as a guideline for further investigations
Catalytically favorable surface patterns in Pt-Au nanoclusters

KAUST Repository

Mokkath, Junais Habeeb; Schwingenschlö gl, Udo

2013-01-01

Motivated by recent experimental demonstrations of novel PtAu nanoparticles with highly enhanced catalytic properties, we present a systematic theoretical study that explores principal catalytic indicators as a function of the particle size
Catalytic Aminohalogenation of Alkenes and Alkynes.

Science.gov (United States)

Chemler, Sherry R; Bovino, Michael T

2013-06-07

Catalytic aminohalogenation methods enable the regio- and stereoselective vicinal difunctionalization of alkynes, allenes and alkenes with amine and halogen moieties. A range of protocols and reaction mechanisms including organometallic, Lewis base, Lewis acid and Brønsted acid catalysis have been disclosed, enabling the regio- and stereoselective synthesis of halogen-functionalized acyclic amines and nitrogen heterocycles. Recent advances including aminofluorination and catalytic enantioselective aminohalogenation reactions are summarized in this review.
Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with the RNA and DNA sequences of the virus populations of their mothers.

Science.gov (United States)

Scarlatti, G; Leitner, T; Halapi, E; Wahlberg, J; Marchisio, P; Clerici-Schoeller, M A; Wigzell, H; Fenyö, E M; Albert, J; Uhlén, M

1993-01-01

We have compared the variable region 3 sequences from 10 human immunodeficiency virus type 1 (HIV-1)-infected infants to virus sequences from the corresponding mothers. The sequences were derived from DNA of uncultured peripheral blood mononuclear cells (PBMC), DNA of cultured PBMC, and RNA from serum collected at or shortly after delivery. The infected infants, in contrast to the mothers, harbored homogeneous virus populations. Comparison of sequences from the children and clones derived from DNA of the corresponding mothers showed that the transmitted virus represented either a minor or a major virus population of the mother. In contrast to an earlier study, we found no evidence of selection of minor virus variants during transmission. Furthermore, the transmitted virus variant did not show any characteristic molecular features. In some cases the transmitted virus was more related to the virus RNA population of the mother and in other cases it was more related to the virus DNA population. This suggests that either cell-free or cell-associated virus may be transmitted. These data will help AIDS researchers to understand the mechanism of transmission and to plan strategies for prevention of transmission. PMID:8446584
Effect of microinjections of subunits of cAMP-dependent protein kinase on development, proliferation, and RNA synthesis in early embryos of the loach Misgurnus fossilis L

International Nuclear Information System (INIS)

Glukhov, A.I.; Benyumov, A.O.; Nesterova, M.V.; Severin, E.S.; Gazaryan, K.G.

1986-01-01

The effect of the catalytic and regulatory subunits of cAMP-dependent protein kinase type II on development, proliferation, and RNA synthesis was studied in loach embryos. It was found that injection of the catalytic subunit in a physiological concentration leads to a disturbance in the course of development and inhibits proliferation and RNA synthesis in the embryos. An increase in the concentration of this protein above the physiological level leads to death of the embryos in the first hours of development. Injection of the regulatory subunit stimulated the incorporation of labeled uridine into the acid-insoluble fraction of the embryos, beginning with the gastrula stage. The cell nuclei of loach embryos injected with subunits of protein kinase type II were transplanted into activated loach egg cells: subunits of protein kinase type I had no effect on the ability of nuclei of undetermined loach embryo cells to provide de novo development and their effect was reversible
Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein

Directory of Open Access Journals (Sweden)

Xu Wanhong

2008-12-01

Full Text Available Abstract Background The orthoreoviruses are infectious agents that possess a genome comprised of 10 double-stranded RNA segments encased in two concentric protein capsids. Like virtually all RNA viruses, an RNA-dependent RNA polymerase (RdRp enzyme is required for viral propagation. RdRp sequences have been determined for the prototype mammalian orthoreoviruses and for several other closely-related reoviruses, including aquareoviruses, but have not yet been reported for any avian orthoreoviruses. Results We determined the L2 genome segment nucleotide sequences, which encode the RdRp proteins, of two different avian reoviruses, strains ARV138 and ARV176 in order to define conserved and variable regions within reovirus RdRp proteins and to better delineate structure/function of this important enzyme. The ARV138 L2 genome segment was 3829 base pairs long, whereas the ARV176 L2 segment was 3830 nucleotides long. Both segments were predicted to encode λB RdRp proteins 1259 amino acids in length. Alignments of these newly-determined ARV genome segments, and their corresponding proteins, were performed with all currently available homologous mammalian reovirus (MRV and aquareovirus (AqRV genome segment and protein sequences. There was ~55% amino acid identity between ARV λB and MRV λ3 proteins, making the RdRp protein the most highly conserved of currently known orthoreovirus proteins, and there was ~28% identity between ARV λB and homologous MRV and AqRV RdRp proteins. Predictive structure/function mapping of identical and conserved residues within the known MRV λ3 atomic structure indicated most identical amino acids and conservative substitutions were located near and within predicted catalytic domains and lining RdRp channels, whereas non-identical amino acids were generally located on the molecule's surfaces. Conclusion The ARV λB and MRV λ3 proteins showed the highest ARV:MRV identity values (~55% amongst all currently known ARV and MRV
Methods for Determination of 2′-O-Me in RNA

DEFF Research Database (Denmark)

Birkedal, Ulf; Krogh, Nicolai; Andersen, Kasper Langebjerg

2016-01-01

mechanism of ribose methylation is found in rRNA of Archaea and Eukarya where a methyltransferase (fibrillarin) use sRNA (Archaea) or box C/D snoRNA (Eukarya) as guide RNAs to specify the site of modification. The general function of these modifications is to promote ribosome biogenesis, in particular...... for mapping modifications and quantitating the fraction of RNA molecules modified in a population until recently remained poorly developed. Here, we review the methods that have been used to study 2′-O-Me in RNA starting with the original approach employing in vivo isotope labeling followed by paper......Ribose methylation is one of the most abundant RNA modifications and is found in all kingdoms of life and all major classes of RNA (rRNA, tRNA, and mRNA). Ribose methylations are introduced by stand-alone enzymes or by generic enzymes guided to the target by small RNA guides. The most abundant...
Novel Metal Nanomaterials and Their Catalytic Applications

Directory of Open Access Journals (Sweden)

Jiaqing Wang

2015-09-01

Full Text Available In the rapidly developing areas of nanotechnology, nano-scale materials as heterogeneous catalysts in the synthesis of organic molecules have gotten more and more attention. In this review, we will summarize the synthesis of several new types of noble metal nanostructures (FePt@Cu nanowires, Pt@Fe2O3 nanowires and bimetallic Pt@Ir nanocomplexes; Pt-Au heterostructures, Au-Pt bimetallic nanocomplexes and Pt/Pd bimetallic nanodendrites; Au nanowires, CuO@Ag nanowires and a series of Pd nanocatalysts and their new catalytic applications in our group, to establish heterogeneous catalytic system in “green” environments. Further study shows that these materials have a higher catalytic activity and selectivity than previously reported nanocrystal catalysts in organic reactions, or show a superior electro-catalytic activity for the oxidation of methanol. The whole process might have a great impact to resolve the energy crisis and the environmental crisis that were caused by traditional chemical engineering. Furthermore, we hope that this article will provide a reference point for the noble metal nanomaterials’ development that leads to new opportunities in nanocatalysis.
Catalytic Organic Transformations Mediated by Actinide Complexes

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Isabell S. R. Karmel

2015-10-01

Full Text Available This review article presents the development of organoactinides and actinide coordination complexes as catalysts for homogeneous organic transformations. This chapter introduces the basic principles of actinide catalysis and deals with the historic development of actinide complexes in catalytic processes. The application of organoactinides in homogeneous catalysis is exemplified in the hydroelementation reactions, such as the hydroamination, hydrosilylation, hydroalkoxylation and hydrothiolation of alkynes. Additionally, the use of actinide coordination complexes for the catalytic polymerization of α-olefins and the ring opening polymerization of cyclic esters is presented. The last part of this review article highlights novel catalytic transformations mediated by actinide compounds and gives an outlook to the further potential of this field.

Modeling and simulation of heterogeneous catalytic processes

CERN Document Server

Dixon, Anthony

2014-01-01

Heterogeneous catalysis and mathematical modeling are essential components of the continuing search for better utilization of raw materials and energy, with reduced impact on the environment. Numerical modeling of chemical systems has progressed rapidly due to increases in computer power, and is used extensively for analysis, design and development of catalytic reactors and processes. This book presents reviews of the state-of-the-art in modeling of heterogeneous catalytic reactors and processes. Reviews by leading authorities in the respective areas Up-to-date reviews of latest techniques in modeling of catalytic processes Mix of US and European authors, as well as academic/industrial/research institute perspectives Connections between computation and experimental methods in some of the chapters.
Catalytic gasification of oil-shales

Energy Technology Data Exchange (ETDEWEB)

Lapidus, A.; Avakyan, T. [I.M. Gubkin Russian State Univ. of Oil and Gas, Moscow (Russian Federation); Strizhakova, Yu. [Samara State Univ. (Russian Federation)

2012-07-01

Nowadays, the problem of complex usage of solid fossil fuels as raw materials for obtaining of motor fuels and chemical products is becoming increasingly important. A one of possible solutions of the problem is their gasification with further processing of gaseous and liquid products. In this work we have investigated the process of thermal and catalytic gasification of Baltic and Kashpir oil-shales. We have shown that, as compared with non-catalytic process, using of nickel catalyst in the reaction increases the yield of gas, as well as hydrogen content in it, and decreases the amount of liquid products. (orig.)
Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea

Science.gov (United States)

Ngugi, David Kamanda; Stingl, Ulrich

2012-01-01

Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24°C throughout the year, and a remarkable uniform temperature (∼22°C) and salinity (∼41 psu) from the mixed layer (∼200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea’s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium. PMID:23185592
Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

KAUST Repository

Ngugi, David

2012-11-20

Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.
Structural stability of human protein tyrosine phosphatase ρ catalytic domain: effect of point mutations.

Directory of Open Access Journals (Sweden)

Alessandra Pasquo

Full Text Available Protein tyrosine phosphatase ρ (PTPρ belongs to the classical receptor type IIB family of protein tyrosine phosphatase, the most frequently mutated tyrosine phosphatase in human cancer. There are evidences to suggest that PTPρ may act as a tumor suppressor gene and dysregulation of Tyr phosphorylation can be observed in diverse diseases, such as diabetes, immune deficiencies and cancer. PTPρ variants in the catalytic domain have been identified in cancer tissues. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of the membrane-proximal catalytic domain of PTPρ. We expressed and purified as soluble recombinant proteins some of the mutants of the membrane-proximal catalytic domain of PTPρ identified in colorectal cancer and in the single nucleotide polymorphisms database. The mutants show a decreased thermal and thermodynamic stability and decreased activation energy relative to phosphatase activity, when compared to wild- type. All the variants show three-state equilibrium unfolding transitions similar to that of the wild- type, with the accumulation of a folding intermediate populated at ~4.0 M urea.
siRNA for Influenza Therapy

Directory of Open Access Journals (Sweden)

Sailen Barik

2010-07-01

Full Text Available Influenza virus is one of the most prevalent and ancient infections in humans. About a fifth of world's population is infected by influenza virus annually, leading to high morbidity and mortality, particularly in infants, the elderly and the immunocompromised. In the US alone, influenza outbreaks lead to roughly 30,000 deaths each year. Current vaccines and anti-influenza drugs are of limited use due to high mutation rate of the virus and side effects. In recent years, RNA interference, triggered by synthetic short interfering RNA (siRNA, has rapidly evolved as a potent antiviral regimen. Properly designed siRNAs have been shown to function as potent inhibitors of influenza virus replication. The siRNAs outperform traditional small molecule antivirals in a number of areas, such as ease of design, modest cost, and fast turnaround. Although specificity and tissue delivery remain major bottlenecks in the clinical applications of RNAi in general, intranasal application of siRNA against respiratory viruses including, but not limited to influenza virus, has experienced significant success and optimism, which is reviewed here.
siRNA for Influenza Therapy.

Science.gov (United States)

Barik, Sailen

2010-07-01

Influenza virus is one of the most prevalent and ancient infections in humans. About a fifth of world's population is infected by influenza virus annually, leading to high morbidity and mortality, particularly in infants, the elderly and the immunocompromised. In the US alone, influenza outbreaks lead to roughly 30,000 deaths each year. Current vaccines and anti-influenza drugs are of limited use due to high mutation rate of the virus and side effects. In recent years, RNA interference, triggered by synthetic short interfering RNA (siRNA), has rapidly evolved as a potent antiviral regimen. Properly designed siRNAs have been shown to function as potent inhibitors of influenza virus replication. The siRNAs outperform traditional small molecule antivirals in a number of areas, such as ease of design, modest cost, and fast turnaround. Although specificity and tissue delivery remain major bottlenecks in the clinical applications of RNAi in general, intranasal application of siRNA against respiratory viruses including, but not limited to influenza virus, has experienced significant success and optimism, which is reviewed here.
Kinetic catalytic studies of scorpion's hemocyanin

International Nuclear Information System (INIS)

Queinnec, E.; Vuillaume, M.; Gardes-Albert, M.; Ferradini, C.; Ducancel, F.

1991-01-01

Hemocyanins are copper proteins which function as oxygen carriers in the haemolymph of Molluscs and Arthropods. They possess enzymatic properties: peroxidatic and catalatic activities, although they have neither iron nor porphyrin ring at the active site. The kinetics of the catalytic reaction is described. The reaction of superoxide anion with hemocyanin has been studied using pulse radiolysis at pH 9. The catalytic rate constant is 3.5 X 10 7 mol -1 .l.s -1 [fr
A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics.

Science.gov (United States)

Smith, Glenna J; Lee, Kang Taek; Qu, Xiaohui; Xie, Zheng; Pesic, Jelena; Sosnick, Tobin R; Pan, Tao; Scherer, Norbert F

2008-05-09

The process of large RNA folding is believed to proceed from many collapsed structures to a unique functional structure requiring precise organization of nucleotides. The diversity of possible structures and stabilities of large RNAs could result in non-exponential folding kinetics (e.g. stretched exponential) under conditions where the molecules have not achieved their native state. We describe a single-molecule fluorescence resonance energy transfer (FRET) study of the collapsed-state region of the free energy landscape of the catalytic domain of RNase P RNA from Bacillus stearothermophilus (C(thermo)). Ensemble measurements have shown that this 260 residue RNA folds cooperatively to its native state at >or=1 mM Mg(2+), but little is known about the conformational dynamics at lower ionic strength. Our measurements of equilibrium conformational fluctuations reveal simple exponential kinetics that reflect a small number of discrete states instead of the expected inhomogeneous dynamics. The distribution of discrete dwell times, collected from an "ensemble" of 300 single molecules at each of a series of Mg(2+) concentrations, fit well to a double exponential, which indicates that the RNA conformational changes can be described as a four-state system. This finding is somewhat unexpected under [Mg(2+)] conditions in which this RNA does not achieve its native state. Observation of discrete well-defined conformations in this large RNA that are stable on the seconds timescale at low [Mg(2+)] (<0.1 mM) suggests that even at low ionic strength, with a tremendous number of possible (weak) interactions, a few critical interactions may produce deep energy wells that allow for rapid averaging of motions within each well, and yield kinetics that are relatively simple.
Tunable preparation of ruthenium nanoparticles with superior size-dependent catalytic hydrogenation properties

Energy Technology Data Exchange (ETDEWEB)

Zhao, Yuan; Luo, Yaodong; Yang, Xuan; Yang, Yaxin; Song, Qijun, E-mail: qsong@jiangnan.edu.cn

2017-06-15

Highlights: • A facile and efficient strategy is firstly developed for the synthesis of Ru NPs. • Ru NPs are stable and uniform with the controllable sizes from 2.6 to 51.5 nm. • Ru NPs exhibit size-dependent and superior catalytic hydrogenation activity. - Abstract: Ruthenium (Ru) featured with an unusual catalytic behavior is of great significance in several heterogeneous and electro-catalytic reactions. The preparation of tractable Ru nanocatalysts and the building of highly active catalytic system at ambient temperature remains a grand challenge. Herein, a facile strategy is developed for the controllable preparation of Ru nanoparticles (NPs) with the sizes ranging from 2.6 to 51.5 nm. Ru NPs show superior size-dependent catalytic performance with the best kinetic rate constant as high as −1.52 min{sup −1}, which could far surpass the other traditional noble metals. Ru NPs exert exceedingly efficient low-temperature catalytic activity and good recyclability in the catalytic reduction of nitroaromatic compounds (NACs) and azo dyes. The developed catalytic system provides a distinguishing insight for the artificial preparation of Ru NPs with desired sizes, and allows for the development of rational design rules for exploring catalysts with superior catalytic performances, potentially broadening the applications of metallic NP-enabled catalytic analysis.
Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans.

Science.gov (United States)

Parrish, S; Fire, A

2001-10-01

RNA interference (RNAi) is a cellular defense mechanism that uses double-stranded RNA (dsRNA) as a sequence-specific trigger to guide the degradation of homologous single-stranded RNAs. RNAi is a multistep process involving several proteins and at least one type of RNA intermediate, a population of small 21-25 nt RNAs (called siRNAs) that are initially derived from cleavage of the dsRNA trigger. Genetic screens in Caenorhabditis elegans have identified numerous mutations that cause partial or complete loss of RNAi. In this work, we analyzed cleavage of injected dsRNA to produce the initial siRNA population in animals mutant for rde-1 and rde-4, two genes that are essential for RNAi but that are not required for organismal viability or fertility. Our results suggest distinct roles for RDE-1 and RDE-4 in the interference process. Although null mutants lacking rde-1 show no phenotypic response to dsRNA, the amount of siRNAs generated from an injected dsRNA trigger was comparable to that of wild-type. By contrast, mutations in rde-4 substantially reduced the population of siRNAs derived from an injected dsRNA trigger. Injection of chemically synthesized 24- or 25-nt siRNAs could circumvent RNAi resistance in rde-4 mutants, whereas no bypass was observed in rde-1 mutants. These results support a model in which RDE-4 is involved before or during production of siRNAs, whereas RDE-1 acts after the siRNAs have been formed.
Orion EFT-1 Catalytic Tile Experiment Overview and Flight Measurements

Science.gov (United States)

Salazar, Giovanni; Amar, Adam; Hyatt, Andrew; Rezin, Marc D.

2016-01-01

This paper describes the design and results of a surface catalysis flight experiment flown on the Orion Multipurpose Crew Vehicle during Exploration Flight Test 1 (EFT1). Similar to previous Space Shuttle catalytic tile experiments, the present test consisted of a highly catalytic coating applied to an instrumented TPS tile. However, the present catalytic tile experiment contained significantly more instrumentation in order to better resolve the heating overshoot caused by the change in surface catalytic efficiency at the interface between two distinct materials. In addition to collecting data with unprecedented spatial resolution of the "overshoot" phenomenon, the experiment was also designed to prove if such a catalytic overshoot would be seen in turbulent flow in high enthalpy regimes. A detailed discussion of the results obtained during EFT1 is presented, as well as the challenges associated with data interpretation of this experiment. Results of material testing carried out in support of this flight experiment are also shown. Finally, an inverse heat conduction technique is employed to reconstruct the flight environments at locations upstream and along the catalytic coating. The data and analysis presented in this work will greatly contribute to our understanding of the catalytic "overshoot" phenomenon, and have a significant impact on the design of future spacecraft.
Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA.

Science.gov (United States)

Swenson, Luke C; Moores, Andrew; Low, Andrew J; Thielen, Alexander; Dong, Winnie; Woods, Conan; Jensen, Mark A; Wynhoven, Brian; Chan, Dennison; Glascock, Christopher; Harrigan, P Richard

2010-08-01

Tropism testing should rule out CXCR4-using HIV before treatment with CCR5 antagonists. Currently, the recombinant phenotypic Trofile assay (Monogram) is most widely utilized; however, genotypic tests may represent alternative methods. Independent triplicate amplifications of the HIV gp120 V3 region were made from either plasma HIV RNA or proviral DNA. These underwent standard, population-based sequencing with an ABI3730 (RNA n = 63; DNA n = 40), or "deep" sequencing with a Roche/454 Genome Sequencer-FLX (RNA n = 12; DNA n = 12). Position-specific scoring matrices (PSSMX4/R5) (-6.96 cutoff) and geno2pheno[coreceptor] (5% false-positive rate) inferred tropism from V3 sequence. These methods were then independently validated with a separate, blinded dataset (n = 278) of screening samples from the maraviroc MOTIVATE trials. Standard sequencing of HIV RNA with PSSM yielded 69% sensitivity and 91% specificity, relative to Trofile. The validation dataset gave 75% sensitivity and 83% specificity. Proviral DNA plus PSSM gave 77% sensitivity and 71% specificity. "Deep" sequencing of HIV RNA detected >2% inferred-CXCR4-using virus in 8/8 samples called non-R5 by Trofile, and <2% in 4/4 samples called R5. Triplicate analyses of V3 standard sequence data detect greater proportions of CXCR4-using samples than previously achieved. Sequencing proviral DNA and "deep" V3 sequencing may also be useful tools for assessing tropism.
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

Directory of Open Access Journals (Sweden)

Cristina Marino Buslje

Full Text Available Identification of catalytic residues (CR is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI, and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls, combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

Science.gov (United States)

Marino Buslje, Cristina; Teppa, Elin; Di Doménico, Tomas; Delfino, José María; Nielsen, Morten

2010-11-04

Identification of catalytic residues (CR) is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI), and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA) database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL) conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI) was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC) was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.
Heterogeneous catalytic degradation of polyacrylamide solution | Hu ...

African Journals Online (AJOL)

Modified with trace metal elements, the catalytic activity of Fe2O3/Al2O3 could be changed greatly. Among various trace metal elements, Fe2O3/Al2O3 catalysts modified with Co and Cu showed great increase on catalytic activity. International Journal of Engineering, Science and Technology, Vol. 2, No. 7, 2010, pp. 110- ...
Multiple RNA processing defects and impaired chloroplast function in plants deficient in the organellar protein-only RNase P enzyme.

Directory of Open Access Journals (Sweden)

Wenbin Zhou

Full Text Available Transfer RNA (tRNA precursors undergo endoribonucleolytic processing of their 5' and 3' ends. 5' cleavage of the precursor transcript is performed by ribonuclease P (RNase P. While in most organisms RNase P is a ribonucleoprotein that harbors a catalytically active RNA component, human mitochondria and the chloroplasts (plastids and mitochondria of seed plants possess protein-only RNase P enzymes (PRORPs. The plant organellar PRORP (PRORP1 has been characterized to some extent in vitro and by transient gene silencing, but the molecular, phenotypic and physiological consequences of its down-regulation in stable transgenic plants have not been assessed. Here we have addressed the function of the dually targeted organellar PRORP enzyme in vivo by generating stably transformed Arabidopsis plants in which expression of the PRORP1 gene was suppressed by RNA interference (RNAi. PRORP1 knock-down lines show defects in photosynthesis, while mitochondrial respiration is not appreciably affected. In both plastids and mitochondria, the effects of PRORP1 knock-down on the processing of individual tRNA species are highly variable. The drastic reduction in the levels of mature plastid tRNA-Phe(GAA and tRNA-Arg(ACG suggests that these two tRNA species limit plastid gene expression in the PRORP1 mutants and, hence, are causally responsible for the mutant phenotype.
SHORT COMMUNICATION CATALYTIC KINETIC ...

African Journals Online (AJOL)

IV) catalyzes the discoloring reaction of DBS-arsenazo oxidized by potassium bromate, a new catalytic kinetic spectrophotometric method for the determination of trace titanium (IV) was developed. The linear range of the determination of ...
Catalytic Kinetic Resolution of Biaryl Compounds.

Science.gov (United States)

Ma, Gaoyuan; Sibi, Mukund P

2015-08-10

Biaryl compounds with axial chirality are very common in synthetic chemistry, especially in catalysis. Axially chiral biaryls are important due to their biological activities and extensive applications in asymmetric catalysis. Thus the development of efficient enantioselective methods for their synthesis has attracted considerable attention. This Minireview discusses the progress made in catalytic kinetic resolution of biaryl compounds and chronicles significant advances made recently in catalytic kinetic resolution of biaryl scaffolds. © 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.
synthesis, characterization, electrical and catalytic studies of some

African Journals Online (AJOL)

B. S. Chandravanshi

catalytic activity of the VO(IV) and Mn(III) complexes have been tested in the epoxidation reaction of styrene ... Vanadyl sulfate pentahydrate, chromium chloride hexahydrate, anhydrous ferric ..... The catalytic oxidation of styrene gives the products styrene oxide, benzaldehyde, benzoic acid, ... bond via a radical mechanism.

CATALYTIC KINETIC SPECTROPHOTOMETRIC DETERMINATION ...

African Journals Online (AJOL)

Preferred Customer

acetylchlorophosphonazo(CPApA) by hydrogen peroxide in 0.10 M phosphoric acid. A novel catalytic kinetic-spectrophotometric method is proposed for the determination of copper based on this principle. Copper(II) can be determined spectrophotometrically ...
Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay.

Directory of Open Access Journals (Sweden)

Jun Yang

Full Text Available Ribosomes are large ribonucleoprotein complexes that are fundamental for protein synthesis. Ribosomes are ribozymes because their catalytic functions such as peptidyl transferase and peptidyl-tRNA hydrolysis depend on the rRNA. rRNA is a heterogeneous biopolymer comprising of at least 112 chemically modified residues that are believed to expand its topological potential. In the present study, we established a comprehensive modification profile of Saccharomyces cerevisiae's 18S and 25S rRNA using a high resolution Reversed-Phase High Performance Liquid Chromatography (RP-HPLC. A combination of mung bean nuclease assay, rDNA point mutants and snoRNA deletions allowed us to systematically map all ribose and base modifications on both rRNAs to a single nucleotide resolution. We also calculated approximate molar levels for each modification using their UV (254nm molar response factors, showing sub-stoichiometric amount of modifications at certain residues. The chemical nature, their precise location and identification of partial modification will facilitate understanding the precise role of these chemical modifications, and provide further evidence for ribosome heterogeneity in eukaryotes.
Isolation of a candidate human telomerase catalytic subunit gene, which reveals complex splicing patterns in different cell types.

Science.gov (United States)

Kilian, A; Bowtell, D D; Abud, H E; Hime, G R; Venter, D J; Keese, P K; Duncan, E L; Reddel, R R; Jefferson, R A

1997-11-01

Telomerase is a multicomponent reverse transcriptase enzyme that adds DNA repeats to the ends of chromosomes using its RNA component as a template for synthesis. Telomerase activity is detected in the germline as well as the majority of tumors and immortal cell lines, and at low levels in several types of normal cells. We have cloned a human gene homologous to a protein from Saccharomyces cerevisiae and Euplotes aediculatus that has reverse transcriptase motifs and is thought to be the catalytic subunit of telomerase in those species. This gene is present in the human genome as a single copy sequence with a dominant transcript of approximately 4 kb in a human colon cancer cell line, LIM1215. The cDNA sequence was determined using clones from a LIM1215 cDNA library and by RT-PCR, cRACE and 3'RACE on mRNA from the same source. We show that the gene is expressed in several normal tissues, telomerase-positive post-crisis (immortal) cell lines and various tumors but is not expressed in the majority of normal tissues analyzed, pre-crisis (non-immortal) cells and telomerase-negative immortal (ALT) cell lines. Multiple products were identified by RT-PCR using primers within the reverse transcriptase domain. Sequencing of these products suggests that they arise by alternative splicing. Strikingly, various tumors, cell lines and even normal tissues (colonic crypt and testis) showed considerable differences in the splicing patterns. Alternative splicing of the telomerase catalytic subunit transcript may be important for the regulation of telomerase activity and may give rise to proteins with different biochemical functions.
Bimetallic Nanoparticles in Alternative Solvents for Catalytic Purposes

Directory of Open Access Journals (Sweden)

Trung Dang-Bao

2017-07-01

Full Text Available Bimetallic nanoparticles represent attractive catalytic systems thanks to the synergy between both partners at the atomic level, mainly induced by electronic effects which in turn are associated with the corresponding structures (alloy, core-shell, hetero-dimer. This type of engineered material can trigger changes in the kinetics of catalyzed processes by variations on the electrophilicity/nucleophilicity of the metal centers involved and also promote cooperative effects to foster organic transformations, including multi-component and multi-step processes. Solvents become a crucial factor in the conception of catalytic processes, not only due to their environmental impact, but also because they can preserve the bimetallic structure during the catalytic reaction and therefore increase the catalyst life-time. In this frame, the present review focuses on the recent works described in the literature concerning the synthesis of bimetallic nanoparticles in non-conventional solvents, i.e., other than common volatile compounds, for catalytic applications.
Catalytic methanol dissociation

International Nuclear Information System (INIS)

Alcinikov, Y.; Fainberg, V.; Garbar, A.; Gutman, M.; Hetsroni, G.; Shindler, Y.; Tatrtakovsky, L.; Zvirin, Y.

1998-01-01

Results of the methanol dissociation study on copper/potassium catalyst with alumina support at various temperatures are presented. The following gaseous and liquid products at. The catalytic methanol dissociation is obtained: hydrogen, carbon monoxide, carbon dioxide, methane, and dimethyl ether. Formation rates of these products are discussed. Activation energies of corresponding reactions are calculated
In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

Science.gov (United States)

Czudnochowski, Nadine; Wang, Amy Liya; Finer-Moore, Janet; Stroud, Robert M

2013-10-23

Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA. Copyright © 2013 Elsevier Ltd. All rights reserved.
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.
Highly Dense Isolated Metal Atom Catalytic Sites

DEFF Research Database (Denmark)

Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei

2015-01-01

-ray diffraction. A combination of electron microscopy images with X-ray absorption spectra demonstrated that the silver atoms were anchored on five-fold oxygen-terminated cavities on the surface of the support to form highly dense isolated metal active sites, leading to excellent reactivity in catalytic oxidation......Atomically dispersed noble-metal catalysts with highly dense active sites are promising materials with which to maximise metal efficiency and to enhance catalytic performance; however, their fabrication remains challenging because metal atoms are prone to sintering, especially at a high metal...... loading. A dynamic process of formation of isolated metal atom catalytic sites on the surface of the support, which was achieved starting from silver nanoparticles by using a thermal surface-mediated diffusion method, was observed directly by using in situ electron microscopy and in situ synchrotron X...
Including lateral interactions into microkinetic models of catalytic reactions

DEFF Research Database (Denmark)

Hellman, Anders; Honkala, Johanna Karoliina

2007-01-01

In many catalytic reactions lateral interactions between adsorbates are believed to have a strong influence on the reaction rates. We apply a microkinetic model to explore the effect of lateral interactions and how to efficiently take them into account in a simple catalytic reaction. Three differ...... different approximations are investigated: site, mean-field, and quasichemical approximations. The obtained results are compared to accurate Monte Carlo numbers. In the end, we apply the approximations to a real catalytic reaction, namely, ammonia synthesis....
Processing and structural characterization of porous reforming catalytic films

International Nuclear Information System (INIS)

Hou Xianghui; Williams, Jey; Choy, Kwang-Leong

2006-01-01

Nickel-based catalysts are often used to reform methanol into hydrogen. The preparation and installation of these catalysts are costly and laborious. As an alternative, directly applying catalytic films onto the separator components can improve the manufacturing efficiency. This paper reports the successful deposition of adherent porous NiO-Al 2 O 3 -based catalytic films with well-controlled stoichiometry, using a single-step Aerosol Assisted Chemical Vapour Deposition (AACVD) method. The microstructure, composition and crystalline phase of the as-deposited catalytic films are characterized using a combination of X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and Fourier Transform Infrared (FTIR) Spectrometer. The results have demonstrated the capability of AACVD to produce porous NiO-Al 2 O 3 -based catalytic films
Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains.

Science.gov (United States)

Harper, Stephen; Gratton, Hayley E; Cornaciu, Irina; Oberer, Monika; Scott, David J; Emsley, Jonas; Dreveny, Ingrid

2014-05-13

The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFβ signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened β-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys(63)-, Lys(6)-, Lys(33)-, and Lys(11)-linked chains over Lys(27)-, Lys(29)-, and Lys(48)-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation.
Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated

DEFF Research Database (Denmark)

Nielsen (Baggesen), Lisbeth Munksgård; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

2013-01-01

. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups......, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see...
Catalytic conversion of ethanol on H-Y zeolite

Directory of Open Access Journals (Sweden)

Čegar Nedeljko

2005-01-01

Full Text Available The catalytic activity of the H-form of synthetic zeolite NaY was examined in this study. The catalytic activity was determined according to the rate of ethanol conversion in a gas phase in the static system. In the conversion of ethanol on synthetic NaY zeolite at 585, 595, and 610 K, on which the reaction develops at an optimal rate, ethene and diethyl ether are evolved in approximately the same quantity. After transforming the NaY zeolite into the H-form, its catalytic activity was extremely increases so, the reaction develops at a significantly lower temperature with a very large increase in the reaction rate. The distribution of the products also changes, so that at lower temperatures diethyl ether is elvolved in most cases, and the development of ethene is favored at higher ones, and after a certain period of time there is almost complete conversion of ethanol into ethene. The increase in catalytic activity, as well as the change of selectivity of conversion of ethanol on the H-form of zeolite, is the result of removing Na+ cations in the NaY zeolite, so that more acidic catalyst is obtained which contains a number of acidic catalytically active centers, as well as a more powerful one compared to the original NaY zeolite.
Catalytic characterization of bi-functional catalysts derived from Pd ...

Indian Academy of Sciences (India)

Unknown

1995; Lyubovsky and Pfefferle 1999; Sales et al 1999;. Hill et al 2000). ... For a catalytic system, whose activity ... catalytic systems containing Pd, supported on various acid- ..... Further studies are needed to optimize a balance between.
A critical role of a cellular membrane traffic protein in poliovirus RNA replication.

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George A Belov

2008-11-01

Full Text Available Replication of many RNA viruses is accompanied by extensive remodeling of intracellular membranes. In poliovirus-infected cells, ER and Golgi stacks disappear, while new clusters of vesicle-like structures form sites for viral RNA synthesis. Virus replication is inhibited by brefeldin A (BFA, implicating some components(s of the cellular secretory pathway in virus growth. Formation of characteristic vesicles induced by expression of viral proteins was not inhibited by BFA, but they were functionally deficient. GBF1, a guanine nucleotide exchange factor for the small cellular GTPases, Arf, is responsible for the sensitivity of virus infection to BFA, and is required for virus replication. Knockdown of GBF1 expression inhibited virus replication, which was rescued by catalytically active protein with an intact N-terminal sequence. We identified a mutation in GBF1 that allows growth of poliovirus in the presence of BFA. Interaction between GBF1 and viral protein 3A determined the outcome of infection in the presence of BFA.
Catalytic membrane in reduction of aqueous nitrates: operational principles and catalytic performance

NARCIS (Netherlands)

Ilinitch, O.M.; Cuperus, F.P.; Nosova, L.V.; Gribov, E.N.

2000-01-01

The catalytic membrane with palladium-copper active component supported over the macroporous ceramic membrane, and a series of γ-Al 2O 3 supported Pd-Cu catalysts were prepared and investigated. In reduction of nitrate ions by hydrogen in water at ambient temperature, pronounced internal diffusion
Hydrogen Production From catalytic reforming of greenhouse gases ...

African Journals Online (AJOL)

ADOWIE PERE

a fixed bed stainless steel reactor. The 20wt%. ... catalytic activity for hydrogen production with the highest yield and selectivity of 32.5% and 17.6% respectively. © JASEM ... CO2 reforming of methane is however not fully developed ..... Design and preparation of .... catalytic nickel membrane for gas to liquid (GTL) process.
Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

Directory of Open Access Journals (Sweden)

Hiraku Takada

Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons
A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms.

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Christiane Noronha Fernandes-Brum

Full Text Available microRNAs (miRNAs are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs are derived from double-stranded RNA (dsRNA or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL in processing the smallRNAs (sRNAs and ARGONAUTE (AGO as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR, Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated, and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.
Ultrasensitive and Facile Detection of MicroRNA via a Portable Pressure Meter.

Science.gov (United States)

Shi, Lu; Lei, Jing; Zhang, Bei; Li, Baoxin; Yang, Chaoyong James; Jin, Yan

2018-04-18

The upregulation of microRNA (miRNA) is highly related with some kinds of tumor, such as breast, prostate, lung, and pancreatic cancers. Therefore, for an important tumor biomarker, the point-of-care testing (POCT) of miRNA is of significant importance and is in great demand for disease diagnosis and clinical prognoses. Herein, a POCT assay for miRNA detection was developed via a portable pressure meter. Two hairpin DNA probes, H1 and H2, were ingeniously designed and functionalized with magnetic beads (MBs) and platinum nanoparticles (PtNPs), respectively, to form MBs-H1 and PtNPs-H2 complexes. In the presence of target microRNA 21 (miR-21), the cyclic strand displacement reaction (SDR) between MBs-H1 and PtNPs-H2 was triggered to continuously form the MBs-H1/PtNPs-H2 duplex. Owing to the amplification of cyclic SDR, numerous PtNPs were enriched onto the surface of MBs to catalytically decompose H 2 O 2 for the generation of much O 2 . The gas pressure value has a linear relationship with the logarithmic value of miR-21 concentration in the range of 10 fM to 10 pM. The limit of detection is 7.6 fM, which is more sensitive than that in a number of previous reports. Hairpin DNA probes and magnetic separation highly ensured the specificity and reliability. Single-base mutation was easily discriminated, and the detection of miR-21 in the serum sample achieved satisfactory result. Therefore, it offers a reliable POCT strategy for the detection of miRNA, which is of great theoretical and practical importance for POCT clinical diagnostics.

The RNA gene information: retroelement-microRNA entangling as the RNA quantum code.

Science.gov (United States)

Fujii, Yoichi Robertus

2013-01-01

MicroRNA (miRNA) and retroelements may be a master of regulator in our life, which are evolutionally involved in the origin of species. To support the Darwinism from the aspect of molecular evolution process, it has tremendously been interested in the molecular information of naive RNA. The RNA wave model 2000 consists of four concepts that have altered from original idea of the miRNA genes for crosstalk among embryonic stem cells, their niche cells, and retroelements as a carrier vesicle of the RNA genes. (1) the miRNA gene as a mobile genetic element induces transcriptional and posttranscriptional silencing via networking-processes (no hierarchical architecture); (2) the RNA information supplied by the miRNA genes expands to intracellular, intercellular, intraorgan, interorgan, intraspecies, and interspecies under the cycle of life into the global environment; (3) the mobile miRNAs can self-proliferate; and (4) cells contain two types information as resident and genomic miRNAs. Based on RNA wave, we have developed an interest in investigation of the transformation from RNA information to quantum bits as physicochemical characters of RNA with the measurement of RNA electron spin. When it would have been given that the fundamental bases for the acquired characters in genetics can be controlled by RNA gene information, it may be available to apply for challenging against RNA gene diseases, such as stress-induced diseases.
Enhanced propylene production in FCC by novel catalytic materials

Energy Technology Data Exchange (ETDEWEB)

Kelkar, C.P.; Harris, D.; Xu, M.; Fu, J. [BASF Catalyst LLC, Iselin, NJ (United States)

2007-07-01

Fluid catalytic cracking is expected to increasingly supply the additional incremental requirements for propylene. The most efficient route to increase propylene yield from an FCC unit is through the use of medium pore zeolites such as ZSM-5. ZSM-5 zeolite cracks near linear olefins in the gasoline range to LPG olefins such as propylene and butylenes. This paper will describe catalytic approaches to increase gasoline range olefins and the chemistry of ZSM-5 to crack those olefins. The paper will also describe novel catalytic materials designed to increase propylene. (orig.)
A study on naphtha catalytic reforming reactor simulation and analysis.

Science.gov (United States)

Liang, Ke-min; Guo, Hai-yan; Pan, Shi-wei

2005-06-01

A naphtha catalytic reforming unit with four reactors in series is analyzed. A physical model is proposed to describe the catalytic reforming radial flow reactor. Kinetics and thermodynamics equations are selected to describe the naphtha catalytic reforming reactions characteristics based on idealizing the complex naphtha mixture by representing the paraffin, naphthene, and aromatic groups by single compounds. The simulation results based above models agree very well with actual operation unit data.
A study on naphtha catalytic reforming reactor simulation and analysis

OpenAIRE

Liang, Ke-min; Guo, Hai-yan; Pan, Shi-wei

2005-01-01

A naphtha catalytic reforming unit with four reactors in series is analyzed. A physical model is proposed to describe the catalytic reforming radial flow reactor. Kinetics and thermodynamics equations are selected to describe the naphtha catalytic reforming reactions characteristics based on idealizing the complex naphtha mixture by representing the paraffin, naphthene, and aromatic groups by single compounds. The simulation results based above models agree very well with actual operation uni...
Catalytic hydrogen recombination for nuclear containments

International Nuclear Information System (INIS)

Koroll, G.W.; Lau, D.W.P.; Dewit, W.A.; Graham, W.R.C.

1994-01-01

Catalytic recombiners appear to be a credible option for hydrogen mitigation in nuclear containments. The passive operation, versatility and ease of back fitting are appealing for existing stations and new designs. Recently, a generation of wet-proofed catalyst materials have been developed at AECL which are highly specific to H 2 -O 2 , are active at ambient temperatures and are being evaluated for containment applications. Two types of catalytic recombiners were evaluated for hydrogen removal in containments based on the AECL catalyst. The first is a catalytic combustor for application in existing air streams such as provided by fans or ventilation systems. The second is an autocatalytic recombiner which uses the enthalpy of reaction to produce natural convective flow over the catalyst elements. Intermediate-scale results obtained in 6 m 3 and 10 m 3 spherical and cylindrical vessels are given to demonstrate self-starting limits, operating limits, removal capacity, scaling parameters, flow resistance, mixing behaviour in the vicinity of an operating recombiner and sensitivity to poisoning, fouling and radiation. (author). 13 refs., 10 figs
Electrochemical catalytic treatment of phenol wastewater

International Nuclear Information System (INIS)

Ma Hongzhu; Zhang Xinhai; Ma Qingliang; Wang Bo

2009-01-01

The slurry bed catalytic treatment of contaminated water appears to be a promising alternative for the oxidation of aqueous organic pollutants. In this paper, the electrochemical oxidation of phenol in synthetic wastewater catalyzed by ferric sulfate and potassium permanganate adsorbed onto active bentonite in slurry bed electrolytic reactor with graphite electrode has been investigated. In order to determine the optimum operating condition, the orthogonal experiments were devised and the results revealed that the system of ferric sulfate, potassium permanganate and active bentonite showed a high catalytic efficiency on the process of electrochemical oxidation phenol in initial pH 5. When the initial concentration of phenol was 0.52 g/L (the initial COD 1214 mg/L), up to 99% chemical oxygen demand (COD) removal was obtained in 40 min. According to the experimental results, a possible mechanism of catalytic degradation of phenol was proposed. Environmental estimation was also done and the results showed that the treated wastewater have little impact on plant growth and could totally be applied to irrigation.
Electrochemical catalytic treatment of phenol wastewater

Energy Technology Data Exchange (ETDEWEB)

Ma Hongzhu, E-mail: hzmachem@snnu.edu.cn [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Zhang Xinhai [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Ma Qingliang [Department of Applied Physics, College of Sciences, Taiyuan University of Technology, 030024 Taiyuan (China); Wang Bo [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China)

2009-06-15

The slurry bed catalytic treatment of contaminated water appears to be a promising alternative for the oxidation of aqueous organic pollutants. In this paper, the electrochemical oxidation of phenol in synthetic wastewater catalyzed by ferric sulfate and potassium permanganate adsorbed onto active bentonite in slurry bed electrolytic reactor with graphite electrode has been investigated. In order to determine the optimum operating condition, the orthogonal experiments were devised and the results revealed that the system of ferric sulfate, potassium permanganate and active bentonite showed a high catalytic efficiency on the process of electrochemical oxidation phenol in initial pH 5. When the initial concentration of phenol was 0.52 g/L (the initial COD 1214 mg/L), up to 99% chemical oxygen demand (COD) removal was obtained in 40 min. According to the experimental results, a possible mechanism of catalytic degradation of phenol was proposed. Environmental estimation was also done and the results showed that the treated wastewater have little impact on plant growth and could totally be applied to irrigation.
Sintering of Catalytic Nanoparticles: Particle Migration or Ostwald Ripening?

DEFF Research Database (Denmark)

Hansen, Thomas Willum; DeLaRiva, Andrew T.; Challa, Sivakumar R.

2013-01-01

deactivation, is an important mechanism for the loss of catalyst activity. This is especially true for high temperature catalytic processes, such as steam reforming, automotive exhaust treatment, or catalytic combustion. With dwindling supplies of precious metals and increasing demand, fundamental...
Catalytic synthesis of ammonia using vibrationally excited nitrogen molecules

DEFF Research Database (Denmark)

Hansen, Flemming Yssing; Henriksen, Niels Engholm; Billing, Gert D.

1992-01-01

The dissociation of nitrogen is the rate-limiting step in the catalytic synthesis of ammonia. Theoretical calculations have shown that the dissociative sticking probability of molecular nitrogen on catalytic active metal surfaces is enhanced by orders of magnitude when the molecules...
The RNA-mediated, asymmetric ring regulatory mechanism of the transcription termination Rho helicase decrypted by time-resolved nucleotide analog interference probing (trNAIP).

Science.gov (United States)

Soares, Emilie; Schwartz, Annie; Nollmann, Marcello; Margeat, Emmanuel; Boudvillain, Marc

2014-08-01

Rho is a ring-shaped, ATP-dependent RNA helicase/translocase that dissociates transcriptional complexes in bacteria. How RNA recognition is coupled to ATP hydrolysis and translocation in Rho is unclear. Here, we develop and use a new combinatorial approach, called time-resolved Nucleotide Analog Interference Probing (trNAIP), to unmask RNA molecular determinants of catalytic Rho function. We identify a regulatory step in the translocation cycle involving recruitment of the 2'-hydroxyl group of the incoming 3'-RNA nucleotide by a Rho subunit. We propose that this step arises from the intrinsic weakness of one of the subunit interfaces caused by asymmetric, split-ring arrangement of primary RNA tethers around the Rho hexamer. Translocation is at highest stake every seventh nucleotide when the weak interface engages the incoming 3'-RNA nucleotide or breaks, depending on RNA threading constraints in the Rho pore. This substrate-governed, 'test to run' iterative mechanism offers a new perspective on how a ring-translocase may function or be regulated. It also illustrates the interest and versatility of the new trNAIP methodology to unveil the molecular mechanisms of complex RNA-based systems. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Novel synthetic Medea selfish genetic elements drive population replacement in Drosophila; a theoretical exploration of Medea-dependent population suppression.

Science.gov (United States)

Akbari, Omar S; Chen, Chun-Hong; Marshall, John M; Huang, Haixia; Antoshechkin, Igor; Hay, Bruce A

2014-12-19

Insects act as vectors for diseases of plants, animals, and humans. Replacement of wild insect populations with genetically modified individuals unable to transmit disease provides a potentially self-perpetuating method of disease prevention. Population replacement requires a gene drive mechanism in order to spread linked genes mediating disease refractoriness through wild populations. We previously reported the creation of synthetic Medea selfish genetic elements able to drive population replacement in Drosophila. These elements use microRNA-mediated silencing of myd88, a maternally expressed gene required for embryonic dorso-ventral pattern formation, coupled with early zygotic expression of a rescuing transgene, to bring about gene drive. Medea elements that work through additional mechanisms are needed in order to be able to carry out cycles of population replacement and/or remove existing transgenes from the population, using second-generation elements that spread while driving first-generation elements out of the population. Here we report the synthesis and population genetic behavior of two new synthetic Medea elements that drive population replacement through manipulation of signaling pathways involved in cellular blastoderm formation or Notch signaling, demonstrating that in Drosophila Medea elements can be generated through manipulation of diverse signaling pathways. We also describe the mRNA and small RNA changes in ovaries and early embryos associated from Medea-bearing females. Finally, we use modeling to illustrate how Medea elements carrying genes that result in diapause-dependent female lethality could be used to bring about population suppression.
Binding interactions between yeast tRNA ligase and a precursor transfer ribonucleic acid containing two photoreactive uridine analogues

International Nuclear Information System (INIS)

Tanner, N.K.; Hanna, M.M.; Abelson, J.

1988-01-01

Yeast tRNA ligase, from Saccharomyces cerevisiae, is one of the protein components that is involved in the splicing reaction of intron-containing yeast precursor tRNAs. It is an unusual protein because it has three distinct catalytic activities. It functions as a polynucleotide kinase, as a cyclic phosphodiesterase, and as an RNA ligase. We have studied the binding interactions between ligase and precursor tRNAs containing two photoreactive uridine analogues, 4-thiouridine and 5-bromouridine. When irradiated with long ultraviolet light, RNA containing these analogues can form specific covalent bonds with associated proteins. In this paper, we show that 4-thiouridine triphosphate and 5-bromouridine triphosphate were readily incorporated into a precursor tRNA(Phe) that was synthesized, in vitro, with bacteriophage T7 RNA polymerase. The analogue-containing precursor tRNAs were authentic substrates for the two splicing enzymes that were tested (endonuclease and ligase), and they formed specific covalent bonds with ligase when they were irradiated with long-wavelength ultraviolet light. We have determined the position of three major cross-links and one minor cross-link on precursor tRNA(Phe) that were located within the intron and near the 3' splice site. On the basis of these data, we present a model for the in vivo splicing reaction of yeast precursor tRNAs
Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

Science.gov (United States)

Weinberg, Marc S.; Michod, Richard E.

2017-01-01

In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3′ end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life. PMID:28989747
Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

Science.gov (United States)

Dhar, Nisha; Weinberg, Marc S.; Michod, Richard E.; Durand, Pierre M.

2017-09-01

In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3' end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life.
Surveillance of siRNA integrity by FRET imaging

Science.gov (United States)

Järve, Anne; Müller, Julius; Kim, Il-Han; Rohr, Karl; MacLean, Caroline; Fricker, Gert; Massing, Ulrich; Eberle, Florian; Dalpke, Alexander; Fischer, Roger; Trendelenburg, Michael F.; Helm, Mark

2007-01-01

Techniques for investigation of exogenous small interfering RNA (siRNA) after penetration of the cell are of substantial interest to the development of efficient transfection methods as well as to potential medical formulations of siRNA. A FRET-based visualization method including the commonplace dye labels fluorescein and tetramethylrhodamin (TMR) on opposing strands of siRNA was found compatible with RNA interference (RNAi). Investigation of spectral properties of three labelled siRNAs with differential FRET efficiencies in the cuvette, including pH dependence and FRET efficiency in lipophilic environments, identified the ratio of red and green fluorescence (R/G-ratio) as a sensitive parameter, which reliably identifies samples containing >90% un-degraded siRNA. Spectral imaging of siRNAs microinjected into cells showed emission spectra indistinguishable from those measured in the cuvette. These were used to establish a calibration curve for assessing the degradation state of siRNA in volume elements inside cells. An algorithm, applied to fluorescence images recorded in standard green and red fluorescence channels, produces R/G-ratio images of high spatial resolution, identifying volume elements in the cell with high populations of intact siRNA with high fidelity. To demonstrate the usefulness of this technique, the movement of intact siRNA molecules are observed after introduction into the cytosol by microinjection, standard transfection and lipofection with liposomes. PMID:17890733
Catalytic Wastewater Treatment Using Pillared Clays

Science.gov (United States)

Perathoner, Siglinda; Centi, Gabriele

After introduction on the use of solid catalysts in wastewater treatment technologies, particularly advanced oxidation processes (AOPs), this review discussed the use of pillared clay (PILC) materials in three applications: (i) wet air catalytic oxidation (WACO), (ii) wet hydrogen peroxide catalytic oxidation (WHPCO) on Cu-PILC and Fe-PILC, and (iii) behavior of Ti-PILC and Fe-PILC in the photocatalytic or photo-Fenton conversion of pollutants. Literature data are critically analyzed to evidence the main direction to further investigate, in particularly with reference to the possible practical application of these technologies to treat industrial, municipal, or agro-food production wastewater.
MicroRNA-encoding long non-coding RNAs

Directory of Open Access Journals (Sweden)

Zhu Xiaopeng

2008-05-01

Full Text Available Abstract Background Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs. Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. Results A few ml-ncRNA have been shown to have genomic loci that overlap with microRNA loci, leading us to suspect that a fraction of ml-ncRNA may encode microRNAs. We therefore developed an algorithm (PriMir for specifically detecting potential microRNA-encoding transcripts in the entire set of 34,030 mouse full-length ml-ncRNAs. In combination with mouse-rat sequence conservation, this algorithm detected 97 (80 of them were novel strong miRNA-encoding candidates, and for 52 of these we obtained experimental evidence for the existence of their corresponding mature microRNA by microarray and stem-loop RT-PCR. Sequence analysis of the microRNA-encoding RNAs revealed an internal motif, whose presence correlates strongly (R2 = 0.9, P-value = 2.2 × 10-16 with the occurrence of stem-loops with characteristics of known pre-miRNAs, indicating the presence of a larger number microRNA-encoding RNAs (from 300 up to 800 in the ml-ncRNAs population. Conclusion Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.
Reactivity of organic compounds in catalytic synthesis

Energy Technology Data Exchange (ETDEWEB)

Minachev, Kh M; Bragin, O V

1978-01-01

A comprehensive review of 1976 Soviet research on catalysis delivered to the 1977 annual session of the USSR Academy of Science Council on Catalysis (Baku 6/16-20/77) covers hydrocarbon reactions, including hydrogenation and hydrogenolysis, dehydrogenation, olefin dimerization and disproportionation, and cyclization and dehydrocyclization (e.g., piperylene cyclization and ethylene cyclotrimerization); catalytic and physicochemical properties of zeolites, including cracking, dehydrogenation, and hydroisomerization catalytic syntheses and conversion of heterocyclic and functional hydrocarbon derivatives, including partial and total oxidation (e.g., of o-xylene to phthalic anhydride); syntheses of thiophenes from alkanes and hydrogen sulfide over certain dehydrogenation catalysts; catalytic syntheses involving carbon oxides ( e.g., the development of a new heterogeneous catalyst for hydroformylation of olefins), and of Co-MgO zeolitic catalysts for synthesis of aliphatic hydrocarbons from carbon dioxide and hydrogen, and fabrication of high-viscosity lubricating oils over bifunctional aluminosilicate catalysts.
Component Development to Accelerate Commercial Implementation of Ultra-Low Emissions Catalytic Combustion

Energy Technology Data Exchange (ETDEWEB)

McCarty, Jon; Berry, Brian; Lundberg, Kare; Anson, Orris

2003-03-31

This final report describes a 2000-2003 program for the development of components and processes to enhance the commercialization of ultra-low emissions catalytic combustion in industrial gas turbines. The range of project tasks includes: development of more durable, lower-cost catalysts and catalytic combustor components; development and design of a catalytic pre-burner and a catalytic pilot burner for gas turbines, and on-site fuel conversion processing for utilization of liquid fuel.
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis

International Nuclear Information System (INIS)

Greenwood, Alexander I.; Rogals, Monique J.; De, Soumya; Lu, Kun Ping; Kovrigin, Evgenii L.; Nicholson, Linda K.

2011-01-01

The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation, rigorous enzymatic assays of isomerization are required. However, most measures of isomerase activity require significant constraints on substrate sequence and only yield rate constants for the cis isomer, k cat cis and apparent Michaelis constants, K M App . By contrast, NMR lineshape analysis is a powerful tool for determining microscopic rates and populations of each state in a complex binding scheme. The isolated catalytic domain of Pin1 was employed as a first step towards elucidating the reaction scheme of the full-length enzyme. A 24-residue phosphopeptide derived from the amyloid precurser protein intracellular domain (AICD) phosphorylated at Thr668 served as a biologically-relevant Pin1 substrate. Specific 13 C labeling at the Pin1-targeted proline residue provided multiple reporters sensitive to individual isomer binding and on-enzyme catalysis. We have performed titration experiments and employed lineshape analysis of phosphopeptide 13 C– 1 H constant time HSQC spectra to determine k cat cis , k cat trans , K D cis , and K D trans for the catalytic domain of Pin1 acting on this AICD substrate. The on-enzyme equilibrium value of [E·trans]/[E·cis] = 3.9 suggests that the catalytic domain of Pin1 is optimized to operate on this substrate near equilibrium in the cellular context. This highlights the power of lineshape analysis for determining the microscopic parameters of enzyme catalysis, and demonstrates the feasibility of future studies of Pin1-PPIase mutants to gain insights on the catalytic mechanism of this important enzyme.

Catalytic Conversion of Biofuels

DEFF Research Database (Denmark)

Jørgensen, Betina

This thesis describes the catalytic conversion of bioethanol into higher value chemicals. The motivation has been the unavoidable coming depletion of the fossil resources. The thesis is focused on two ways of utilising ethanol; the steam reforming of ethanol to form hydrogen and the partial oxida...
Direct catalytic hydrothermal liquefaction of spirulina to biofuels with hydrogen

Science.gov (United States)

Zeng, Qin; Liao, Hansheng; Zhou, Shiqin; Li, Qiuping; Wang, Lu; Yu, Zhihao; Jing, Li

2018-01-01

We report herein on acquiring biofuels from direct catalytic hydrothermal liquefaction of spirulina. The component of bio-oil from direct catalytic hydrothermal liquefaction was similar to that from two independent processes (including liquefaction and upgrading of biocrude). However, one step process has higher carbon recovery, due to the less loss of carbons. It was demonstrated that the yield and HHV of bio-oil from direct catalytic algae with hydrothermal condition is higher than that from two independent processes.
Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

Science.gov (United States)

Hardcastle, Thomas J; Müller, Sebastian Y; Baulcombe, David C

2018-04-20

Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.
Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2.

Science.gov (United States)

Absmeier, Eva; Becke, Christian; Wollenhaupt, Jan; Santos, Karine F; Wahl, Markus C

2017-01-02

RNA helicase Brr2 is implicated in multiple phases of pre-mRNA splicing and thus requires tight regulation. Brr2 can be auto-inhibited via a large N-terminal region folding back onto its helicase core and auto-activated by a catalytically inactive C-terminal helicase cassette. Furthermore, it can be regulated in trans by the Jab1 domain of the Prp8 protein, which can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Presently it is unclear, whether these regulatory mechanisms functionally interact and to which extent they are evolutionarily conserved. Here, we report crystal structures of Saccharomyces cerevisiae and Chaetomium thermophilum Brr2-Jab1 complexes, demonstrating that Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented via organism-specific molecular contacts. Moreover, the structures show that Brr2 auto-inhibition can act in concert with Jab1-mediated inhibition, and suggest that the N-terminal region influences how the Jab1 C-terminal tail interacts at the RNA-binding tunnel. Systematic RNA binding and unwinding studies revealed that the N-terminal region and the Jab1 C-terminal tail specifically interfere with accommodation of double-stranded and single-stranded regions of an RNA substrate, respectively, mutually reinforcing each other. Additionally, such analyses show that regulation based on the N-terminal region requires the presence of the inactive C-terminal helicase cassette. Together, our results outline an intricate system of regulatory mechanisms, which control Brr2 activities during snRNP assembly and splicing.
Novel Synthetic Medea selfish genetic elements drive population replacement in Drosophila, and a theoretical exploration of Medea-dependent population suppression

Science.gov (United States)

Akbari, Omar S.; Chen, Chun-Hong; Marshall, John M.; Huang, Haixia; Antoshechkin, Igor; Hay, Bruce A.

2013-01-01

Insects act as vectors for diseases of plants, animals and humans. Replacement of wild insect populations with genetically modified individuals unable to transmit disease provides a potentially self-perpetuating method of disease prevention. Population replacement requires a gene drive mechanism in order to spread linked genes mediating disease refractoriness through wild populations. We previously reported the creation of synthetic Medea selfish genetic elements able to drive population replacement in Drosophila. These elements use microRNA-mediated silencing of myd88, a maternally expressed gene required for embryonic dorso-ventral pattern formation, coupled with early zygotic expression of a rescuing transgene, to bring about gene drive. Medea elements that work through additional mechanisms are needed in order to be able to carry out cycles of population replacement and/or remove existing transgenes from the population, using second-generation elements that spread while driving first-generation elements out of the population. Here we report the synthesis and population genetic behavior of two new synthetic Medea elements that drive population replacement through manipulation of signaling pathways involved in cellular blastoderm formation or Notch signaling, demonstrating that in Drosophila Medea elements can be generated through manipulation of diverse signaling pathways. We also describe the mRNA and small RNA changes in ovaries and early embryos associated from Medea-bearing females. Finally, we use modeling to illustrate how Medea elements carrying genes that result in diapause-dependent female lethality could be used to bring about population suppression. PMID:23654248
Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1.

Directory of Open Access Journals (Sweden)

Luis Apolonia

2015-01-01

Full Text Available The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 proteins are cell-encoded cytidine deaminases, some of which, such as APOBEC3G (A3G and APOBEC3F (A3F, act as potent human immunodeficiency virus type-1 (HIV-1 restriction factors. These proteins require packaging into HIV-1 particles to exert their antiviral activities, but the molecular mechanism by which this occurs is incompletely understood. The nucleocapsid (NC region of HIV-1 Gag is required for efficient incorporation of A3G and A3F, and the interaction between A3G and NC has previously been shown to be RNA-dependent. Here, we address this issue in detail by first determining which RNAs are able to bind to A3G and A3F in HV-1 infected cells, as well as in cell-free virions, using the unbiased individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP method. We show that A3G and A3F bind many different types of RNA, including HIV-1 RNA, cellular mRNAs and small non-coding RNAs such as the Y or 7SL RNAs. Interestingly, A3G/F incorporation is unaffected when the levels of packaged HIV-1 genomic RNA (gRNA and 7SL RNA are reduced, implying that these RNAs are not essential for efficient A3G/F packaging. Confirming earlier work, HIV-1 particles formed with Gag lacking the NC domain (Gag ΔNC fail to encapsidate A3G/F. Here, we exploit this system by demonstrating that the addition of an assortment of heterologous RNA-binding proteins and domains to Gag ΔNC efficiently restored A3G/F packaging, indicating that A3G and A3F have the ability to engage multiple RNAs to ensure viral encapsidation. We propose that the rather indiscriminate RNA binding characteristics of A3G and A3F promote functionality by enabling recruitment into a wide range of retroviral particles whose packaged RNA genomes comprise divergent sequences.
Highly efficient catalytic systems based on Pd-coated microbeads

Science.gov (United States)

Lim, Jin Hyun; Cho, Ahyoung; Lee, Seung Hwan; Park, Bumkyo; Kang, Dong Woo; Koo, Chong Min; Yu, Taekyung; Park, Bum Jun

2018-01-01

The efficiency of two prototype catalysis systems using palladium (Pd)-coated microparticles was investigated with regard to the recovery and recyclability of the catalytic particles. One such system was the interface-adsorption method, in which polymer particles coated with Pd nanoparticles strongly and irreversibly attach to the oil-water interface. Due to the irreversible adsorption of the catalytic particles to the interface, particle loss was completely prevented while mixing the aqueous solution and while collecting the products. The other system was based on the magnetic field-associated particle recovery method. The use of polymeric microparticles containing Pd nanoparticles and magnetite nanoparticles accelerated the sedimentation of the particles in the aqueous phase by applying a strong magnetic field, consequently suppressing drainage of the particles from the reactor along the product stream. Upon multiple runs of the catalytic reactions, it was found that conversion does not change significantly, demonstrating the excellent recyclability and performance efficiency in the catalytic processes.
Catalytic pyrolysis of microalgae to high-quality liquid bio-fuels

International Nuclear Information System (INIS)

Babich, I.V.; Hulst, M. van der; Lefferts, L.; Moulijn, J.A.; O'Connor, P.; Seshan, K.

2011-01-01

The pyrolytic conversion of chlorella algae to liquid fuel precursor in presence of a catalyst (Na 2 CO 3 ) has been studied. Thermal decomposition studies of the algae samples were performed using TGA coupled with MS. Liquid oil samples were collected from pyrolysis experiments in a fixed-bed reactor and characterized for water content and heating value. The oil composition was analyzed by GC-MS. Pretreatment of chlorella with Na 2 CO 3 influences the primary conversion of chlorella by shifting the decomposition temperature to a lower value. In the presence of Na 2 CO 3 , gas yield increased and liquid yield decreased when compared with non-catalytic pyrolysis at the same temperatures. However, pyrolysis oil from catalytic runs carries higher heating value and lower acidity. Lower content of acids in the bio-oil, higher aromatics, combined with higher heating value show promise for production of high-quality bio-oil from algae via catalytic pyrolysis, resulting in energy recovery in bio-oil of 40%. -- Highlights: → The pyrolytic catalytic conversion of chlorella algae to liquid fuel precursor. → Na 2 CO 3 as a catalyst for the primary conversion of chlorella. → Pyrolysis oil from catalytic runs carries higher heating value and lower acidity. → High-quality bio-oil from algae via catalytic pyrolysis with energy recovery in bio-oil of 40%.
Multi-Stage Selective Catalytic Reduction of NOx in Lean-Burn Engine Exhaust

National Research Council Canada - National Science Library

Penetrante, B

1997-01-01

.... A plasma can also be used to oxidize NO to NO2. This paper compares the multi-stage catalytic scheme with the plasma-assisted catalytic scheme for reduction of NOx in lean-burn engine exhausts. The advantages of plasma oxidation over catalytic oxidation are presented.
RNA-SSPT: RNA Secondary Structure Prediction Tools.

Science.gov (United States)

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.
Green technology for conversion of renewable hydrocarbon based on plasma-catalytic approach

Science.gov (United States)

Fedirchyk, Igor; Nedybaliuk, Oleg; Chernyak, Valeriy; Demchina, Valentina

2016-09-01

The ability to convert renewable biomass into fuels and chemicals is one of the most important steps on our path to green technology and sustainable development. However, the complex composition of biomass poses a major problem for established conversion technologies. The high temperature of thermochemical biomass conversion often leads to the appearance of undesirable byproducts and waste. The catalytic conversion has reduced yield and feedstock range. Plasma-catalytic reforming technology opens a new path for biomass conversion by replacing feedstock-specific catalysts with free radicals generated in the plasma. We studied the plasma-catalytic conversion of several renewable hydrocarbons using the air plasma created by rotating gliding discharge. We found that plasma-catalytic hydrocarbon conversion can be conducted at significantly lower temperatures (500 K) than during the thermochemical ( 1000 K) and catalytic (800 K) conversion. By using gas chromatography, we determined conversion products and found that conversion efficiency of plasma-catalytic conversion reaches over 85%. We used obtained data to determine the energy yield of hydrogen in case of plasma-catalytic reforming of ethanol and compared it with other plasma-based hydrogen-generating systems.
Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

Energy Technology Data Exchange (ETDEWEB)

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.
A Novel Regulator of Activation-Induced Cytidine Deaminase/APOBECs in Immunity and Cancer: Schrödinger’s CATalytic Pocket

Directory of Open Access Journals (Sweden)

Mani Larijani

2017-04-01

Full Text Available Activation-induced cytidine deaminase (AID and its relative APOBEC3 cytidine deaminases boost immune response by mutating immune or viral genes. Because of their genome-mutating activities, AID/APOBECs are also drivers of tumorigenesis. Due to highly charged surfaces, extensive non-specific protein–protein/nucleic acid interactions, formation of polydisperse oligomers, and general insolubility, structure elucidation of these proteins by X-ray crystallography and NMR has been challenging. Hence, almost all available AID/APOBEC structures are of mutated and/or truncated versions. In 2015, we reported a functional structure for AID using a combined computational–biochemical approach. In so doing, we described a new regulatory mechanism that is a first for human DNA/RNA-editing enzymes. This mechanism involves dynamic closure of the catalytic pocket. Subsequent X-ray and NMR studies confirmed our discovery by showing that other APOBEC3s also close their catalytic pockets. Here, we highlight catalytic pocket closure as an emerging and important regulatory mechanism of AID/APOBEC3s. We focus on three sub-topics: first, we propose that variable pocket closure rates across AID/APOBEC3s underlie differential activity in immunity and cancer and review supporting evidence. Second, we discuss dynamic pocket closure as an ever-present internal regulator, in contrast to other proposed regulatory mechanisms that involve extrinsic binding partners. Third, we compare the merits of classical approaches of X-ray and NMR, with that of emerging computational–biochemical approaches, for structural elucidation specifically for AID/APOBEC3s.
Catalytic Upgrading of Sugars to Hydrocarbons Technology Pathway

Energy Technology Data Exchange (ETDEWEB)

Biddy, M.; Jones, S.

2013-03-01

This technology pathway case investigates the catalytic conversion of solubilized carbohydrate streams to hydrocarbon biofuels, utilizing data from recent efforts within the National Advanced Biofuels Consortium (NABC) in collaboration with Virent, Inc. Technical barriers and key research needs that should be pursued for the catalytic conversion of sugars pathway to be competitive with petroleum-derived gasoline-, diesel-, and jet-range hydrocarbon blendstocks have been identified.
Zinc-mediated binding of a low-molecular-weight stabilizer of the host anti-viral factor apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G.

Science.gov (United States)

Radwan, Mohamed O; Sonoda, Sachiko; Ejima, Tomohiko; Tanaka, Ayumi; Koga, Ryoko; Okamoto, Yoshinari; Fujita, Mikako; Otsuka, Masami

2016-09-15

Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G, A3G), is a human anti-virus restriction protein which works deaminase-dependently and -independently. A3G is known to be ubiquitinated by HIV-1 viral infectivity factor (Vif) protein, leading to proteasomal degradation. A3G contains two zinc ions at the N-terminal domain and the C-terminal domain. Four lysine residues, K(297), K(301), K(303), and K(334), are known to be required for Vif-mediated A3G ubiquitination and degradation. Previously, we reported compound SN-1, a zinc chelator that increases steady-state expression level of A3G in the presence of Vif. In this study, we prepared Biotin-SN-1, a biotinylated derivative of SN-1, to study the SN-1-A3G interaction. A pull-down assay revealed that Biotin-SN-1 bound A3G. A zinc-abstraction experiment indicated that SN-1 binds to the zinc site of A3G. We carried out a SN-1-A3G docking study using molecular operating environment. The calculations revealed that SN-1 binds to the C-terminal domain through Zn(2+), H(216), P(247), C(288), and Y(315). Notably, SN-1-binding covers the H(257), E(259), C(288), and C(291) residues that participate in zinc-mediated deamination, and the ubiquitination regions of A3G. The binding of SN-1 presumably perturbs the secondary structure between C(288) and Y(315), leading to less efficient ubiquitination. Copyright © 2016 Elsevier Ltd. All rights reserved.
Combinatorics of RNA-RNA interaction

DEFF Research Database (Denmark)

Li, Thomas J X; Reidys, Christian

2012-01-01

RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...
Janus droplet as a catalytic micromotor

Science.gov (United States)

Shklyaev, Sergey

2015-06-01

Self-propulsion of a Janus droplet in a solution of surfactant, which reacts on a half of a drop surface, is studied theoretically. The droplet acts as a catalytic motor creating a concentration gradient, which generates its surface-tension-driven motion; the self-propulsion speed is rather high, 60 μ \\text{m/s} and more. This catalytic motor has several advantages over other micromotors: simple manufacturing, easily attained neutral buoyancy. In contrast to a single-fluid droplet, which demonstrates a self-propulsion as a result of symmetry breaking instability, for the Janus one no stability threshold exists; hence, the droplet radius can be scaled down to micrometers.
Hydrogen production via catalytic processing of renewable feedstocks

International Nuclear Information System (INIS)

Nazim Muradov; Franklyn Smith; Ali T-Raissi

2006-01-01

Landfill gas (LFG) and biogas can potentially become important feedstocks for renewable hydrogen production. The objectives of this work were: (1) to develop a catalytic process for direct reforming of CH 4 -CO 2 gaseous mixture mimicking LFG, (2) perform thermodynamic analysis of the reforming process using AspenPlus chemical process simulator, (3) determine operational conditions for auto-thermal (or thermo-neutral) reforming of a model CH 4 -CO 2 feedstock, and (4) fabricate and test a bench-scale hydrogen production unit. Experimental data obtained from catalytic reformation of the CH 4 -CO 2 and CH 4 -CO 2 -O 2 gaseous mixtures using Ni-catalyst were in a good agreement with the simulation results. It was demonstrated that catalytic reforming of LFG-mimicking gas produced hydrogen with the purity of 99.9 vol.%. (authors)
Heterogeneous-catalytic redox reactions in nitrate - formate systems

International Nuclear Information System (INIS)

Ananiev, A.V.; Shilov, V.P.; Tananaev, I.G.; Brossard, Ph.; Broudic, J.Ch.

2000-01-01

It was found that an intensive destruction of various organic and mineral substances - usual components of aqueous waste solutions (oxalic acid, complexones, urea, hydrazine, ammonium nitrate, etc.) takes place under the conditions of catalytic denitration. Kinetics and mechanisms of urea and ammonium nitrate decomposition in the system HNO 3 - HCOOH - Pt/SiO 2 are comprehensively investigated. The behaviour of uranium, neptunium and plutonium under the conditions of catalytic denitration is studied. It is shown, that under the certain conditions the formic acid is an effective reducer of the uranium (VI), neptunium (VI, V) and plutonium (VI, IV) ions. Kinetics of heterogeneous-catalytic red-ox reactions of uranium (VI), neptunium (VI, V) and plutonium (VI, IV) with formic acid are investigated. The mechanisms of the appropriate reactions are evaluated. (authors)
Catalytic flash pyrolysis of oil-impregnated-wood and jatropha cake using sodium based catalysts

NARCIS (Netherlands)

Ali Imran, A.; Bramer, Eduard A.; Seshan, Kulathuiyer; Brem, Gerrit

2016-01-01

Catalytic pyrolysis of wood with impregnated vegetable oil was investigated and compared with catalytic pyrolysis of jatropha cake making use of sodium based catalysts to produce a high quality bio-oil. The catalytic pyrolysis was carried out in two modes: in-situ catalytic pyrolysis and post

Two regulatory RNA elements affect TisB-dependent depolarization and persister formation.

Science.gov (United States)

Berghoff, Bork A; Hoekzema, Mirthe; Aulbach, Lena; Wagner, E Gerhart H

2017-03-01

Bacterial survival strategies involve phenotypic diversity which is generated by regulatory factors and noisy expression of effector proteins. The question of how bacteria exploit regulatory RNAs to make decisions between phenotypes is central to a general understanding of these universal regulators. We investigated the TisB/IstR-1 toxin-antitoxin system of Escherichia coli to appreciate the role of the RNA antitoxin IstR-1 in TisB-dependent depolarization of the inner membrane and persister formation. Persisters are phenotypic variants that have become transiently drug-tolerant by arresting growth. The RNA antitoxin IstR-1 sets a threshold for TisB-dependent depolarization under DNA-damaging conditions, resulting in two sub-populations: polarized and depolarized cells. Furthermore, our data indicate that an inhibitory 5' UTR structure in the tisB mRNA serves as a regulatory RNA element that delays TisB translation to avoid inappropriate depolarization when DNA damage is low. Investigation of the persister sub-population further revealed that both regulatory RNA elements affect persister levels as well as persistence time. This work provides an intriguing example of how bacteria exploit regulatory RNAs to control phenotypic heterogeneity. © 2016 John Wiley & Sons Ltd.
Catalytic copyrolysis of cork oak and bio-oil distillation residue

Science.gov (United States)

Lee, Yejin; Oh, Daejun; Kim, Young-Min; Jae, Jungho; Jung, Sang-Chul; Jeon, Jong-Ki; Kim, Sang Chai; Park, Young-Kwon

2018-01-01

The atmospheric distillation residue (ADR) of cork oak (CO) pyrolysis oil was used as the co-feeding material for the catalytic pyrolysis of CO over HZSM-5 catalysts to improve the formation of aromatic hydrocarbons. Although the non-catalytic copyrolysis of CO and ADR did not improve the formation of aromatic hydrocarbons, the catalytic copyrolysis of CO and ADR promoted the synergistic formation of aromatic hydrocarbons. HZSM-5(30), having a lower SiO2/Al2O3(30), showed better performance for the formation of aromatic hydrocarbons than HZSM-5(80) because of its higher acidity. The catalytic copyrolysis of CO and ADR also decreased the formation of coke. The largest quantity of aromatic hydrocarbons was obtained from the catalytic copyrolysis of CO and ADR over HZSM-5 (30) at 600 °C, whereas the lowest coke yield was achieved at 700 °C. When the catalyst to sample ratio was increased from 2:1 to 5:1, the synergistic formation of aromatic hydrocarbons was limited, resulting in a lower experimental yield of aromatic hydrocarbons than the theoretical yield. A lower coke yield was also achieved at a high catalyst to sample ratio (5:1).
Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.

Directory of Open Access Journals (Sweden)

Pablo Cordero

2015-11-01

Full Text Available Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral infection [corrected]. We report herein that high-throughput chemical experiments can isolate an RNA's multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2 and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states' structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10% and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization.
Screening of Active Lyssavirus Infection in Wild Bat Populations by Viral RNA Detection on Oropharyngeal Swabs

Science.gov (United States)

Echevarría, Juan E.; Avellón, Ana; Juste, Javier; Vera, Manuel; Ibáñez, Carlos

2001-01-01

Brain analysis cannot be used for the investigation of active lyssavirus infection in healthy bats because most bat species are protected by conservation directives. Consequently, serology remains the only tool for performing virological studies on natural bat populations; however, the presence of antibodies merely reflects past exposure to the virus and is not a valid marker of active infection. This work describes a new nested reverse transcription (RT)-PCR technique specifically designed for the detection of the European bat virus 1 on oropharyngeal swabs obtained from bats but also able to amplify RNA from the remaining rabies-related lyssaviruses in brain samples. The technique was successfully used for surveillance of a serotine bat (Eptesicus serotinus) colony involved in a case of human exposure, in which 15 out of 71 oropharyngeal swabs were positive. Lyssavirus infection was detected on 13 oropharyngeal swabs but in only 5 brains out of the 34 animals from which simultaneous brain and oropharyngeal samples had been taken. The lyssavirus involved could be rapidly identified by automatic sequencing of the RT-PCR products obtained from 14 brains and three bat oropharyngeal swabs. In conclusion, RT-PCR using oropharyngeal swabs will permit screening of wild bat populations for active lyssavirus infection, for research or epidemiological purposes, in line not only with conservation policies but also in a more efficient manner than classical detection techniques used on the brain. PMID:11574590
Thermal and catalytic pyrolysis of plastic waste

Directory of Open Access Journals (Sweden)

Débora Almeida

2016-02-01

Full Text Available Abstract The amount of plastic waste is growing every year and with that comes an environmental concern regarding this problem. Pyrolysis as a tertiary recycling process is presented as a solution. Pyrolysis can be thermal or catalytical and can be performed under different experimental conditions. These conditions affect the type and amount of product obtained. With the pyrolysis process, products can be obtained with high added value, such as fuel oils and feedstock for new products. Zeolites can be used as catalysts in catalytic pyrolysis and influence the final products obtained.
Using electron beams to investigate catalytic materials

International Nuclear Information System (INIS)

Zhang, Bingsen; Su, Dang Sheng

2014-01-01

Transmission Electron microscopy (TEM) enables us, not only to reveal the morphology, but also to provide structural, chemical and electronic information about solid catalysts at the atomic level, providing a dramatic driving force for the development of heterogeneous catalysis. Almost all catalytic materials have been studied with TEM in order to obtain information about their structures, which can help us to establish the synthesis-structure-property relationships and to design catalysts with new structures and desired properties. Herein, several examples will be reviewed to illustrate the investigation of catalytic materials by using electron beams. (authors)
Engineering reactors for catalytic reactions

Indian Academy of Sciences (India)

126, No. 2, March 2014, pp. 341–351. c Indian Academy of Sciences. ... enhancement was realized by catalyst design, appropriate choice of reactor, better injection and .... Gas–liquid and liquid–solid transport processes in catalytic reactors.5.
Schizosaccharomyces pombe Polysome Profile Analysis and RNA Purification.

Science.gov (United States)

Wolf, Dieter A; Bähler, Jürg; Wise, Jo Ann

2017-04-03

Polysome profile analysis is widely used by investigators studying the mechanism and regulation of translation. The method described here uses high-velocity centrifugation of whole cell extracts on linear sucrose gradients to separate 40S and 60S ribosomal subunits from 80S monosomes and polysomes. Cycloheximide is included in the lysis buffer to "freeze" polysomes by blocking translation. After centrifugation, the gradient is fractionated and RNA (and/or protein) is prepared from each fraction for subsequent analysis of individual species using northern or western blots. The entire RNA population in each fraction can be analyzed by hybridization to microarrays or by high-throughput RNA sequencing, and the proteins present can be identified by mass spectrometry analysis. © 2017 Cold Spring Harbor Laboratory Press.
Materials for High-Temperature Catalytic Combustion

Energy Technology Data Exchange (ETDEWEB)

Ersson, Anders

2003-04-01

Catalytic combustion is an environmentally friendly technique to combust fuels in e.g. gas turbines. Introducing a catalyst into the combustion chamber of a gas turbine allows combustion outside the normal flammability limits. Hence, the adiabatic flame temperature may be lowered below the threshold temperature for thermal NO{sub X} formation while maintaining a stable combustion. However, several challenges are connected to the application of catalytic combustion in gas turbines. The first part of this thesis reviews the use of catalytic combustion in gas turbines. The influence of the fuel has been studied and compared over different catalyst materials. The material section is divided into two parts. The first concerns bimetallic palladium catalysts. These catalysts showed a more stable activity compared to their pure palladium counterparts for methane combustion. This was verified both by using an annular reactor at ambient pressure and a pilot-scale reactor at elevated pressures and flows closely resembling the ones found in a gas turbine combustor. The second part concerns high-temperature materials, which may be used either as active or washcoat materials. A novel group of materials for catalysis, i.e. garnets, has been synthesised and tested in combustion of methane, a low-heating value gas and diesel fuel. The garnets showed some interesting abilities especially for combustion of low-heating value, LHV, gas. Two other materials were also studied, i.e. spinels and hexa aluminates, both showed very promising thermal stability and the substituted hexa aluminates also showed a good catalytic activity. Finally, deactivation of the catalyst materials was studied. In this part the sulphur poisoning of palladium, platinum and the above-mentioned complex metal oxides has been studied for combustion of a LHV gas. Platinum and surprisingly the garnet were least deactivated. Palladium was severely affected for methane combustion while the other washcoat materials were
The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

Science.gov (United States)

Mohorianu, Irina; Stocks, Matthew Benedict; Applegate, Christopher Steven; Folkes, Leighton; Moulton, Vincent

2017-01-01

RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed
Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction.

Science.gov (United States)

Yang, Yuedong; Li, Xiaomei; Zhao, Huiying; Zhan, Jian; Wang, Jihua; Zhou, Yaoqi

2017-01-01

As most RNA structures are elusive to structure determination, obtaining solvent accessible surface areas (ASAs) of nucleotides in an RNA structure is an important first step to characterize potential functional sites and core structural regions. Here, we developed RNAsnap, the first machine-learning method trained on protein-bound RNA structures for solvent accessibility prediction. Built on sequence profiles from multiple sequence alignment (RNAsnap-prof), the method provided robust prediction in fivefold cross-validation and an independent test (Pearson correlation coefficients, r, between predicted and actual ASA values are 0.66 and 0.63, respectively). Application of the method to 6178 mRNAs revealed its positive correlation to mRNA accessibility by dimethyl sulphate (DMS) experimentally measured in vivo (r = 0.37) but not in vitro (r = 0.07), despite the lack of training on mRNAs and the fact that DMS accessibility is only an approximation to solvent accessibility. We further found strong association across coding and noncoding regions between predicted solvent accessibility of the mutation site of a single nucleotide variant (SNV) and the frequency of that variant in the population for 2.2 million SNVs obtained in the 1000 Genomes Project. Moreover, mapping solvent accessibility of RNAs to the human genome indicated that introns, 5' cap of 5' and 3' cap of 3' untranslated regions, are more solvent accessible, consistent with their respective functional roles. These results support conformational selections as the mechanism for the formation of RNA-protein complexes and highlight the utility of genome-scale characterization of RNA tertiary structures by RNAsnap. The server and its stand-alone downloadable version are available at http://sparks-lab.org. © 2016 Yang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Catalytic enantioselective Reformatsky reaction with ketones

NARCIS (Netherlands)

Fernandez-Ibanez, M. Angeles; Macia, Beatriz; Minnaard, Adriaan J.; Feringa, Ben L.

2008-01-01

Chiral tertiary alcohols were obtained with good yields and enantioselectivities via a catalytic Reformatsky reaction with ketones, including the challenging diaryl ketones, using chiral BINOL derivatives.
Catalytic dehydration of ethanol using transition metal oxide catalysts.

Science.gov (United States)

Zaki, T

2005-04-15

The aim of this work is to study catalytic ethanol dehydration using different prepared catalysts, which include Fe(2)O(3), Mn(2)O(3), and calcined physical mixtures of both ferric and manganese oxides with alumina and/or silica gel. The physicochemical properties of these catalysts were investigated via X-ray powder diffraction (XRD), acidity measurement, and nitrogen adsorption-desorption at -196 degrees C. The catalytic activities of such catalysts were tested through conversion of ethanol at 200-500 degrees C using a catalytic flow system operated under atmospheric pressure. The results obtained indicated that the dehydration reaction on the catalyst relies on surface acidity, whereas the ethylene production selectivity depends on the catalyst chemical constituents.
Novel Catalytic Membrane Reactors

Energy Technology Data Exchange (ETDEWEB)

Stuart Nemser, PhD

2010-10-01

There are many industrial catalytic organic reversible reactions with amines or alcohols that have water as one of the products. Many of these reactions are homogeneously catalyzed. In all cases removal of water facilitates the reaction and produces more of the desired chemical product. By shifting the reaction to right we produce more chemical product with little or no additional capital investment. Many of these reactions can also relate to bioprocesses. Given the large number of water-organic compound separations achievable and the ability of the Compact Membrane Systems, Inc. (CMS) perfluoro membranes to withstand these harsh operating conditions, this is an ideal demonstration system for the water-of-reaction removal using a membrane reactor. Enhanced reaction synthesis is consistent with the DOE objective to lower the energy intensity of U.S. industry 25% by 2017 in accord with the Energy Policy Act of 2005 and to improve the United States manufacturing competitiveness. The objective of this program is to develop the platform technology for enhancing homogeneous catalytic chemical syntheses.
Iron induced RNA-oxidation in the general population and in mouse tissue

DEFF Research Database (Denmark)

Cejvanovic, Vanja; Kjær, Laura Kofoed; Bergholdt, Helle Kirstine Mørup

2018-01-01

Iron promotes formation of hydroxyl radicals by the Fenton reaction, subsequently leading to potential oxidatively generated damage of nucleic acids. Oxidatively generated damage to RNA, measured as 8-oxo-7,8-dihydroguanosine (8-oxoGuo) in urine, is increased in patients with genetic iron overloa...
Catalytic Reactor for Inerting of Aircraft Fuel Tanks

Science.gov (United States)

1974-06-01

Aluminum Panels After Triphase Corrosion Test 79 35 Inerting System Flows in Various Flight Modes 82 36 High Flow Reactor Parametric Data 84 37 System...AD/A-000 939 CATALYTIC REACTOR FOR INERTING OF AIRCRAFT FUEL TANKS George H. McDonald, et al AiResearch Manufacturing Company Prepared for: Air Force...190th Street 2b. GROUP Torrance, California .. REPORT TITLE CATALYTIC REACTOR FOR INERTING OF AIRCRAFT FUEL TANKS . OESCRIP TIVE NOTEs (Thpe of refpoft
Aerobic, catalytic oxidation of alcohols in ionic liquids

Directory of Open Access Journals (Sweden)

Souza Roberto F. de

2006-01-01

Full Text Available An efficient and simple catalytic system based on RuCl3 dissolved in ionic liquids has been developed for the oxidation of alcohols into aldehydes and ketones under mild conditions. A new fluorinated ionic liquid, 1-n-butyl-3-methylimidazolium pentadecafluorooctanoate, was synthesized and demonstrated better performance that the other ionic liquids employed. Moreover this catalytic system utilizes molecular oxygen as an oxidizing agent, producing water as the only by-product.
Potential roles of placental human beta-defensin-3 and apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3G in prevention of intrauterine transmission of hepatitis B virus.

Science.gov (United States)

Bai, Xiaoxia; Tian, Ting; Wang, Peng; Yang, Xiaofu; Wang, Zhengping; Dong, Minyue

2015-03-01

Approximately 5% of newborns were infected by hepatitis B virus (HBV) via intrauterine transmission and this is the main reason for high prevalence of HBV in endemic regions. However, the mechanisms by which intrauterine transmission is avoided in most cases remain elusive and placental natural anti-microbial factors may play a role in the prevention of HBV intrauterine transmission. The expression levels of human β-defensin-3 (HBD-3), apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3G (A3G) and mannose binding lectin (MBL) were determined in the placenta of 30 HBV-seronegative pregnant women (controls), 7 HBV-seropositive pregnant women with infants infected via intrauterine transmission (infected group) and 30 HBV-seropositive pregnant women with non-infected infants (non-infected group). The expression of HBD-3, A3G, and MBL of placental trophoblast cell line Swan71 was determined after exposed to HBV. There were significant differences in placental HBD-3 and A3G levels among three groups, but the expression of MBL did not significantly differ. The expressions of HBD-3 and A3G were higher in non-infected group than controls and infected group, but not significantly different between infected group and controls. The exposure to HBV increased significantly the expression of HBD-3, A3G, and MBL by Swan 71. It may be concluded HBV up-regulates HBD-3 and A3G expression in vivo and in vitro in placental trophoblast and lack of this up-regulation is possibly associated with intrauterine transmission of HBV. © 2014 Wiley Periodicals, Inc.
Iron Toxicity in the Retina Requires Alu RNA and the NLRP3 Inflammasome

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Bradley D. Gelfand

2015-06-01

Full Text Available Excess iron induces tissue damage and is implicated in age-related macular degeneration (AMD. Iron toxicity is widely attributed to hydroxyl radical formation through Fenton’s reaction. We report that excess iron, but not other Fenton catalytic metals, induces activation of the NLRP3 inflammasome, a pathway also implicated in AMD. Additionally, iron-induced degeneration of the retinal pigmented epithelium (RPE is suppressed in mice lacking inflammasome components caspase-1/11 or Nlrp3 or by inhibition of caspase-1. Iron overload increases abundance of RNAs transcribed from short interspersed nuclear elements (SINEs: Alu RNAs and the rodent equivalent B1 and B2 RNAs, which are inflammasome agonists. Targeting Alu or B2 RNA prevents iron-induced inflammasome activation and RPE degeneration. Iron-induced SINE RNA accumulation is due to suppression of DICER1 via sequestration of the co-factor poly(C-binding protein 2 (PCBP2. These findings reveal an unexpected mechanism of iron toxicity, with implications for AMD and neurodegenerative diseases associated with excess iron.
Catalytic applications of bio-inspired nanomaterials

Science.gov (United States)

Pacardo, Dennis Kien Balaong

The biomimetic synthesis of Pd nanoparticles was presented using the Pd4 peptide, TSNAVHPTLRHL, isolated from combinatorial phage display library. Using this approach, nearly monodisperse and spherical Pd nanoparticles were generated with an average diameter of 1.9 +/- 0.4 nm. The peptide-based nanocatalyst were employed in the Stille coupling reaction under energy-efficient and environmentally friendly reaction conditions of aqueous solvent, room temperature and very low catalyst loading. To this end, the Pd nanocatalyst generated high turnover frequency (TOF) value and quantitative yields using ≥ 0.005 mol% Pd as well as catalytic activities with different aryl halides containing electron-withdrawing and electron-donating groups. The Pd4-capped Pd nanoparticles followed the atom-leaching mechanism and were found to be selective with respect to substrate identity. On the other hand, the naturally-occurring R5 peptide (SSKKSGSYSGSKGSKRRIL) was employed in the synthesis of biotemplated Pd nanomaterials which showed morphological changes as a function of Pd:peptide ratio. TOF analysis for hydrogenation of olefinic alcohols showed similar catalytic activity regardless of nanomorphology. Determination of catalytic properties of these bio-inspired nanomaterials are important as they serve as model system for alternative green catalyst with applications in industrially important transformations.

Vapor-Driven Propulsion of Catalytic Micromotors

Science.gov (United States)

Dong, Renfeng; Li, Jinxing; Rozen, Isaac; Ezhilan, Barath; Xu, Tailin; Christianson, Caleb; Gao, Wei; Saintillan, David; Ren, Biye; Wang, Joseph

2015-08-01

Chemically-powered micromotors offer exciting opportunities in diverse fields, including therapeutic delivery, environmental remediation, and nanoscale manufacturing. However, these nanovehicles require direct addition of high concentration of chemical fuel to the motor solution for their propulsion. We report the efficient vapor-powered propulsion of catalytic micromotors without direct addition of fuel to the micromotor solution. Diffusion of hydrazine vapor from the surrounding atmosphere into the sample solution is instead used to trigger rapid movement of iridium-gold Janus microsphere motors. Such operation creates a new type of remotely-triggered and powered catalytic micro/nanomotors that are responsive to their surrounding environment. This new propulsion mechanism is accompanied by unique phenomena, such as the distinct off-on response to the presence of fuel in the surrounding atmosphere, and spatio-temporal dependence of the motor speed borne out of the concentration gradient evolution within the motor solution. The relationship between the motor speed and the variables affecting the fuel concentration distribution is examined using a theoretical model for hydrazine transport, which is in turn used to explain the observed phenomena. The vapor-powered catalytic micro/nanomotors offer new opportunities in gas sensing, threat detection, and environmental monitoring, and open the door for a new class of environmentally-triggered micromotors.
Comprehensive characterization of lncRNA-mRNA related ceRNA network across 12 major cancers

Science.gov (United States)

Feng, Li; Li, Feng; Sun, Zeguo; Wu, Tan; Shi, Xinrui; Li, Jing; Li, Xia

2016-01-01

Recent studies indicate that long noncoding RNAs (lncRNAs) can act as competing endogenous RNAs (ceRNAs) to indirectly regulate mRNAs through shared microRNAs, which represents a novel layer of RNA crosstalk and plays critical roles in the development of tumor. However, the global regulation landscape and characterization of these lncRNA related ceRNA crosstalk in cancers is still largely unknown. Here, we systematically characterized the lncRNA related ceRNA interactions across 12 major cancers and the normal physiological states by integrating multidimensional molecule profiles of more than 5000 samples. Our study suggest the large difference of ceRNA regulation between normal and tumor states and the higher similarity across similar tissue origin of tumors. The ceRNA related molecules have more conserved features in tumor networks and they play critical roles in both the normal and tumorigenesis processes. Besides, lncRNAs in the pan-cancer ceRNA network may be potential biomarkers of tumor. By exploring hub lncRNAs, we found that these conserved key lncRNAs dominate variable tumor hallmark processes across pan-cancers. Network dynamic analysis highlights the critical roles of ceRNA regulation in tumorigenesis. By analyzing conserved ceRNA interactions, we found that miRNA mediate ceRNA regulation showed different patterns across pan-cancer; while analyzing the cancer specific ceRNA interactions reveal that lncRNAs synergistically regulated tumor driver genes of cancer hallmarks. Finally, we found that ceRNA modules have the potential to predict patient survival. Overall, our study systematically dissected the lncRNA related ceRNA networks in pan-cancer that shed new light on understanding the molecular mechanism of tumorigenesis. PMID:27580177
Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

Science.gov (United States)

Martos, Laura; Fernández-Pardo, Álvaro; Oto, Julia; Medina, Pilar; España, Francisco; Navarro, Silvia

2017-01-01

microRNAs are promising biomarkers in biological fluids in several diseases. Different plasma RNA isolation protocols and carriers are available, but their efficiencies have been scarcely compared. Plasma microRNAs were isolated using a phenol and column-based procedure and a column-based procedure, in the presence or absence of two RNA carriers (yeast RNA and MS2 RNA). We evaluated the presence of PCR inhibitors and the relative abundance of certain microRNAs by qRT-PCR. Furthermore, we analyzed the association between different isolation protocols, the relative abundance of the miRNAs in the sample, the GC content and the free energy of microRNAs. In all microRNAs analyzed, the addition of yeast RNA as a carrier in the different isolation protocols used gave lower raw Cq values, indicating higher microRNA recovery. Moreover, this increase in microRNAs recovery was dependent on their own relative abundance in the sample, their GC content and the free-energy of their own most stable secondary structure. Furthermore, the normalization of microRNA levels by an endogenous microRNA is more reliable than the normalization by plasma volume, as it reduced the difference in microRNA fold abundance between the different isolation protocols evaluated. Our thorough study indicates that a standardization of pre- and analytical conditions is necessary to obtain reproducible inter-laboratory results in plasma microRNA studies. PMID:29077772
Association between tuberculosis and circulating microRNA hsa-let-7b and hsa-miR-30b: A pilot study in a Chinese population.

Science.gov (United States)

Xin, Henan; Yang, Yu; Liu, Jianmin; Li, Xiangwei; Li, Mufei; Feng, Boxuan; Li, Zhen; Zhang, Haoran; Li, Hengjing; Shen, Fei; Guan, Ling; Gao, Lei

2016-07-01

Tuberculosis remains one of the world's deadliest communicable diseases. Limitations in the current diagnosis tools have heavily slowed down the step to eliminate TB. The objective of this study was to identify potential circulating miRNA associated with tuberculosis (TB) infection and disease development. Agilent human miRNA microarray was used to estimate the circulating levels of 1887 miRNAs among 34 study participants (10 patients with pulmonary TB, 13 controls with latent TB infection and 11 non-infected healthy controls). The identified miRNAs were subsequently verified by real-time qPCR. Target gene prediction and miRNA-gene network construction were further explored. A total of 119 miRNAs were identified to be in different levels between any two groups of the study population by microarray (Fold Change>2, p < 0.01). 11 most promising miRNAs were then selected for verification by real-time qPCR. The levels of hsa-let-7b-5p and hsa-miR-30b-5p were confirmed to be significantly up-regulated in pulmonary TB patients as compared to both control groups (p < 0.01). Caspase 3 was predicted to be one common target gene for these two miRNAs. None of the selected miRNA was confirmed to be related with the infection status. This pilot study suggested circulating hsa-let-7b and hsa-miR-30b might be associated with TB development by regulating the target genes involved in TLR-NF-kB mediated signal pathway. Copyright © 2016 Elsevier Ltd. All rights reserved.
Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

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Yunpeng Zhang

2015-01-01

Full Text Available Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it is important to identify subtype specific miRNA-mRNA modules. In this study, we integrated the Ping-Pong algorithm and multiobjective genetic algorithm to identify subtype specific miRNA-mRNA functional regulatory modules (MFRMs through integrative analysis of three biological data sets: GO biological processes, miRNA target information, and matched miRNA and mRNA expression data. We applied our method on a heterogeneous disease, multiple myeloma (MM, to identify MM subtype specific MFRMs. The constructed miRNA-mRNA regulatory networks provide modular outlook at subtype specific miRNA-mRNA interactions. Furthermore, clustering analysis demonstrated that heterogeneous MFRMs were able to separate corresponding MM subtypes. These subtype specific MFRMs may aid in the further elucidation of the pathogenesis of each subtype and may serve to guide MM subtype diagnosis and treatment.
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

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Wasik Szymon

2010-05-01

Full Text Available Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA
Simulation on Toxic Gases in Vehicle Exhaust Equipped with Modified Catalytic Converter : A Review

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Leman A.M.

2016-01-01

Full Text Available Air pollution and global warming is a major issue nowadays. One of the main contributors to be the emission of harmful gases produced by vehicle exhausts lines. The harmful gases like NOx, CO, unburned HC and particulate matter increases the global warming, so catalytic converter plays a vital role in reducing harmful gases. Catalytic converters are used on most vehicles on the road today. This research deals with the gas emission flow in the catalytic converter involving the heat transfer, velocity flow, back pressure and others chemical reaction in the modified catalytic converter by using FeCrAl as a substrate that is treated using the ultrasonic bath and electroplating techniques. The objective of this study is to obtain a quantitative description of the gas emission in the catalytic converter system of automobile exhaust gas using ANSYS Software. The description of the gas emission in the catalytic converter system of automobile exhaust gas using ANSYS Software was simulated in this research in order to provide better efficiency and ease the reusability of the catalytic converter by comparing experimental data with software analysing data. The result will be expected to demonstrate a good approximation of gas emission in the modified catalytic converter simulation data compared to experimental data in order to verify the effectiveness of modified catalytic converter. Therefore studies on simulation of flow through the modified catalytic converter are very important to increase the accuracy of the obtained emission result.
Intellectual disabilities, neuronal posttranscriptional RNA metabolism, and RNA-binding proteins: three actors for a complex scenario.

Science.gov (United States)

Bardoni, Barbara; Abekhoukh, Sabiha; Zongaro, Samantha; Melko, Mireille

2012-01-01

Intellectual disability (ID) is the most frequent cause of serious handicap in children and young adults and interests 2-3% of worldwide population, representing a serious problem from the medical, social, and economic points of view. The causes are very heterogeneous. Genes involved in ID have various functions altering different pathways important in neuronal function. Regulation of mRNA metabolism is particularly important in neurons for synaptic structure and function. Here, we review ID due to alteration of mRNA metabolism. Functional absence of some RNA-binding proteins--namely, FMRP, FMR2P, PQBP1, UFP3B, VCX-A--causes different forms of ID. These proteins are involved in different steps of RNA metabolism and, even if a detailed analysis of their RNA targets has been performed so far only for FMRP, it appears clear that they modulate some aspects (translation, stability, transport, and sublocalization) of a subset of RNAs coding for proteins, whose function must be relevant for neurons. Two other proteins, DYRK1A and CDKL5, involved in Down syndrome and Rett syndrome, respectively, have been shown to have an impact on splicing efficiency of specific mRNAs. Both proteins are kinases and their effect is indirect. Interestingly, both are localized in nuclear speckles, the nuclear domains where splicing factors are assembled, stocked, and recycled and influence their biogenesis and/or their organization. Copyright © 2012 Elsevier B.V. All rights reserved.
Ionic Liquids: The Synergistic Catalytic Effect in the Synthesis of Cyclic Carbonates

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Flora T.T. Ng

2013-10-01

Full Text Available This review presents the synergistic effect in the catalytic system of ionic liquids (ILs for the synthesis of cyclic carbonate from carbon dioxide and epoxide. The emphasis of this review is on three aspects: the catalytic system of metal-based ionic liquids, the catalytic system of hydrogen bond-promoted ionic liquids and supported ionic liquids. Metal and ionic liquids show a synergistic effect on the cycloaddition reactions of epoxides. The cations and anions of ionic liquids show a synergistic effect on the cycloaddition reactions. The functional groups in cations or supports combined with the anions have a synergistic effect on the cycloaddition reactions. Synergistic catalytic effects of ILs play an important role of promoting the cycloaddition reactions of epoxides. The design of catalytic system of ionic liquids will be possible if the synergistic effect on a molecular level is understood.
Oscillatory behaviour of catalytic properties, structure and temperature during the catalytic partial oxidation of methane on Pd/Al2O3

DEFF Research Database (Denmark)

Kimmerle, B.; Baiker, A.; Grunwaldt, Jan-Dierk

2010-01-01

Pd/Al2O3 catalysts showed an oscillatory behaviour during the catalytic partial oxidation (CPO) of methane, which was investigated simultaneously by IR-thermography, X-ray absorption spectroscopy, and online mass-spectrometry to correlate the temperature, state of the catalyst and catalytic...... to self-reduction leading to extinction of the process. The latter was the key driver for the oscillations and thus gave additional insight into the mechanism of partial methane oxidation....
Ribosomal proteins L11 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23 S rRNA backbone in the ribosomal GTPase centre

DEFF Research Database (Denmark)

Rosendahl, G; Douthwaite, S

1993-01-01

RNA, and to investigate how this interaction is influenced by other ribosomal components. Complexes were characterized in both naked 23 S rRNA and ribosomes from an E. coli L11-minus strain, before and after reconstitution with L11. The protein protects 17 riboses between positions 1058 and 1085 in the naked 23 S r......The Escherichia coli ribosomal protein (r-protein) L11 and its binding site on 23 S ribosomal RNA (rRNA) are associated with ribosomal hydrolysis of guanosine 5'-triphosphate (GTP). We have used hydroxyl radical footprinting to map the contacts between L11 and the backbone riboses in 23 S r......)4 and other proteins within the ribosome. The antibiotics thiostrepton and micrococcin inhibit the catalytic functions of this region by slotting in between the accessible loops and interacting with nucleotides there....
Methods of using structures including catalytic materials disposed within porous zeolite materials to synthesize hydrocarbons

Science.gov (United States)

Rollins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

2011-02-01

Catalytic structures include a catalytic material disposed within a zeolite material. The catalytic material may be capable of catalyzing a formation of methanol from carbon monoxide and/or carbon dioxide, and the zeolite material may be capable of catalyzing a formation of hydrocarbon molecules from methanol. The catalytic material may include copper and zinc oxide. The zeolite material may include a first plurality of pores substantially defined by a crystal structure of the zeolite material and a second plurality of pores dispersed throughout the zeolite material. Systems for synthesizing hydrocarbon molecules also include catalytic structures. Methods for synthesizing hydrocarbon molecules include contacting hydrogen and at least one of carbon monoxide and carbon dioxide with such catalytic structures. Catalytic structures are fabricated by forming a zeolite material at least partially around a template structure, removing the template structure, and introducing a catalytic material into the zeolite material.
Surface composition of carburized tungsten trioxide and its catalytic activity

International Nuclear Information System (INIS)

Nakazawa, M.; Okamoto, H.

1985-01-01

The surface composition and electronic structure of carburized tungsten trioxide are investigated using x-ray photoelectron spectroscopy (XPS). The relationship between the surface composition and the catalytic activity for methanol electro-oxidation is clarified. The tungsten carbide concentration in the surface layer increases with the carburization time. The formation of tungsten carbide enhances the catalytic activity. On the other hand, the presence of free carbon or tungsten trioxide in the surface layer reduces the activity remarkably. It is also shown that, the higher the electronic density of states near the Fermi level, the higher the catalytic activity
antaRNA: ant colony-based RNA sequence design.

Science.gov (United States)

Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

2015-10-01

RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.
Poisoning of bubble propelled catalytic micromotors: the chemical environment matters.

Science.gov (United States)

Zhao, Guanjia; Sanchez, Samuel; Schmidt, Oliver G; Pumera, Martin

2013-04-07

Self-propelled catalytic microjets have attracted considerable attention in recent years and these devices have exhibited the ability to move in complex media. The mechanism of propulsion is via the Pt catalysed decomposition of H2O2 and it is understood that the Pt surface is highly susceptible to poisoning by sulphur-containing molecules. Here, we show that important extracellular thiols as well as basic organic molecules can significantly hamper the motion of catalytic microjet engines. This is due to two different mechanisms: (i) molecules such as dimethyl sulfoxide can quench the hydroxyl radicals produced at Pt surfaces and reduce the amount of oxygen gas generated and (ii) molecules containing -SH, -SSR, and -SCH3 moieties can poison the catalytically active platinum surface, inhibiting the motion of the jet engines. It is essential that the presence of such molecules in the environment be taken into consideration for future design and operation of catalytic microjet engines. We show this effect on catalytic micromotors prepared by both rolled-up and electrodeposition approaches, demonstrating that such poisoning is universal for Pt catalyzed micromotors. We believe that our findings will contribute significantly to this field to develop alternative systems or catalysts for self-propulsion when practical applications in the real environment are considered.
Hepatitis C virus (HCV) RNA profiles among chronic HIV/HCV-coinfected individuals in ESPRIT; spontaneous HCV RNA clearance observed in nine individuals.

Science.gov (United States)

Grint, D; Tedaldi, E; Peters, L; Mocroft, A; Edlin, B; Gallien, S; Klinker, H; Boesecke, C; Kokordelis, P; Rockstroh, J K

2017-07-01

Studies have shown that hepatitis C virus (HCV) RNA levels remain stable over time in HIV/HCV-coinfected individuals taking combination antiretroviral therapy (cART), while spontaneous clearance of HCV RNA during the persistent infection phase has been documented only rarely among those with the CC interleukin (IL)-28B genotype. This study describes HCV RNA profiles and factors associated with changes over time in HCV RNA levels in the ESPRIT study. HIV/HCV-coinfected individuals positive for HCV RNA were included in the study. Follow-up was counted from the first HCV RNA positive test and censored at the initiation of interferon-based treatment. HCV RNA and IL-28B measurements were performed in the same reference laboratory. Random effects mixed models were used to analyse changes over time in HCV RNA. A total of 312 ESPRIT patients were included in the study (151 in the arm receiving subcutaneous recombinant IL-2 and 161 in the control arm). Most of the patients were white (89%) and male (76%), and they had a median of 5 HCV RNA measurements per person [interquartile range (IQR) 3-6; range 1-9]. Median follow-up was 5 years (IQR: 2-6 years). At baseline, 96% of patients were taking cART and 93% had undetectable HIV RNA. Mean HCV RNA levels decreased by 13% per year over the study period [95% confidence interval (CI) 8-18%; P < 0.0001]. Baseline HCV RNA levels and the change over time in HCV RNA did not differ by randomization arm (P = 0.16 and P = 0.56, respectively). Nine individuals spontaneously cleared HCV RNA during follow-up [IL-28B genotypes: CC, five patients (56%); CT, four patients (44%)]. HCV RNA levels decreased over time in this population with well-controlled HIV infection. Spontaneous clearance of HCV RNA was documented in five individuals with IL-28B genotype CC and four with the CT genotype. © 2016 British HIV Association.
The L7Ae protein binds to two kink-turns in the Pyrococcus furiosus RNase P RNA

Science.gov (United States)

Lai, Stella M.; Lai, Lien B.; Foster, Mark P.; Gopalan, Venkat

2014-01-01

The RNA-binding protein L7Ae, known for its role in translation (as part of ribosomes) and RNA modification (as part of sn/oRNPs), has also been identified as a subunit of archaeal RNase P, a ribonucleoprotein complex that employs an RNA catalyst for the Mg2+-dependent 5′ maturation of tRNAs. To better understand the assembly and catalysis of archaeal RNase P, we used a site-specific hydroxyl radical-mediated footprinting strategy to pinpoint the binding sites of Pyrococcus furiosus (Pfu) L7Ae on its cognate RNase P RNA (RPR). L7Ae derivatives with single-Cys substitutions at residues in the predicted RNA-binding interface (K42C/C71V, R46C/C71V, V95C/C71V) were modified with an iron complex of EDTA-2-aminoethyl 2-pyridyl disulfide. Upon addition of hydrogen peroxide and ascorbate, these L7Ae-tethered nucleases were expected to cleave the RPR at nucleotides proximal to the EDTA-Fe–modified residues. Indeed, footprinting experiments with an enzyme assembled with the Pfu RPR and five protein cofactors (POP5, RPP21, RPP29, RPP30 and L7Ae–EDTA-Fe) revealed specific RNA cleavages, localizing the binding sites of L7Ae to the RPR's catalytic and specificity domains. These results support the presence of two kink-turns, the structural motifs recognized by L7Ae, in distinct functional domains of the RPR and suggest testable mechanisms by which L7Ae contributes to RNase P catalysis. PMID:25361963
From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.

Science.gov (United States)

Michelini, Flavia; Jalihal, Ameya P; Francia, Sofia; Meers, Chance; Neeb, Zachary T; Rossiello, Francesca; Gioia, Ubaldo; Aguado, Julio; Jones-Weinert, Corey; Luke, Brian; Biamonti, Giuseppe; Nowacki, Mariusz; Storici, Francesca; Carninci, Piero; Walter, Nils G; Fagagna, Fabrizio d'Adda di

2018-03-30

Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
The prognostic value of microRNA-126 and microvessel density in patients with stage II colon cancer

DEFF Research Database (Denmark)

Hansen, Torben Frøstrup; Kjær-Frifeldt, Sanne; Morgenthaler, Søren

2014-01-01

BACKGROUND: Angiogenesis plays a pivotal role in malignant tumour growth and the metastatic process. We analysed the prognostic value of two angiogenesis parameters, microRNA-126 (miRNA-126) and microvessel density (MVD), in a population based cohort of patients operated for stage II colon cancer...... estimate was not associated with either RF-CSS, p = 0.49, or OS, p = 0.94.CONCLUSION: The current population based study of patients operated for stage II colon cancer demonstrated correlations between several prognostic unfavourable characteristics and miRNA-126 and argues for a possible prognostic impact...
Catalytic Fast Pyrolysis: A Review

Directory of Open Access Journals (Sweden)

Theodore Dickerson

2013-01-01

Full Text Available Catalytic pyrolysis is a promising thermochemical conversion route for lignocellulosic biomass that produces chemicals and fuels compatible with current, petrochemical infrastructure. Catalytic modifications to pyrolysis bio-oils are geared towards the elimination and substitution of oxygen and oxygen-containing functionalities in addition to increasing the hydrogen to carbon ratio of the final products. Recent progress has focused on both hydrodeoxygenation and hydrogenation of bio-oil using a variety of metal catalysts and the production of aromatics from bio-oil using cracking zeolites. Research is currently focused on developing multi-functional catalysts used in situ that benefit from the advantages of both hydrodeoxygenation and zeolite cracking. Development of robust, highly selective catalysts will help achieve the goal of producing drop-in fuels and petrochemical commodities from wood and other lignocellulosic biomass streams. The current paper will examine these developments by means of a review of existing literature.

Chemically-modified cellulose paper as a microstructured catalytic reactor.

Science.gov (United States)

Koga, Hirotaka; Kitaoka, Takuya; Isogai, Akira

2015-01-15

We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.
Chemically-Modified Cellulose Paper as a Microstructured Catalytic Reactor

Directory of Open Access Journals (Sweden)

Hirotaka Koga

2015-01-01

Full Text Available We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.
34A, miRNA-944, miRNA-101 and miRNA-218 in cervical cancer

African Journals Online (AJOL)

RNAs (21 - 24 nucleotides in length) that are critical for many important processes such as development, ... RNA extraction and reverse transcription. Total RNA was extracted from each of the experimental groups using ... used as an endogenous control to normalize the expression of miRNA-143, miRNA-34A, miRNA-.
Enzymatic synthesis of tRNA-peptide conjugates and spectroscopic studies of fluorine-modified RNA

International Nuclear Information System (INIS)

Graber, D.

2010-01-01

possess the naturally occurring nucleoside modifications. Hence, an alternative process for access to 5'-fragments containing these modifications was needed. Starting from wild-type tRNA, a DNA-enzyme mediated position-specific cleavage at the desired cleavage site was elaborated. For quantitative cleavage, the introduction of repeated temperature cycles was inevitable. Dephosphorylation of the so obtained 2',3'-cyclophosphate cleavage products had to be performed prior to ligating the wild-type 5'-fragment by T4 RNA ligase to the chimeric 3'-fragment yielding the fully modified tRNA-peptide conjugate. The broad applicability of that approach was demonstrated by successful ligation of various tRNA, and tRNA from different species. In the second part of this thesis fluorinated nucleic acids were applied to 19F NMR spectroscopic investigations. One subproject concerned fluorinated nucleic acids for probing secondary structures. For that reason, a 2,4-difluorotoluyl-ribofuranose phosphoramidite was synthesized and site-specifically incorporated into oligonucleotides. As a proof of principle, the differentiation between monomolecular and bimolecular melting transitions was demonstrated by monitoring the temperature dependent alterations in the chemical shift signatures. It was also shown that oligonucleotides of self-complementary sequences - which simultaneously adopt different secondary structures - can be analyzed in terms of quantification of the coexisting populations. Moreover, melting temperatures determined by 19F NMR spectroscopy were in excellent accordance with those found using traditional UV-techniques. In another subproject, the interaction of tRNA pseudouridine synthase (TruB) with its TΨC loop tRNA substrate was studied using 19F NMR spectroscopy. So far, published contributions have focused on 5-fluorouridine substrate/enzyme reactions which were expected to result in a stable covalently linked RNA-enzyme complex. However, the enzyme was capable of
Oxyfuel combustion using a catalytic ceramic membrane reactor

Energy Technology Data Exchange (ETDEWEB)

Tan, Xiaoyao; Li, K. [Department of Chemical Engineering, Imperial College London, University of London, South Kensington, London SW7 2AZ (United Kingdom); Thursfield, A.; Metcalfe, I.S. [School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, NE1 7RU (United Kingdom)

2008-02-29

Membrane catalytic combustion (MCC) is an environmentally friendly technique for heat and power generation from methane. This work demonstrates the performances of a MCC perovskite hollow fibre membrane reactor for the catalytic combustion of methane. The ionic-electronic La{sub 0.6}Sr{sub 0.4}Co{sub 0.2}Fe{sub 0.8}O{sub 3-{alpha}} (LSCF6428) mixed conductor, in the form of an oxygen-permeable hollow fibre membrane, has been prepared successfully by means of a phase-inversion spinning/sintering technique. For this process polyethersulfone (PESf) was used as a binder, N-methyl-2-pyrrollidone (NMP) as solvent and polyvinylpyrrolidone (PVP, K16-18) as an additive. With the prepared LSCF6428 hollow fibre membranes packed with catalyst, hollow fibre membrane reactors (HFMRs) have been assembled to perform the catalytic combustion of methane. A simple mathematical model that combines the local oxygen permeation rate with approximate catalytic reaction kinetics has been developed and can be used to predict the performance of the HFMRs for methane combustion. The effects of operating temperature and methane and air feed flow rates on the performance of the HFMR have been investigated both experimentally and theoretically. Both the methane conversion and oxygen permeation rate can be improved by means of coating platinum on the air side of the hollow fibre membranes. (author)
Preventive Activity against Influenza (H1N1 Virus by Intranasally Delivered RNA-Hydrolyzing Antibody in Respiratory Epithelial Cells of Mice

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Seungchan Cho

2015-09-01

Full Text Available The antiviral effect of a catalytic RNA-hydrolyzing antibody, 3D8 scFv, for intranasal administration against avian influenza virus (H1N1 was described. The recombinant 3D8 scFv protein prevented BALB/c mice against H1N1 influenza virus infection by degradation of the viral RNA genome through its intrinsic RNA-hydrolyzing activity. Intranasal administration of 3D8 scFv (50 μg/day for five days prior to infection demonstrated an antiviral activity (70% survival against H1N1 infection. The antiviral ability of 3D8 scFv to penetrate into epithelial cells from bronchial cavity via the respiratory mucosal layer was confirmed by immunohistochemistry, qRT-PCR, and histopathological examination. The antiviral activity of 3D8 scFv against H1N1 virus infection was not due to host immune cytokines or chemokines, but rather to direct antiviral RNA-hydrolyzing activity of 3D8 scFv against the viral RNA genome. Taken together, our results suggest that the RNase activity of 3D8 scFv, coupled with its ability to penetrate epithelial cells through the respiratory mucosal layer, directly prevents H1N1 virus infection in a mouse model system.
Extracellular RNA Communication (ExRNA)

Data.gov (United States)

Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...
COAL CONVERSION WASTEWATER TREATMENT BY CATALYTIC OXIDATION IN SUPERCRITICAL WATER; FINAL

International Nuclear Information System (INIS)

Phillip E. Savage

1999-01-01

Wastewaters from coal-conversion processes contain phenolic compounds in appreciable concentrations. These compounds need to be removed so that the water can be discharged or re-used. Catalytic oxidation in supercritical water is one potential means of treating coal-conversion wastewaters, and this project examined the reactions of phenol over different heterogeneous oxidation catalysts in supercritical water. More specifically, we examined the oxidation of phenol over a commercial catalyst and over bulk MnO(sub 2), bulk TiO(sub 2), and CuO supported on Al(sub 2) O(sub 3). We used phenol as the model pollutant because it is ubiquitous in coal-conversion wastewaters and there is a large database for non-catalytic supercritical water oxidation (SCWO) with which we can contrast results from catalytic SCWO. The overall objective of this research project is to obtain the reaction engineering information required to evaluate the utility of catalytic supercritical water oxidation for treating wastes arising from coal conversion processes. All four materials were active for catalytic supercritical water oxidation. Indeed, all four materials produced phenol conversions and CO(sub 2) yields in excess of those obtained from purely homogeneous, uncatalyzed oxidation reactions. The commercial catalyst was so active that we could not reliably measure reaction rates that were not limited by pore diffusion. Therefore, we performed experiments with bulk transition metal oxides. The bulk MnO(sub 2) and TiO(sub 2) catalysts enhance both the phenol disappearance and CO(sub 2) formation rates during SCWO. MnO(sub 2) does not affect the selectivity to CO(sub 2), or to the phenol dimers at a given phenol conversion. However, the selectivities to CO(sub 2) are increased and the selectivities to phenol dimers are decreased in the presence of TiO(sub 2) , which are desirable trends for a catalytic SCWO process. The role of the catalyst appears to be accelerating the rate of formation of
Catalytic destruction of tar in biomass derived producer gas

International Nuclear Information System (INIS)

Zhang Ruiqin; Brown, Robert C.; Suby, Andrew; Cummer, Keith

2004-01-01

The purpose of this study is to investigate catalytic destruction of tar formed during gasification of biomass, with the goal of improving the quality of the producer gas. This work focuses on nickel based catalysts treated with alkali in an effort to promote steam gasification of the coke that deposits on catalyst surfaces. A tar conversion system consisting of a guard bed and catalytic reactor was designed to treat the producer gas from an air blown, fluidized bed biomass gasifier. The guard bed used dolomite to crack the heavy tars. The catalytic reactor was used to evaluate three commercial steam reforming catalysts. These were the ICI46-1 catalyst from Imperial Chemical Industry and Z409 and RZ409 catalysts from Qilu Petrochemical Corp. in China. A 0.5-3 l/min slipstream from a 5 tpd biomass gasifier was used to test the tar conversion system. Gas and tar were sampled before and after the tar conversion system to evaluate the effectiveness of the system. Changes in gas composition as functions of catalytic bed temperature, space velocity and steam/TOC (total organic carbon) ratio are presented. Structural changes in the catalysts during the tests are also described
Catalytic Activity Control via Crossover between Two Different Microstructures

KAUST Repository

Zhou, Yuheng

2017-09-08

Metal nanocatalysts hold great promise for a wide range of heterogeneous catalytic reactions, while the optimization strategy of catalytic activity is largely restricted by particle size or shape control. Here, we demonstrate that a reversible microstructural control through the crossover between multiply-twinned nanoparticle (MTP) and single crystal (SC) can be readily achieved by solvent post-treatment on gold nanoparticles (AuNPs). Polar solvents (e.g. water, methanol) direct the transformation from MTP to SC accompanied by the disappearance of twinning and stacking faults. A reverse transformation from SC to MTP is achieved in non-polar solvent (e.g. toluene) mixed with thiol ligands. The transformation between two different microstructures is directly observed by in-situ TEM and leads to a drastic modulation of catalytic activity towards the gas-phase selective oxidation of alcohols. There is a quasi-linear relationship between TOFs and MTP concentrations. Based on the combined experimental and theoretical investigations of alcohol chemisorption on these nanocatalysts, we propose that the exposure of {211}-like microfacets associated with twin boundaries and stack faults accounts for the strong chemisorption of alcohol molecules on MTP AuNPs and thus the exceptionally high catalytic activity.
RNA Crystallization

Science.gov (United States)

Golden, Barbara L.; Kundrot, Craig E.

2003-01-01

RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.
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.
Identifying microRNA/mRNA dysregulations in ovarian cancer.

Science.gov (United States)

Miles, Gregory D; Seiler, Michael; Rodriguez, Lorna; Rajagopal, Gunaretnam; Bhanot, Gyan

2012-03-27

MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory mechanisms. Our findings identify
Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1.

Science.gov (United States)

Stamogiannos, Athanasios; Maben, Zachary; Papakyriakou, Athanasios; Mpakali, Anastasia; Kokkala, Paraskevi; Georgiadis, Dimitris; Stern, Lawrence J; Stratikos, Efstratios

2017-03-14

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that is important for the generation of antigenic epitopes and major histocompatibility class I-restricted adaptive immune responses. ERAP1 processes a vast variety of different peptides but still shows length and sequence selectivity, although the mechanism behind these properties is poorly understood. X-ray crystallographic analysis has revealed that ERAP1 can assume at least two distinct conformations in which C-terminal domain IV is either proximal or distal to active site domain II. To improve our understanding of the role of this conformational change in the catalytic mechanism of ERAP1, we used site-directed mutagenesis to perturb key salt bridges between domains II and IV. Enzymatic analysis revealed that these mutations, although located away from the catalytic site, greatly reduce the catalytic efficiency and change the allosteric kinetic behavior. The variants were more efficiently activated by small peptides and bound a competitive inhibitor with weaker affinity and faster dissociation kinetics. Molecular dynamics analysis suggested that the mutations affect the conformational distribution of ERAP1, reducing the population of closed states. Small-angle X-ray scattering indicated that both the wild type and the ERAP1 variants are predominantly in an open conformational state in solution. Overall, our findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site. The extent of domain opening in ERAP1 probably underlies its specialization for antigenic peptide precursors and should be taken into account in inhibitor development efforts.
Natural RNA circles function as efficient microRNA sponges

DEFF Research Database (Denmark)

Hansen, Thomas Birkballe; Jensen, Trine I; Clausen, Bettina Hjelm

2013-01-01

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called comp......MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so......-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more...... sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA....
RNA Origami

DEFF Research Database (Denmark)

Sparvath, Steffen Lynge

introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...
PINGU: PredIction of eNzyme catalytic residues usinG seqUence information.

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Priyadarshini P Pai

Full Text Available Identification of catalytic residues can help unveil interesting attributes of enzyme function for various therapeutic and industrial applications. Based on their biochemical roles, the number of catalytic residues and sequence lengths of enzymes vary. This article describes a prediction approach (PINGU for such a scenario. It uses models trained using physicochemical properties and evolutionary information of 650 non-redundant enzymes (2136 catalytic residues in a support vector machines architecture. Independent testing on 200 non-redundant enzymes (683 catalytic residues in predefined prediction settings, i.e., with non-catalytic per catalytic residue ranging from 1 to 30, suggested that the prediction approach was highly sensitive and specific, i.e., 80% or above, over the incremental challenges. To learn more about the discriminatory power of PINGU in real scenarios, where the prediction challenge is variable and susceptible to high false positives, the best model from independent testing was used on 60 diverse enzymes. Results suggested that PINGU was able to identify most catalytic residues and non-catalytic residues properly with 80% or above accuracy, sensitivity and specificity. The effect of false positives on precision was addressed in this study by application of predicted ligand-binding residue information as a post-processing filter. An overall improvement of 20% in F-measure and 0.138 in Correlation Coefficient with 16% enhanced precision could be achieved. On account of its encouraging performance, PINGU is hoped to have eventual applications in boosting enzyme engineering and novel drug discovery.
Branched RNA: A New Architecture for RNA Interference

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Anna Aviñó

2011-01-01

Full Text Available Branched RNAs with two and four strands were synthesized. These structures were used to obtain branched siRNA. The branched siRNA duplexes had similar inhibitory capacity as those of unmodified siRNA duplexes, as deduced from gene silencing experiments of the TNF-α protein. Branched RNAs are considered novel structures for siRNA technology, and they provide an innovative tool for specific gene inhibition. As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems.
Small regulatory RNA-induced growth rate heterogeneity of Bacillus subtilis.

Science.gov (United States)

Mars, Ruben A T; Nicolas, Pierre; Ciccolini, Mariano; Reilman, Ewoud; Reder, Alexander; Schaffer, Marc; Mäder, Ulrike; Völker, Uwe; van Dijl, Jan Maarten; Denham, Emma L

2015-03-01

Isogenic bacterial populations can consist of cells displaying heterogeneous physiological traits. Small regulatory RNAs (sRNAs) could affect this heterogeneity since they act by fine-tuning mRNA or protein levels to coordinate the appropriate cellular behavior. Here we show that the sRNA RnaC/S1022 from the Gram-positive bacterium Bacillus subtilis can suppress exponential growth by modulation of the transcriptional regulator AbrB. Specifically, the post-transcriptional abrB-RnaC/S1022 interaction allows B. subtilis to increase the cell-to-cell variation in AbrB protein levels, despite strong negative autoregulation of the abrB promoter. This behavior is consistent with existing mathematical models of sRNA action, thus suggesting that induction of protein expression noise could be a new general aspect of sRNA regulation. Importantly, we show that the sRNA-induced diversity in AbrB levels generates heterogeneity in growth rates during the exponential growth phase. Based on these findings, we hypothesize that the resulting subpopulations of fast- and slow-growing B. subtilis cells reflect a bet-hedging strategy for enhanced survival of unfavorable conditions.
RNA Catalysis, Thermodynamics and the Origin of Life

Directory of Open Access Journals (Sweden)

William G. Scott

2014-04-01

Full Text Available The RNA World Hypothesis posits that the first self-replicating molecules were RNAs. RNA self-replicases are, in general, assumed to have employed nucleotide 5ʹ-polyphosphates (or their analogues as substrates for RNA polymerization. The mechanism by which these substrates might be synthesized with sufficient abundance to supply a growing and evolving population of RNAs is problematic for evolutionary hypotheses because non-enzymatic synthesis and assembly of nucleotide 5ʹ-triphosphates (or other analogously activated phosphodiester species is inherently difficult. However, nucleotide 2ʹ,3ʹ-cyclic phosphates are also phosphodiesters, and are the natural and abundant products of RNA degradation. These have previously been dismissed as viable substrates for prebiotic RNA synthesis. We propose that the arguments for their dismissal are based on a flawed assumption, and that nucleotide 2ʹ,3ʹ-cyclic phosphates in fact possess several significant, advantageous properties that indeed make them particularly viable substrates for prebiotic RNA synthesis. An RNA World hypothesis based upon the polymerization of nucleotide 2ʹ,3ʹ-cyclic phosphates possesses additional explanatory power in that it accounts for the observed ribozyme “fossil record”, suggests a viable mechanism for substrate transport across lipid vesicle boundaries of primordial proto-cells, circumvents the problems of substrate scarcity and implausible synthetic pathways, provides for a primitive but effective RNA replicase editing mechanism, and definitively explains why RNA, rather than DNA, must have been the original catalyst. Finally, our analysis compels us to propose that a fundamental and universal property that drives the evolution of living systems, as well as pre-biotic replicating molecules (be they composed of RNA or protein, is that they exploit chemical reactions that already possess competing kinetically-preferred and thermodynamically-preferred pathways in a

Antibody proteases: induction of catalytic response.

Science.gov (United States)

Gabibov, A G; Friboulet, A; Thomas, D; Demin, A V; Ponomarenko, N A; Vorobiev, I I; Pillet, D; Paon, M; Alexandrova, E S; Telegin, G B; Reshetnyak, A V; Grigorieva, O V; Gnuchev, N V; Malishkin, K A; Genkin, D D

2002-10-01

Most of the data accumulated throughout the years on investigation of catalytic antibodies indicate that their production increases on the background of autoimmune abnormalities. The different approaches to induction of catalytic response toward recombinant gp120 HIV-1 surface protein in mice with various autoimmune pathologies are described. The peptidylphosphonate conjugate containing structural part of gp120 molecule is used for reactive immunization of NZB/NZW F1, MRL, and SJL mice. The specific modification of heavy and light chains of mouse autoantibodies with Val-Ala-Glu-Glu-Glu-Val-PO(OPh)2 reactive peptide was demonstrated. Increased proteolytic activity of polyclonal antibodies in SJL mice encouraged us to investigate the production of antigen-specific catalytic antibodies on the background of induced experimental autoimmune encephalomyelitis (EAE). The immunization of autoimmune-prone mice with the engineered fusions containing the fragments of gp120 and encephalitogenic epitope of myelin basic protein (MBP(89-104)) was made. The proteolytic activity of polyclonal antibodies isolated from the sera of autoimmune mice immunized by the described antigen was shown. Specific immune response of SJL mice to these antigens was characterized. Polyclonal antibodies purified from sera of the immunized animals revealed proteolytic activity. The antiidiotypic approach to raise the specific proteolytic antibody as an "internal image" of protease is described. The "second order" monoclonal antibodies toward subtilisin Carlsberg revealed pronounced proteolytic activity.
Plant RNA Regulatory Network and RNA Granules in Virus Infection

Directory of Open Access Journals (Sweden)

Kristiina Mäkinen

2017-12-01

Full Text Available Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and
Plant RNA Regulatory Network and RNA Granules in Virus Infection.

Science.gov (United States)

Mäkinen, Kristiina; Lõhmus, Andres; Pollari, Maija

2017-01-01

Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual
Effect of Catalytic Layer Thickness on Diameter of Vertically Aligned Individual Carbon Nanotubes

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Hyun Kyung Jung

2014-01-01

Full Text Available The effect of catalytic thin film thickness on the diameter control of individual carbon nanotubes grown by plasma enhanced chemical vapor deposition was investigated. Individual carbon nanotubes were grown on catalytic nanodot arrays, which were fabricated by e-beam lithography and e-beam evaporation. During e-beam evaporation of the nanodot pattern, more catalytic metal was deposited at the edge of the nanodots than the desired catalyst thickness. Because of this phenomenon, carbon atoms diffused faster near the center of the dots than at the edge of the dots. The carbon atoms, which were gathered at the interface between the catalytic nanodot and the diffusion barrier, accumulated near the center of the dot and lifted the catalyst off. From the experiments, an individual carbon nanotube with the same diameter as that of the catalytic nanodot was obtained from a 5 nm thick catalytic nanodot; however, an individual carbon nanotube with a smaller diameter (~40% reduction was obtained from a 50 nm thick nanodot. We found that the thicker the catalytic layer, the greater the reduction in diameter of the carbon nanotubes. The diameter-controlled carbon nanotubes could have applications in bio- and nanomaterial scanning and as a contrast medium for magnetic resonance imaging.
The successes and future prospects of the linear antisense RNA amplification methodology.

Science.gov (United States)

Li, Jifen; Eberwine, James

2018-05-01

It has been over a quarter of a century since the introduction of the linear RNA amplification methodology known as antisense RNA (aRNA) amplification. Whereas most molecular biology techniques are rapidly replaced owing to the fast-moving nature of development in the field, the aRNA procedure has become a base that can be built upon through varied uses of the technology. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. In this Perspective we detail the linear aRNA amplification procedure and its use in assessing various components of a cell's chemical phenotype. This procedure is particularly useful in efforts to multiplex the simultaneous detection of various cellular processes. These efforts are necessary to identify the quantitative chemical phenotype of cells that underlies cellular function.
I.C. Engine emission reduction by copper oxide catalytic converter

Science.gov (United States)

Venkatesan, S. P.; Shubham Uday, Desai; Karan Hemant, Borana; Rajarshi Kushwanth Goud, Kagita; Lakshmana Kumar, G.; Pavan Kumar, K.

2017-05-01

The toxic gases emitted from diesel engines are more than petrol engines. Predicting the use of diesel engines, even more in future, this system is developed and can be used to minimize the harmful gases. Toxic gases include NOX, CO, HC and Smoke which are harmful to the atmosphere as well as to the human beings. The main aim of this work is to fabricate system, where the level of intensity of toxic gases is controlled through chemical reaction to more agreeable level. This system acts itself as an exhaust system; hence there is no needs to fit separate the silencer. The whole assembly is fitted in the exhaust pipe from engine. In this work, catalytic converter with copper oxide as a catalyst, by replacing noble catalysts such as platinum, palladium and rhodium is fabricated and fitted in the engine exhaust. With and without catalytic converter, the experimentations are carried out at different loads such as 0%, 25%, 50%, 75%, and 100% of maximum rated load. From the experimental results it is found that the maximum reduction is 32%, 61% and 21% for HC, NOx and CO respectively at 100% of maximum rated load when compared to that of without catalytic converter. This catalytic converter system is cash effective and more economical than the existing catalytic converter.
Catalytic antibodies in clinical and experimental pathology: human and mouse models.

Science.gov (United States)

Ponomarenko, Natalya A; Durova, Oxana M; Vorobiev, Ivan I; Aleksandrova, Elena S; Telegin, Georgy B; Chamborant, Olga G; Sidorik, Lyudmila L; Suchkov, Sergei V; Alekberova, Zemfira S; Gnuchev, Nikolay V; Gabibov, Alexander G

2002-11-01

Most of the data accumulated through studies on natural catalytic autoantibodies indicate that production scales up markedly in pathological abnormalities. We have previously described an increased level of DNA-hydrolyzing autoantibodies in the sera of patients with various autoimmune disorders [systemic lupus erythematosus (SLE), rheumatoid arthritis, scleroderma], HIV infection and lymphoproliferative diseases accompanied by autoimmune manifestations. In the present study, we show that an increased level of catalytic activity of autoantibodies can be observed in the sera of autoimmune mice, thus providing a fundamental insight into the medical relevance of abzymes. Polyclonal autoantibodies purified from sera of NZB/W, MRL-lpr/lpr and SJL/J mice show proteolytic and DNA-hydrolyzing activities, as opposed to those harvested from non-autoimmune BALB/c mice. The expressiveness of the catalytic activity was strongly dependent on the age of the animal. The highest levels of catalytic activity were found in the sera of mice aged between 8 and 12 months; the lowest level was typical of younger animals whose age ranged from 6 to 8 weeks. Specific inhibition assays of the catalytic activities were performed to throw light on the nature of the abzyme activity. Within a cohort of aging animals, a strong correlation between marked autoimmune abnormalities and levels of catalytic activities has been established. Nonimmunized SJL/J mice revealed specific immune responses to myelin basic protein (MBP), skeletal muscle myosin (skMyo) and cardiac myosin (Myo), and highly purified antibodies from their serum show specific proteolytic attack against the target antigens. This finding prompted us to undertake a more detailed study of specific antibody-mediated proteolysis in diseased humans. A targeted catalytic response was originally demonstrated against MBP and Myo in multiple sclerosis and myocarditis patients, respectively.
Minotaur is critical for primary piRNA biogenesis.

Science.gov (United States)

Vagin, Vasily V; Yu, Yang; Jankowska, Anna; Luo, Yicheng; Wasik, Kaja A; Malone, Colin D; Harrison, Emily; Rosebrock, Adam; Wakimoto, Barbara T; Fagegaltier, Delphine; Muerdter, Felix; Hannon, Gregory J

2013-08-01

Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to silence transposon targets and, as such, form a molecular code that discriminates transposons from endogenous genes. Information ultimately carried by piRNAs is encoded within genomic loci, termed piRNA clusters. These give rise to long, single-stranded, primary transcripts that are processed into piRNAs. Despite the biological importance of this pathway, neither the characteristics that define a locus as a source of piRNAs nor the mechanisms that catalyze primary piRNA biogenesis are well understood. We searched an EMS-mutant collection annotated for fertility phenotypes for genes involved in the piRNA pathway. Twenty-seven homozygous sterile strains showed transposon-silencing defects. One of these, which strongly impacted primary piRNA biogenesis, harbored a causal mutation in CG5508, a member of the Drosophila glycerol-3-phosphate O-acetyltransferase (GPAT) family. These enzymes catalyze the first acylation step on the path to the production of phosphatidic acid (PA). Though this pointed strongly to a function for phospholipid signaling in the piRNA pathway, a mutant form of CG5508, which lacks the GPAT active site, still functions in piRNA biogenesis. We have named this new biogenesis factor Minotaur.
Minotaur is critical for primary piRNA biogenesis

Science.gov (United States)

Vagin, Vasily V.; Yu, Yang; Jankowska, Anna; Luo, Yicheng; Wasik, Kaja A.; Malone, Colin D.; Harrison, Emily; Rosebrock, Adam; Wakimoto, Barbara T.; Fagegaltier, Delphine; Muerdter, Felix; Hannon, Gregory J.

2013-01-01

Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to silence transposon targets and, as such, form a molecular code that discriminates transposons from endogenous genes. Information ultimately carried by piRNAs is encoded within genomic loci, termed piRNA clusters. These give rise to long, single-stranded, primary transcripts that are processed into piRNAs. Despite the biological importance of this pathway, neither the characteristics that define a locus as a source of piRNAs nor the mechanisms that catalyze primary piRNA biogenesis are well understood. We searched an EMS-mutant collection annotated for fertility phenotypes for genes involved in the piRNA pathway. Twenty-seven homozygous sterile strains showed transposon-silencing defects. One of these, which strongly impacted primary piRNA biogenesis, harbored a causal mutation in CG5508, a member of the Drosophila glycerol-3-phosphate O-acetyltransferase (GPAT) family. These enzymes catalyze the first acylation step on the path to the production of phosphatidic acid (PA). Though this pointed strongly to a function for phospholipid signaling in the piRNA pathway, a mutant form of CG5508, which lacks the GPAT active site, still functions in piRNA biogenesis. We have named this new biogenesis factor Minotaur. PMID:23788724
Methylated nucleosides in tRNA and tRNA methyltransferases

Directory of Open Access Journals (Sweden)

Hiroyuki eHori

2014-05-01

Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
CRM1 and its ribosome export adaptor NMD3 localize to the nucleolus and affect rRNA synthesis.

Science.gov (United States)

Bai, Baoyan; Moore, Henna M; Laiho, Marikki

2013-01-01

CRM1 is an export factor that together with its adaptor NMD3 transports numerous cargo molecules from the nucleus to cytoplasm through the nuclear pore. Previous studies have suggested that CRM1 and NMD3 are detected in the nucleolus. However, their localization with subnucleolar domains or participation in the activities of the nucleolus are unclear. We demonstrate here biochemically and using imaging analyses that CRM1 and NMD3 co-localize with nucleolar marker proteins in the nucleolus. In particular, their nucleolar localization is markedly increased by inhibition of RNA polymerase I (Pol I) transcription by actinomycin D or by silencing Pol I catalytic subunit, RPA194. We show that CRM1 nucleolar localization is dependent on its activity and the expression of NMD3, whereas NMD3 nucleolar localization is independent of CRM1. This suggests that NMD3 provides nucleolar tethering of CRM1. While inhibition of CRM1 by leptomycin B inhibited processing of 28S ribosomal (r) RNA, depletion of NMD3 did not, suggesting that their effects on 28S rRNA processing are distinct. Markedly, depletion of NMD3 and inhibition of CRM1 reduced the rate of pre-47S rRNA synthesis. However, their inactivation did not lead to nucleolar disintegration, a hallmark of Pol I transcription stress, suggesting that they do not directly regulate transcription. These results indicate that CRM1 and NMD3 have complex functions in pathways that couple rRNA synthetic and processing engines and that the rRNA synthesis rate may be adjusted according to proficiency in rRNA processing and export.
Catalytic flash pyrolysis of oil-impregnated-wood and jatropha cake using sodium based catalysts

KAUST Repository

Imran, Ali; Bramer, Eddy A.; Seshan, Kulathuiyer; Brem, Gerrit

2015-01-01

Catalytic pyrolysis of wood with impregnated vegetable oil was investigated and compared with catalytic pyrolysis of jatropha cake making use of sodium based catalysts to produce a high quality bio-oil. The catalytic pyrolysis was carried out in two
RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

International Nuclear Information System (INIS)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

2012-01-01

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a
RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

Energy Technology Data Exchange (ETDEWEB)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

2012-04-15

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino
Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components.

Science.gov (United States)

Lu, Qiaosheng; Wierzbicki, Sara; Krasilnikov, Andrey S; Schmitt, Mark E

2010-03-01

RNase MRP is a ribonucleoprotein endoribonuclease found in three cellular locations where distinct substrates are processed: the mitochondria, the nucleolus, and the cytoplasm. Cytoplasmic RNase MRP is the nucleolar enzyme that is transiently relocalized during mitosis. Nucleolar RNase MRP (NuMRP) was purified to homogeneity, and we extensively purified the mitochondrial RNase MRP (MtMRP) to a single RNA component identical to the NuMRP RNA. Although the protein components of the NuMRP were identified by mass spectrometry successfully, none of the known NuMRP proteins were found in the MtMRP preparation. Only trace amounts of the core NuMRP protein, Pop4, were detected in MtMRP by Western blot. In vitro activity of the two enzymes was compared. MtMRP cleaved only mitochondrial ORI5 substrate, while NuMRP cleaved all three substrates. However, the NuMRP enzyme cleaved the ORI5 substrate at sites different than the MtMRP enzyme. In addition, enzymatic differences in preferred ionic strength confirm these enzymes as distinct entities. Magnesium was found to be essential to both enzymes. We tested a number of reported inhibitors including puromycin, pentamidine, lithium, and pAp. Puromycin inhibition suggested that it binds directly to the MRP RNA, reaffirming the role of the RNA component in catalysis. In conclusion, our study confirms that the NuMRP and MtMRP enzymes are distinct entities with differing activities and protein components but a common RNA subunit, suggesting that the RNA must be playing a crucial role in catalytic activity.
MysiRNA-designer: a workflow for efficient siRNA design.

Directory of Open Access Journals (Sweden)

Mohamed Mysara

Full Text Available The design of small interfering RNA (siRNA is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.
Plasma-activated core-shell gold nanoparticle films with enhanced catalytic properties

Energy Technology Data Exchange (ETDEWEB)

Llorca, Jordi, E-mail: jordi.llorca@upc.edu; Casanovas, Albert; Dominguez, Montserrat; Casanova, Ignasi [Universitat Politecnica de Catalunya, Institut de Tecniques Energetiques (Spain); Angurell, Inmaculada; Seco, Miquel; Rossell, Oriol [Universitat de Barcelona, Departament de Quimica Inorganica (Spain)

2008-03-15

Catalytically active gold nanoparticle films have been prepared from core-shell nanoparticles by plasma-activation and characterized by high-resolution transmission electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Methane can be selectively oxidized into formic acid with an O{sub 2}-H{sub 2} mixture in a catalytic wall reactor functionalized with plasma-activated gold nanoparticle films containing well-defined Au particles of about 3.5 nm in diameter. No catalytic activity was recorded over gold nanoparticle films prepared by thermal decomposition of core-shell nanoparticles due to particle agglomeration.
Plasma-activated core-shell gold nanoparticle films with enhanced catalytic properties

International Nuclear Information System (INIS)

Llorca, Jordi; Casanovas, Albert; Dominguez, Montserrat; Casanova, Ignasi; Angurell, Inmaculada; Seco, Miquel; Rossell, Oriol

2008-01-01

Catalytically active gold nanoparticle films have been prepared from core-shell nanoparticles by plasma-activation and characterized by high-resolution transmission electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Methane can be selectively oxidized into formic acid with an O 2 -H 2 mixture in a catalytic wall reactor functionalized with plasma-activated gold nanoparticle films containing well-defined Au particles of about 3.5 nm in diameter. No catalytic activity was recorded over gold nanoparticle films prepared by thermal decomposition of core-shell nanoparticles due to particle agglomeration
RNA binding and replication by the poliovirus RNA polymerase

International Nuclear Information System (INIS)

Oberste, M.S.

1988-01-01

RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to 32 P-labeled ribohomopolymeric RNAs was examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K a for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 x 10 9 M -1 . The polymerase binds to a subgenomic RNAs which contain the 3' end of the genome with a K a similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3' noncoding region
Generation of Human Induced Pluripotent Stem Cells Using RNA-Based Sendai Virus System and Pluripotency Validation of the Resulting Cell Population.

Science.gov (United States)

Chichagova, Valeria; Sanchez-Vera, Irene; Armstrong, Lyle; Steel, David; Lako, Majlinda

2016-01-01

Human induced pluripotent stem cells (hiPSCs) provide a platform for studying human disease in vitro, increase our understanding of human embryonic development, and provide clinically relevant cell types for transplantation, drug testing, and toxicology studies. Since their discovery, numerous advances have been made in order to eliminate issues such as vector integration into the host genome, low reprogramming efficiency, incomplete reprogramming and acquisition of genomic instabilities. One of the ways to achieve integration-free reprogramming is by using RNA-based Sendai virus. Here we describe a method to generate hiPSCs with Sendai virus in both feeder-free and feeder-dependent culture systems. Additionally, we illustrate methods by which to validate pluripotency of the resulting stem cell population.

From biomass to advanced bio-fuel by catalytic pyrolysis/hydro-processing: hydrodeoxygenation of bio-oil derived from biomass catalytic pyrolysis.

Science.gov (United States)

Wang, Yuxin; He, Tao; Liu, Kaituo; Wu, Jinhu; Fang, Yunming

2012-03-01

Compared hydrodeoxygenation experimental studies of both model compounds and real bio-oil derived from biomass fast pyrolysis and catalytic pyrolysis was carried out over two different supported Pt catalysts. For the model compounds, the deoxygenation degree of dibenzofuran was higher than that of cresol and guaiacol over both Pt/Al(2)O(3) and the newly developed Pt supported on mesoporous zeolite (Pt/MZ-5) catalyst, and the deoxygenation degree of cresol over Pt/MZ-5 was higher than that over Pt/Al(2)O(3). The results indicated that hydrodeoxygenation become much easier upon oxygen reduction. Similar to model compounds study, the hydrodeoxygenation of the real bio-oil derived from catalytic pyrolysis was much easier than that from fast pyrolysis over both Pt catalysts, and the Pt/MZ-5 again shows much higher deoxygenation ability than Pt/Al(2)O(3). Clearly synergy between catalytic pyrolysis and bio-oil hydro-processing was found in this paper and this finding will lead an advanced biofuel production pathway in the future. Copyright © 2012 Elsevier Ltd. All rights reserved.
Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme.

Science.gov (United States)

Vallecillo-Viejo, Isabel C; Liscovitch-Brauer, Noa; Montiel-Gonzalez, Maria Fernanda; Eisenberg, Eli; Rosenthal, Joshua J C

2018-01-02

Site-directed RNA editing (SDRE) is a general strategy for making targeted base changes in RNA molecules. Although the approach is relatively new, several groups, including our own, have been working on its development. The basic strategy has been to couple the catalytic domain of an adenosine (A) to inosine (I) RNA editing enzyme to a guide RNA that is used for targeting. Although highly efficient on-target editing has been reported, off-target events have not been rigorously quantified. In this report we target premature termination codons (PTCs) in messages encoding both a fluorescent reporter protein and the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein transiently transfected into human epithelial cells. We demonstrate that while on-target editing is efficient, off-target editing is extensive, both within the targeted message and across the entire transcriptome of the transfected cells. By redirecting the editing enzymes from the cytoplasm to the nucleus, off-target editing is reduced without compromising the on-target editing efficiency. The addition of the E488Q mutation to the editing enzymes, a common strategy for increasing on-target editing efficiency, causes a tremendous increase in off-target editing. These results underscore the need to reduce promiscuity in current approaches to SDRE.
RNA.

Science.gov (United States)

Darnell, James E., Jr.

1985-01-01

Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…
Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

OpenAIRE

Zhang, Yunpeng; Liu, Wei; Xu, Yanjun; Li, Chunquan; Wang, Yingying; Yang, Haixiu; Zhang, Chunlong; Su, Fei; Li, Yixue; Li, Xia

2015-01-01

Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it i...
OPERATING SPECIFICATIONS OF CATALYTIC CLEANING OF GAS FROM BIOMASS GASIFICATION

Directory of Open Access Journals (Sweden)

Martin Lisý

2015-12-01

Full Text Available The paper focuses on the theoretical description of the cleaning of syngas from biomass and waste gasification using catalytic methods, and on the verification of the theory through experiments. The main obstruction to using syngas from fluid gasification of organic matter is the presence of various high-boiling point hydrocarbons (i.e., tar in the gas. The elimination of tar from the gas is a key factor in subsequent use of the gas in other technologies for cogeneration of electrical energy and heat. The application of a natural or artificial catalyst for catalytic destruction of tar is one of the methods of secondary elimination of tar from syngas. In our experiments, we used a natural catalyst (dolomite or calcium magnesium carbonate from Horní Lánov with great mechanical and catalytic properties, suitable for our purposes. The advantages of natural catalysts in contrast to artificial catalysts include their availability, low purchase prices and higher resilience to the so-called catalyst poison. Natural calcium catalysts may also capture undesired compounds of sulphure and chlorine. Our paper presents a theoretical description and analysis of catalytic destruction of tar into combustible gas components, and of the impact of dolomite calcination on its efficiency. The efficiency of the technology is verified in laboratories. The facility used for verification was a 150 kW pilot gasification unit with a laboratory catalytic filter. The efficiency of tar elimination reached 99.5%, the tar concentration complied with limits for use of the gas in combustion engines, and the tar content reached approximately 35 mg/mn3. The results of the measurements conducted in laboratories helped us design a pilot technology for catalytic gas cleaning.
Fuel Flexible, Low Emission Catalytic Combustor for Opportunity Fuel Applications

Energy Technology Data Exchange (ETDEWEB)

Eteman, Shahrokh

2013-06-30

Limited fuel resources, increasing energy demand and stringent emission regulations are drivers to evaluate process off-gases or process waste streams as fuels for power generation. Often these process waste streams have low energy content and/or highly reactive components. Operability of low energy content fuels in gas turbines leads to issues such as unstable and incomplete combustion. On the other hand, fuels containing higher-order hydrocarbons lead to flashback and auto-ignition issues. Due to above reasons, these fuels cannot be used directly without modifications or efficiency penalties in gas turbine engines. To enable the use of these wide variety of fuels in gas turbine engines a rich catalytic lean burn (RCL®) combustion system was developed and tested in a subscale high pressure (10 atm.) rig. The RCL® injector provided stability and extended turndown to low Btu fuels due to catalytic pre-reaction. Previous work has shown promise with fuels such as blast furnace gas (BFG) with LHV of 85 Btu/ft3 successfully combusted. This program extends on this work by further modifying the combustor to achieve greater catalytic stability enhancement. Fuels containing low energy content such as weak natural gas with a Lower Heating Value (LHV) of 6.5 MJ/m3 (180 Btu/ft3 to natural gas fuels containing higher hydrocarbon (e.g ethane) with LHV of 37.6 MJ/m3 (1010 Btu/ft3) were demonstrated with improved combustion stability; an extended turndown (defined as the difference between catalytic and non-catalytic lean blow out) of greater than 250oF was achieved with CO and NOx emissions lower than 5 ppm corrected to 15% O2. In addition, for highly reactive fuels the catalytic region preferentially pre-reacted the higher order hydrocarbons with no events of flashback or auto-ignition allowing a stable and safe operation with low NOx and CO emissions.
microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein.

Science.gov (United States)

Pinder, Benjamin D; Smibert, Craig A

2013-01-01

Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.
Catalytic gasification in fluidized bed, of orange waste. Comparison with non catalytic gasification

International Nuclear Information System (INIS)

Aguiar Trujillo, Leonardo; Marquez Montesinos, Francisco; Ramos Robaina, Boris A.; Guerra Reyes, Yanet; Arauzo Perez, Jesus; Gonzalo Callejo, Alberto; Sanchez Cebrian, Jose L

2011-01-01

The industry processing of the orange, generates high volumes of solid waste. This waste has been used as complement in the animal feeding, in biochemical processes; but their energy use has not been valued by means of the gasification process. They were carried out gasification studies with air in catalytic fluidized bed (using dolomite and olivine as catalysts in a secondary reactor, also varying the temperature of the secondary reactor and the catalyst mass), of the solid waste of orange and the results are compared with those obtained in the gasification with non catalytic air. In the processes we use a design of complete factorial experiment of 2k, valuing the influence of the independent variables and their interactions in the answers, using the software Design-Expert version 7 and a grade of significance of 95 %. The results demonstrate the qualities of the solid waste of orange in the energy use by means of the gasification process for the treatment of these residuals, obtaining a gas of low caloric value. The use of catalysts also diminishes the yield of tars obtained in the gasification process, being more active the dolomite that the olivine in this process. (author)
RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

Directory of Open Access Journals (Sweden)

Andronescu Mirela

2008-08-01

Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.
MicroRNA from tuberculosis RNA: A bioinformatics study

OpenAIRE

Wiwanitkit, Somsri; Wiwanitkit, Viroj

2012-01-01

The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...
Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

Science.gov (United States)

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
Studying RNA-protein interactions in vivo by RNA immunoprecipitation

DEFF Research Database (Denmark)

Selth, Luke A; Close, Pierre; Svejstrup, Jesper Q

2011-01-01

and have significant effects on gene expression. RNA immunoprecipitation (RIP) is a powerful technique used to detect direct and indirect interactions between individual proteins and specific RNA molecules in vivo. Here, we describe RIP methods for both yeast and mammalian cells.......The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases...
RNA SURVEILLANCE– AN EMERGING ROLE FOR RNA REGULATORY NETWORKS IN AGING

OpenAIRE

Montano, Monty; Long, Kimberly

2010-01-01

In this review, we describe recent advances in the field of RNA regulatory biology and relate these advances to aging science. We introduce a new term, RNA surveillance, an RNA regulatory process that is conserved in metazoans, and describe how RNA surveillance represents molecular cross-talk between two emerging RNA regulatory systems – RNA interference and RNA editing. We discuss how RNA surveillance mechanisms influence mRNA and microRNA expression and activity during lifespan. Additionall...
Mechanisms of catalytic activity in heavily coated hydrocracking catalysts

Energy Technology Data Exchange (ETDEWEB)

Millan, M.; Adell, C.; Hinojosa, C.; Herod, A.A.; Kandiyoti, R. [University of London Imperial College Science Technology & Medicine, London (United Kingdom). Dept. of Chemical Engineering

2008-01-15

Catalyst deactivation by coke deposition has a direct impact on the economic viability of heavy hydrocarbon upgrading processes, such as coal liquefaction and oil residue hydroprocessing. Coke deposition is responsible for rapid loss of catalytic activity and it mostly takes place in the early stages of hydrocracking. The effect of carbonaceous deposition on the catalytic activity of a chromium pillared montmorillonite has been studied in the present work. Its catalytic activity in hydrocracking a coal extract was evaluated based on the boiling point distributions of feed and products obtained by thermogravimetric analysis (TGA), and their characterisation by size exclusion chromatography (SEC) and UV-Fluorescence spectroscopy (UV-F). A large deposition on the catalyst was observed after two successive 2-hour long runs in which the catalyst recovered from the first run was reused in the second. The pillared clay retained its activity even though it showed high carbon loading, a large drop in surface area and complete apparent pore blockage. Some observations may contribute to explain this persistent catalytic activity. First, there is evidence suggesting the dynamic nature of the carbonaceous deposits, which continuously exchange material with the liquid, allowing catalytic activity to continue. Secondly, Scanning Electron Microscopy (SEM) on the used Cr montmorillonite has shown preferential deposition on some regions of the catalyst, which leaves a fraction of the surface relatively exposed. Finally, evidence from SEM coupled to X-ray microanalysis also suggest that deposits are thinner in areas where the active phase of the catalyst is present in higher concentrations. Hydrogenation on the active sites would make the deposits more soluble in the liquid cleaning of surrounding area from deposits.
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.
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.
Challenges of the movement of catalytic micromotors in blood.

Science.gov (United States)

Zhao, Guanjia; Viehrig, Marlitt; Pumera, Martin

2013-05-21

Catalytic microjet bubble-propelled engines have attracted a large amount of interest for their potential applications in biomedicine, environmental sciences and natural resources discovery. One of the current efforts in this field is focused on the search of biocompatible fuels. However, only a minimal amount of effort has been made to assess the challenges facing the movement of such devices in a real world environment, especially with regards to the components of blood and their interactions with the catalytic microjets. Herein, we will show the limitations on the movement of catalytic microengines prepared via the rolled-up, as well as the templated-electrochemical deposition method, in an artificial blood sample, due to the presence of two main components of animal blood: the cellular component (red blood cells in this study) and serum. We will show that the motion of catalytic microjets is only possible in highly diluted dispersions of the red blood cells and serum. This finding has a profound implication on the development of the whole field, where the components found in real environments have to be considered carefully, and issues arising from the presence of such components have to be resolved prior to deploying these devices in real world applications.
sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline.

Science.gov (United States)

Wu, Xiaogang; Kim, Taek-Kyun; Baxter, David; Scherler, Kelsey; Gordon, Aaron; Fong, Olivia; Etheridge, Alton; Galas, David J; Wang, Kai

2017-12-01

Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline-sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline

Science.gov (United States)

Kim, Taek-Kyun; Baxter, David; Scherler, Kelsey; Gordon, Aaron; Fong, Olivia; Etheridge, Alton; Galas, David J.

2017-01-01

Abstract Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline—sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/. PMID:29069500
Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

NARCIS (Netherlands)

Kluiver, Joost; Gibcus, Johan H.; Hettinga, Chris; Adema, Annelies; Richter, Mareike K. S.; Halsema, Nancy; Slezak-Prochazka, Izabella; Ding, Ye; Kroesen, Bart-Jan; van den Berg, Anke

2012-01-01

MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and

Photolytic AND Catalytic Destruction of Organic Waste Water Pollutants

Science.gov (United States)

Torosyan, V. F.; Torosyan, E. S.; Kryuchkova, S. O.; Gromov, V. E.

2017-01-01

The system: water supply source - potable and industrial water - wastewater - sewage treatment - water supply source is necessary for water supply and efficient utilization of water resources. Up-to-date technologies of waste water biological treatment require for special microorganisms, which are technologically complex and expensive but unable to solve all the problems. Application of photolytic and catalytically-oxidizing destruction is quite promising. However, the most reagents are strong oxidizers in catalytic oxidation of organic substances and can initiate toxic substance generation. Methodic and scientific approaches to assess bread making industry influence on the environment have been developed in this paper in order to support forecasting and taking technological decisions concerning reduction of this influence. Destructive methods have been tested: ultra violet irradiation and catalytic oxidation for extraction of organic compounds from waste water by natural reagents.
Catalytic Ammonia Decomposition Over Ruthenium Nanoparticles Supported on Nano-Titanates

DEFF Research Database (Denmark)

Klerke, Asbjørn; Klitgaard, Søren Kegnæs; Fehrmann, Rasmus

2009-01-01

Nanosized Na2Ti3O7, K2Ti6O13 and Cs2Ti6O13 materials were prepared and used as supports of ruthenium nanoparticles for catalytic ammonia decomposition. It is shown that these catalysts exhibit higher catalytic activity than ruthenium supported on TiO2 nanoparticles promoted with cesium. The diffe...
The ApaH-like phosphatase TbALPH1 is the major mRNA decapping enzyme of trypanosomes.

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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.
Catalytical Properties of Free and Immobilized Aspergillus niger Tannase

OpenAIRE

Abril Flores-Maltos; Luis V. Rodríguez-Durán; Jacqueline Renovato; Juan C. Contreras; Raúl Rodríguez; Cristóbal N. Aguilar

2011-01-01

A fungal tannase was produced, recovered, and immobilized by entrapment in calcium alginate beads. Catalytical properties of the immobilized enzyme were compared with those of the free one. Tannase was produced intracellularly by the xerophilic fungus Aspergillus niger GH1 in a submerged fermentation system. Enzyme was recovered by cell disruption and the crude extract was partially purified. The catalytical properties of free and immobilized tannase were evaluated using tannic acid and methy...
MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.

Science.gov (United States)

Corrêa, Régis L; Steiner, Florian A; Berezikov, Eugene; Ketting, René F

2010-04-08

RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi-related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.
Plant RNA binding proteins for control of RNA virus infection

Directory of Open Access Journals (Sweden)

Sung Un eHuh

2013-12-01

Full Text Available Plant RNA viruses have effective strategies to infect host plants through either direct or indirect interactions with various host proteins, thus suppressing the host immune system. When plant RNA viruses enter host cells exposed RNAs of viruses are recognized by the host immune system through processes such as siRNA-dependent silencing. Interestingly, some host RNA binding proteins have been involved in the inhibition of RNA virus replication, movement, and translation through RNA-specific binding. Host plants intensively use RNA binding proteins for defense against viral infections in nature. In this mini review, we will summarize the function of some host RNA binding proteins which act in a sequence-specific binding manner to the infecting virus RNA. It is important to understand how plants effectively suppresses RNA virus infections via RNA binding proteins, and this defense system can be potentially developed as a synthetic virus defense strategy for use in crop engineering.
Chemistry and engineering of catalytic hydrodesulfurization

NARCIS (Netherlands)

Schuit, G.C.A.; Gates, B.C.

1973-01-01

A review with 74 refs. on catalytic hydrodesulfurization of pure compds. and petroleum feedstocks, with emphasis on reaction intermediates and structures of Al2O3-supported Ni-W and Co-Mo catalysts. [on SciFinder (R)
Kinetic and catalytic performance of a BI-porous composite material in catalytic cracking and isomerisation reactions

KAUST Repository

Al-Khattaf, S.; Odedairo, T.; Balasamy, R. J.

2012-01-01

Catalytic behaviour of pure zeolite ZSM-5 and a bi-porous composite material (BCM) were investigated in transformation of m-xylene, while zeolite HY and the bi-porous composite were used in the cracking of 1,3,5-triisopropylbenzene (TIPB). The micro
Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems

Science.gov (United States)

Szilágyi, András; Kun, Ádám; Könnyű, Balázs; Czárán, Tamás

2017-01-01

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future. PMID:29186916
Effective Anti-miRNA Oligonucleotides Show High Releasing Rate of MicroRNA from RNA-Induced Silencing Complex.

Science.gov (United States)

Ariyoshi, Jumpei; Matsuyama, Yohei; Kobori, Akio; Murakami, Akira; Sugiyama, Hiroshi; Yamayoshi, Asako

2017-10-01

MicroRNAs (miRNAs) regulate gene expression by forming RNA-induced silencing complexes (RISCs) and have been considered as promising therapeutic targets. MiRNA is an essential component of RISC for the modulation of gene expression. Therefore, the release of miRNA from RISC is considered as an effective method for the inhibition of miRNA functions. In our previous study, we reported that anti-miRNA oligonucleotides (AMOs), which are composed of the 2'-O-methyl (2'-OMe) RNA, could induce the release of miRNA from RISC. However, the mechanisms underlying the miRNA-releasing effects of chemically modified AMOs, which are conventionally used as anti-cancer drugs, are still unclear. In this study, we investigated the relationship between the miRNA releasing rate from RISC and the inhibitory effect on RISC activity (IC 50 ) using conventional chemically modified AMOs. We demonstrated that the miRNA-releasing effects of AMOs are directly proportional to the IC 50 values, and AMOs, which have an ability to promote the release of miRNA from RISC, can effectively inhibit RISC activity in living cells.
Enhancing chemosensitivity to gemcitabine via RNA interference targeting the catalytic subunits of protein kinase CK2 in human pancreatic cancer cells

International Nuclear Information System (INIS)

Kreutzer, Jan N; Ruzzene, Maria; Guerra, Barbara

2010-01-01

Pancreatic cancer is a complex genetic disorder that is characterized by rapid progression, invasiveness, resistance to treatment and high molecular heterogeneity. Various agents have been used in clinical trials showing only modest improvements with respect to gemcitabine-based chemotherapy, which continues to be the standard first-line treatment for this disease. However, owing to the overwhelming molecular alterations that have been reported in pancreatic cancer, there is increasing focus on targeting molecular pathways and networks, rather than individual genes or gene-products with a combination of novel chemotherapeutic agents. Cells were transfected with small interfering RNAs (siRNAs) targeting the individual CK2 subunits. The CK2 protein expression levels were determined and the effect of its down-regulation on chemosensitization of pancreatic cancer cells was investigated. The present study examined the impact on cell death following depletion of the individual protein kinase CK2 catalytic subunits alone or in combination with gemcitabine and the molecular mechanisms by which this effect is achieved. Depletion of the CK2α or -α' subunits in combination with gemcitabine resulted in marked apoptotic and necrotic cell death in PANC-1 cells. We show that the mechanism of cell death is associated with deregulation of distinct survival signaling pathways. Cellular depletion of CK2α leads to phosphorylation and activation of MKK4/JNK while down-regulation of CK2α' exerts major effects on the PI3K/AKT pathway. Results reported here show that the two catalytic subunits of CK2 contribute differently to enhance gemcitabine-induced cell death, the reduced level of CK2α' being the most effective and that simultaneous reduction in the expression of CK2 and other survival factors might be an effective therapeutic strategy for enhancing the sensitivity of human pancreatic cancer towards chemotherapeutic agents
Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

DEFF Research Database (Denmark)

Kruhøffer, Mogens; Andersen, Lars Dyrskjøt; Voss, Thorsten

2007-01-01

We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood...... and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated micro......RNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis....
The Role of RNA Interference (RNAi in Arbovirus-Vector Interactions

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Carol D. Blair

2015-02-01

Full Text Available RNA interference (RNAi was shown over 18 years ago to be a mechanism by which arbovirus replication and transmission could be controlled in arthropod vectors. During the intervening period, research on RNAi has defined many of the components and mechanisms of this antiviral pathway in arthropods, yet a number of unexplored questions remain. RNAi refers to RNA-mediated regulation of gene expression. Originally, the term described silencing of endogenous genes by introduction of exogenous double-stranded (dsRNA with the same sequence as the gene to be silenced. Further research has shown that RNAi comprises three gene regulation pathways that are mediated by small RNAs: the small interfering (siRNA, micro (miRNA, and Piwi-interacting (piRNA pathways. The exogenous (exo-siRNA pathway is now recognized as a major antiviral innate immune response of arthropods. More recent studies suggest that the piRNA and miRNA pathways might also have important roles in arbovirus-vector interactions. This review will focus on current knowledge of the role of the exo-siRNA pathway as an arthropod vector antiviral response and on emerging research into vector piRNA and miRNA pathway modulation of arbovirus-vector interactions. Although it is assumed that arboviruses must evade the vector’s antiviral RNAi response in order to maintain their natural transmission cycles, the strategies by which this is accomplished are not well defined. RNAi is also an important tool for arthropod gene knock-down in functional genomics studies and in development of arbovirus-resistant mosquito populations. Possible arbovirus strategies for evasion of RNAi and applications of RNAi in functional genomics analysis and arbovirus transmission control will also be reviewed.
IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions.

Science.gov (United States)

Mann, Martin; Wright, Patrick R; Backofen, Rolf

2017-07-03

The IntaRNA algorithm enables fast and accurate prediction of RNA-RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA-RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Catalytic reforming methods

Science.gov (United States)

Tadd, Andrew R; Schwank, Johannes

2013-05-14

A catalytic reforming method is disclosed herein. The method includes sequentially supplying a plurality of feedstocks of variable compositions to a reformer. The method further includes adding a respective predetermined co-reactant to each of the plurality of feedstocks to obtain a substantially constant output from the reformer for the plurality of feedstocks. The respective predetermined co-reactant is based on a C/H/O atomic composition for a respective one of the plurality of feedstocks and a predetermined C/H/O atomic composition for the substantially constant output.
Genetic relatedness of orbiviruses by RNA-RNA blot hybridization

International Nuclear Information System (INIS)

Bodkin, D.K.

1985-01-01

RNA-RNA blot hybridization was developed in order to identify type-specific genes among double-stranded (ds) RNA viruses, to assess the genetic relatedness of dsRNA viruses and to classify new strains. Viral dsRNA segments were electrophoresed through 10% polyacrylamide gels, transferred to membranes, and hybridized to [5' 32 P]-pCp labeled genomic RNA from a related strain. Hybridization was performed at 52 0 C, 50% formamide, 5X SSC. Under these conditions heterologous RNA species must share ≥ 74% sequence homology in order to form stable dsRNA hybrids. Cognate genes of nine members of the Palyam serogroup of orbiviruses were identified and their sequence relatedness to the prototype. Palyam virus, was determined. Reciprocal blot hybridizations were performed using radiolabeled genomic RNA of all members of the Palyam serogroup. Unique and variant genes were identified by lack of cross-homology or by weak homology between segments. Since genes 2 and 6 exhibited the highest degree of sequence variability, response to the vertebrate immune system may be a major cause of sequence divergence among members of a single serogroup. Changuinola serogroup isolates were compared by dot-blot hybridization, while Colorado tick fever (CTF) serogroup isolates were compared by the RNA-RNA blot hybridization procedure described for reovirus and Palyam serogroup isolates. Preliminary blot hybridization data were also obtained on the relatedness of members of different Orbivirus serogroups
Heterogeneous kinetic modeling of the catalytic conversion of cycloparaffins

Science.gov (United States)

Al-Sabawi, Mustafa N.

The limited availability of high value light hydrocarbon feedstocks along with the rise in crude prices has resulted in the international recognition of the vast potential of Canada's oil sands. With the recent expansion of Canadian bitumen production come, however, many technical challenges, one of which is the significant presence of aromatics and cycloparaffins in bitumen-derived feedstocks. In addition to their negative environmental impact, aromatics limit fluid catalytic cracking (FCC) feedstock conversion, decrease the yield and quality of valuable products such as gasoline and middle distillates, increase levels of polyaromatic hydrocarbons prone to form coke on the catalyst, and ultimately compromise the FCC unit performance. Although cycloparaffins do not have such negative impacts, they are precursors of aromatics as they frequently undergo hydrogen transfer reactions. However, cycloparaffin cracking chemistry involves other competing reactions that are complex and need much investigation. This dissertation provides insights and understanding of the fundamentals of the catalytic cracking of cycloparaffins using carefully selected model compounds such as methylcyclohexane (MCH) and decalin. Thermal and catalytic cracking of these cycloparaffins on FCC-type catalysts are carried out using the CREC Riser Simulator under operating conditions similar to those of the industrial FCC units in terms of temperature, reaction time, reactant partial pressure and catalyst-to-hydrocarbon ratio. The crystallite size of the supported zeolites is varied between 0.4 and 0.9 microns, with both activity and selectivity being monitored. Catalytic conversions ranged between 4 to 16 wt% for MCH and between 8 to 27 wt% for decalin. Reaction pathways of cycloparaffins are determined, and these include ring-opening, protolytic cracking, isomerization, hydrogen transfer and transalkylation. The yields and selectivities of over 60 and 140 products, formed during MCH and decalin
The crystal structure and RNA-binding of an orthomyxovirus nucleoprotein.

Directory of Open Access Journals (Sweden)

Wenjie Zheng

2013-09-01

Full Text Available Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV (genus Isavirus. As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ~12 nts of RNA, shorter than the 24-28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions.
A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

Directory of Open Access Journals (Sweden)

Baodong Wu

2009-03-01

Full Text Available Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.
Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach

Directory of Open Access Journals (Sweden)

Galiano V

2016-10-01

Full Text Available Vicente Galiano,1 Pablo Garcia-Valtanen,2 Vicente Micol,3,4 José Antonio Encinar3 1Physics and Computer Architecture Department, Miguel Hernández University (UMH, Elche, Spain; 2Experimental Therapeutics Laboratory, Hanson and Sansom Institute for Health Research, School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia; 3Molecular and Cell Biology Institute, Miguel Hernández University (UMH, Elche, Spain; 4CIBER: CB12/03/30038, Physiopathology of the Obesity and Nutrition, CIBERobn, Instituto de Salud Carlos III, Palma de Mallorca, Spain Abstract: The dengue virus (DENV nonstructural protein 5 (NS5 contains both an N-terminal methyltransferase domain and a C-terminal RNA-dependent RNA polymerase domain. Polymerase activity is responsible for viral RNA synthesis by a de novo initiation mechanism and represents an attractive target for antiviral therapy. The incidence of DENV has grown rapidly and it is now estimated that half of the human population is at risk of becoming infected with this virus. Despite this, there are no effective drugs to treat DENV infections. The present in silico study aimed at finding new inhibitors of the NS5 RNA-dependent RNA polymerase of the four serotypes of DENV. We used a chemical library comprising 372,792 nonnucleotide compounds (around 325,319 natural compounds to perform molecular docking experiments against a binding site of the RNA template tunnel of the virus polymerase. Compounds with high negative free energy variation (ΔG <-10.5 kcal/mol were selected as putative inhibitors. Additional filters for favorable druggability and good absorption, distribution, metabolism, excretion, and toxicity were applied. Finally, after the screening process was completed, we identified 39 compounds as lead DENV polymerase inhibitor candidates. Potentially, these compounds could act as efficient DENV polymerase inhibitors in vitro and in vivo. Keywords: virtual screening, molecular

Non-Specific dsRNA-Mediated Antiviral Response in the Honey Bee

Science.gov (United States)

Flenniken, Michelle L.; Andino, Raul

2013-01-01

Honey bees are essential pollinators of numerous agricultural crops. Since 2006, honey bee populations have suffered considerable annual losses that are partially attributed to Colony Collapse Disorder (CCD). CCD is an unexplained phenomenon that correlates with elevated incidence of pathogens, including RNA viruses. Honey bees are eusocial insects that live in colonies of genetically related individuals that work in concert to gather and store nutrients. Their social organization provides numerous benefits, but also facilitates pathogen transmission between individuals. To investigate honey bee antiviral defense mechanisms, we developed an RNA virus infection model and discovered that administration of dsRNA, regardless of sequence, reduced virus infection. Our results suggest that dsRNA, a viral pathogen associated molecular pattern (PAMP), triggers an antiviral response that controls virus infection in honey bees. PMID:24130869
Seryl-tRNA Synthetases from Methanogenic Archaea: Suppression of Bacterial Amber Mutation and Heterologous Toxicity

Directory of Open Access Journals (Sweden)

Drasko Boko

2010-01-01

Full Text Available Methanogenic archaea possess unusual seryl-tRNA synthetases (SerRS, evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. Our recent X-ray structural analysis of Methanosarcina barkeri SerRS revealed an idiosyncratic N-terminal domain and catalytic zinc ion in the active site. To shed further light on substrate discrimination by methanogenic-type SerRS, we set up to explore in vivo the interaction of methanogenic-type SerRSs with their cognate tRNAs in Escherichia coli or Saccharomyces cerevisiae. The expression of various methanogenic-type SerRSs was toxic for E. coli, resulting in the synthesis of erroneous proteins, as revealed by β-galactosidase stability assay. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precluded the complementation of endogenous SerRS function in both, E. coli and S. cerevisiae. However, despite the observed toxicity, coexpression of methanogenic-type SerRS with its cognate tRNA suppressed bacterial amber mutation.
Catalytic copyrolysis of particle board and polypropylene over Al-MCM-48

Energy Technology Data Exchange (ETDEWEB)

Kim, Hannah; Choi, Suek Ju [School of Environmental Engineering, University of Seoul, Seoul 02504 (Korea, Republic of); Kim, Ji Man [Department of Chemistry, Sungkyunkwan University, Suwon 16419 (Korea, Republic of); Jeon, Jong-Ki [Department of Chemical Engineering, Kongju National University, Cheonan 31080 (Korea, Republic of); Park, Sung Hoon; Jung, Sang-Chul [Department of Environmental Engineering, Sunchon National University, Suncheon 57922 (Korea, Republic of); Kim, Sang Chai [Department of Environmental Education, Mokpo National University, Muan 58554 (Korea, Republic of); Park, Young-Kwon, E-mail: catalica@uos.ac.kr [School of Environmental Engineering, University of Seoul, Seoul 02504 (Korea, Republic of)

2016-10-15

Highlights: • Al-MCM-48 was used for catalytic copyrolysis of particle board and polypropylene. • Catalytic produced mainly hydrocarbons. • The hydrocarbons produced were mainly in the diesel range. - Abstract: Particle board and polypropylene (PP) at a mixing ratio of 1:1 were copyrolyzed over two Al-MCM-48 catalysts with Si/Al ratios of 20 and 80. The catalyst characteristics were examined by measuring the Brunauer-Emmett-Teller surface area, temperature programmed desorption of ammonia, and X-ray diffraction. The main pyrolysis products of particle board were oxygenates, acids, and phenolics, whereas a large quantity of hydrocarbons within the diesel fuel range was produced from copyrolysis with polypropylene. The catalytic copyrolysis of particle board and PP over the Al-MCM-48 catalysts produced bio-oil with a much larger hydrocarbon content than that from the catalytic pyrolysis of particle board only. The hydrocarbons produced were mainly in the diesel range, highlighting the potential for the production of high-quality fuel.
Aligned carbon nanotube with electro-catalytic activity for oxygen reduction reaction

Science.gov (United States)

Liu, Di-Jia; Yang, Junbing; Wang, Xiaoping

2010-08-03

A catalyst for an electro-chemical oxygen reduction reaction (ORR) of a bundle of longitudinally aligned carbon nanotubes having a catalytically active transition metal incorporated longitudinally in said nanotubes. A method of making an electro-chemical catalyst for an oxygen reduction reaction (ORR) having a bundle of longitudinally aligned carbon nanotubes with a catalytically active transition metal incorporated throughout the nanotubes, where a substrate is in a first reaction zone, and a combination selected from one or more of a hydrocarbon and an organometallic compound containing an catalytically active transition metal and a nitrogen containing compound and an inert gas and a reducing gas is introduced into the first reaction zone which is maintained at a first reaction temperature for a time sufficient to vaporize material therein. The vaporized material is then introduced to a second reaction zone maintained at a second reaction temperature for a time sufficient to grow longitudinally aligned carbon nanotubes over the substrate with a catalytically active transition metal incorporated throughout the nanotubes.
Bifurcations in the interplay of messenger RNA, protein and nonprotein coding RNA

International Nuclear Information System (INIS)

Zhdanov, Vladimir P

2008-01-01

The interplay of messenger RNA (mRNA), protein, produced via translation of this RNA, and nonprotein coding RNA (ncRNA) may include regulation of the ncRNA production by protein and (i) ncRNA-protein association resulting in suppression of the protein regulatory activity or (ii) ncRNA-mRNA association resulting in degradation of the miRNA-mRNA complex. The kinetic models describing these two scenarios are found to predict bistability provided that protein suppresses the ncRNA formation
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...
Formalization of hydrocarbon conversion scheme of catalytic cracking for mathematical model development

Science.gov (United States)

Nazarova, G.; Ivashkina, E.; Ivanchina, E.; Kiseleva, S.; Stebeneva, V.

2015-11-01

The issue of improving the energy and resource efficiency of advanced petroleum processing can be solved by the development of adequate mathematical model based on physical and chemical regularities of process reactions with a high predictive potential in the advanced petroleum refining. In this work, the development of formalized hydrocarbon conversion scheme of catalytic cracking was performed using thermodynamic parameters of reaction defined by the Density Functional Theory. The list of reaction was compiled according to the results of feedstock structural-group composition definition, which was done by the n-d-m-method, the Hazelvuda method, qualitative composition of feedstock defined by gas chromatography-mass spectrometry and individual composition of catalytic cracking gasoline fraction. Formalized hydrocarbon conversion scheme of catalytic cracking will become the basis for the development of the catalytic cracking kinetic model.
High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea.

Science.gov (United States)

Srivastava, Sangeeta; Zheng, Yun; Kudapa, Himabindu; Jagadeeswaran, Guru; Hivrale, Vandana; Varshney, Rajeev K; Sunkar, Ramanjulu

2015-06-01

Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs/phasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5' RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA-target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.
A catalytic distillation process for light gas oil hydrodesulfurization

Energy Technology Data Exchange (ETDEWEB)

Vargas-Villamil, F.D.; Marroquin, J.O.; Paz, C. de la; Rodriguez, E. [Prog. de Matematicas Aplicadas y Computacion, Prog. de Tratamiento de Crudo Maya, Instituto Mexicano del Petroleo, Mexico City, DF (Mexico)

2004-07-01

A light gas oil hydrodesulfurization process via catalytic distillation is developed and compared to a conventional process. By integrating the separation and reaction into a single unit, the catalytic distillation may produce a diesel with low concentration of sulfur compounds at a lower cost than the traditional reaction/separation process. The process proposed in this work is compared to an optimised conventional hydrodesulfurization unit which represents fairly well a plant that belongs to the National System of Refineries. During the optimisation of the conventional process, a compromise is established among the production of diesel and naphtha and the operating costs. The results show that the light gas oil hydrodesulfurization via catalytic distillation is as or more efficient than the conventional process. However, the removal of the sulfur compounds is carried out under less rigorous conditions. This design reduces the fix and operational costs. (author)
Electro-catalytic degradation of sulfisoxazole by using graphene anode.

Science.gov (United States)

Wang, Yanyan; Liu, Shuan; Li, Ruiping; Huang, Yingping; Chen, Chuncheng

2016-05-01

Graphite and graphene electrodes were prepared by using pure graphite as precursor. The electrode materials were characterized by a scanning electron microscope (SEM), X-ray diffraction (XRD) and cyclic voltammetry (CV) measurements. The electro-catalytic activity for degradation of sulfisoxazole (SIZ) was investigated by using prepared graphene or graphite anode. The results showed that the degradation of SIZ was much more rapid on the graphene than that on the graphite electrode. Moreover, the graphene electrode exhibited good stability and recyclability. The analysis on the intermediate products and the measurement of active species during the SIZ degradation demonstrated that indirect oxidation is the dominant mechanism, involving the electro-catalytic generation of OH and O2(-) as the main active oxygen species. This study implies that graphene is a promising potential electrode material for long-term application to electro-catalytic degradation of organic pollutants. Copyright © 2015. Published by Elsevier B.V.
Silencing of the hTERT gene by shRNA inhibits colon cancer SW480 cell growth in vitro and in vivo.

Directory of Open Access Journals (Sweden)

Ai-Qun Liu

Full Text Available Human telomerase reverse transcriptase (hTERT is the key enzyme responsible for synthesizing and maintaining the telomeres on the ends of chromosomes, and it is essential for cell proliferation. This has made hTERT a focus of oncology research and an attractive target for anticancer drug development. In this study, we designed a small interfering RNA (siRNA targeting the catalytic subunit of hTERT and tested its effects on the growth of telomerase-positive human colon carcinoma SW480 cells in vitro, as well as on the tumorigenicity of these cells in nude mice. Transient and stable transfection of hTERT siRNA into colon cancer SW480 cells suppressed hTERT expression, reduced telomerase activity and inhibited cell growth and proliferation. Knocking down hTERT expression in SW480 tumors xenografted into nude mice significantly slowed tumor growth and promoted tumor cell apoptosis. Our results suggest that hTERT is involved in carcinogenesis of human colon carcinoma, and they highlight the therapeutic potential of a hTERT knock-down approach.
Catalytic Oxidation of CO and Soot over Ce-Zr-Pr Mixed Oxides Synthesized in a Multi-Inlet Vortex Reactor: Effect of Structural Defects on the Catalytic Activity.

Science.gov (United States)

Bensaid, Samir; Piumetti, Marco; Novara, Chiara; Giorgis, Fabrizio; Chiodoni, Angelica; Russo, Nunzio; Fino, Debora

2016-12-01

In the present work, ceria, ceria-zirconia (Ce = 80 at.%, Zr = 20 at.%), ceria praseodymia (Ce = 80 at.%, Pr = 20 at.%) and ceria-zirconia-praseodymia catalysts (Ce = 80 at.%, Zr = 10 at.% and Pr = 10 at.%) have been prepared by the multi-inlet vortex reactor (MIVR). For each set of samples, two inlet flow rates have been used during the synthesis (namely, 2 ml min -1 , and 20 ml min -1 ) in order to obtain different particle sizes. Catalytic activity of the prepared materials has been investigated for CO and soot oxidation reactions. As a result, when the catalysts exhibit similar crystallite sizes (in the 7.7-8.8 nm range), it is possible to observe a direct correlation between the O v /F 2g vibrational band intensity ratios and the catalytic performance for the CO oxidation. This means that structural (superficial) defects play a key role for this process. The incorporation of Zr and Pr species into the ceria lattice increases the population of structural defects, as measured by Raman spectroscopy, according to the order: CeO 2 oxidation activity for these catalysts, in contrast with nanostructured ones (e.g., Ce-Zr-O nanopolyhedra, Ce-Pr-O nanocubes) described elsewhere (Andana et al. Appl. Catal. B 197: 125-137, 2016; Piumetti et al., Appl Catal B 180: 271-282, 2016).
Enhanced catalytic behavior of Ni alloys in steam methane reforming

Science.gov (United States)

Yoon, Yeongpil; Kim, Hanmi; Lee, Jaichan

2017-08-01

The dissociation process of methane on Ni and Ni alloys are investigated by density functional theory (DFT) in terms of catalytic efficiency and carbon deposition. Examining the dissociation to CH3, CH2, CH, C, and H is not sufficient to properly predict the catalytic efficiency and carbon deposition, and further investigation of the CO gas-evolving reaction is required to completely understand methane dissociation in steam. The location of alloying element in Ni alloy needed be addressed from the results of ab-inito molecular dynamics (MD). The reaction pathway of methane dissociation associated with CO gas evolution is traced by performing first-principles calculations of the adsorption and activation energies of each dissociation step. During the dissociation process, two alternative reaction steps producing adsorbed C and H or adsorbed CO are critically important in determining coking inhibition as well as H2 gas evolution (i.e., the catalytic efficiency). The theoretical calculations presented here suggest that alloying Ni with Ru is an effective way to reduce carbon deposition and enhance the catalytic efficiency of H2 fueling in solid oxide fuel cells (SOFCs).
Simulation and calculation of three-reactor system of catalytic reforming

International Nuclear Information System (INIS)

Rikalovska, Tatjana; Markovska, Liljana; Meshko, Vera; Poposka, Filimena

1999-01-01

The process of catalytic reforming has been operated for quite a long time, one can not always find real data for the kinetics and thermodynamics of the reactions that take place during the catalytic reforming process in order to facilitate the designing of reactor system or its simulation in a wide:ran e of process parameters. Kinetic and thermodynamic data have been collected for the reactions that take place during the catalytic reforming process. The stress has been pointed on four major reactions: dehydrogenation of naphthenes (aromatization), dehydrocyclization of paraffins and hydrocracking of naphthenes and paraffins. On the base of such a kinetic model, the reforming process has been described with a system of differential equations. For the purpose of solving these equations computer programs for simulation of a three-reactor system for adiabatic operation of the reactors. The computer simulation of the mathematical model of this three-reactor system has been accomplished by use of the ISIM-dynamic simulator. The results obtained out of the simulation agree very good with the data of the real process of catalytic reforming in OKTA Crude Oil Refinery in Skopje, Macedonia. (Author)
The catalytic cracking mechanism of lignite pyrolysis char on tar

International Nuclear Information System (INIS)

Lei, Z.; Huibin, H.; Xiangling, S.; Zhenhua, M.; Lei, Z.

2017-01-01

The influence of different pyrolysis conditions for tar catalytic cracking will be analyzed according to the lignite pyrolysis char as catalyst on pyrolytic tar in this paper. The pyrolysis char what is the by-product of the cracking of coal has an abundant of pore structure and it has good catalytic activity. On this basis, making the modified catalyst when the pyrolysis char is activation and loads Fe by impregnation method. The cracking mechanism of lignite pyrolytic tar is explored by applying gas chromatograph to analyze splitting products of tar. The experimental results showed that: (1) The effect of tar cracking as the pyrolysis temperature, the heating rate, the volatilization of pyrolysis char and particle size increasing is better and better. The effect of the catalytic and cracking of lignite pyrolysis char in tar is best when the heating rate, the pyrolysis temperature, the volatiles of pyrolysis char, particle size is in specific conditions.(2) The activation of pyrolysis char can improve the catalytic effect of pyrolysis char on the tar cracking. But it reduces the effect of the tar cracking when the pyrolysis char is activation loading Fe. (author)
Catalytic ozonation of fenofibric acid over alumina-supported manganese oxide

Energy Technology Data Exchange (ETDEWEB)

Rosal, Roberto, E-mail: roberto.rosal@uah.es [Departamento de Quimica Analitica e Ingenieria Quimica, Universidad de Alcala, E-28771 Alcala de Henares (Spain); Gonzalo, Maria S.; Rodriguez, Antonio; Garcia-Calvo, Eloy [Departamento de Quimica Analitica e Ingenieria Quimica, Universidad de Alcala, E-28771 Alcala de Henares (Spain)

2010-11-15

The catalytic ozonation of fenofibric acid was studied using activated alumina and alumina-supported manganese oxide in a semicontinuous reactor. The rate constants at 20 deg. C for the non-catalytic reaction of fenofibric acid with ozone and hydroxyl radicals were 3.43 {+-} 0.20 M{sup -1} s{sup -1} and (6.55 {+-} 0.33) x 10{sup 9} M{sup -1} s{sup -1}, respectively. The kinetic constant for the catalytic reaction between fenofibric acid and hydroxyl radicals did not differ significantly from that of homogeneous ozonation, either using Al{sub 2}O{sub 3} or MnO{sub x}/Al{sub 2}O{sub 3}. The results showed a considerable increase in the generation of hydroxyl radicals due to the use of catalysts even in the case of catalytic runs performed using a real wastewater matrix. Both catalysts promoted the decomposition of ozone in homogeneous phase, but the higher production of hydroxyl radicals corresponded to the catalyst with more activity in terms of ozone decomposition. We did not find evidence of the catalysts having any effect on rate constants, which suggests that the reaction may not involve the adsorption of organics on catalyst surface.
Bubble Driven Quasioscillatory Translational Motion of Catalytic Micromotors

Science.gov (United States)

Manjare, Manoj; Yang, Bo; Zhao, Y.-P.

2012-09-01

A new quasioscillatory translational motion has been observed for big Janus catalytic micromotors with a fast CCD camera. Such motional behavior is found to coincide with both the bubble growth and burst processes resulting from the catalytic reaction, and the competition of the two processes generates a net forward motion. Detailed physical models have been proposed to describe the above processes. It is suggested that the bubble growth process imposes a growth force moving the micromotor forward, while the burst process induces an instantaneous local pressure depression pulling the micromotor backward. The theoretic predictions are consistent with the experimental data.
Catalytic Oxidation of Allylic Alcohols to Methyl Esters

DEFF Research Database (Denmark)

Gallas-Hulin, Agata; Kotni, Rama Krishna; Nielsen, Martin

2017-01-01

Aerobic oxidation of allylic alcohols to methyl esters using gold nanoparticles supported on different metal oxide carriers has been performed successfully under mild conditions (room temperature, 0.1 MPa O2) without significant loss of catalytic activity. The effects of different reaction...... parameters are studied to find the suitable reaction conditions. All catalysts are characterised by XRD, XRF and TEM. Among these catalysts, Au/TiO2 showed the most efficient catalytic activity towards the selective oxidation of allylic alcohols to the corresponding esters. Moreover, the same Au/TiO2...... to synthesize methyl esters from allylic alcohols....
Crystallization and preliminary X-ray diffraction analysis of the P3 RNA domain of yeast ribonuclease MRP in a complex with RNase P/MRP protein components Pop6 and Pop7.

Science.gov (United States)

Perederina, Anna; Esakova, Olga; Quan, Chao; Khanova, Elena; Krasilnikov, Andrey S

2010-01-01

Eukaryotic ribonucleases P and MRP are closely related RNA-based enzymes which contain a catalytic RNA component and several protein subunits. The roles of the protein subunits in the structure and function of eukaryotic ribonucleases P and MRP are not clear. Crystals of a complex that included a circularly permuted 46-nucleotide-long P3 domain of the RNA component of Saccharomyces cerevisiae ribonuclease MRP and selenomethionine derivatives of the shared ribonuclease P/MRP protein components Pop6 (18.2 kDa) and Pop7 (15.8 kDa) were obtained using the sitting-drop vapour-diffusion method. The crystals belonged to space group P4(2)22 (unit-cell parameters a = b = 127.2, c = 76.8 A, alpha = beta = gamma = 90 degrees ) and diffracted to 3.25 A resolution.
Determination of organic bases in non-aqueous solvents by catalytic thermometric titration.

Science.gov (United States)

Vajgand, V J; Kiss, T A; Gaál, F F; Zsigrai, I J

1968-07-01

Catalytic thermometric titrations have been developed for bases (brucine, diethylaniline, potassium acetate and triethylamine) in acetic acid by continuous and discontinuous addition of the standard solution and automatic temperature recording. The determination of weak bases, e.g., antipyrine, unsuccessful in acetic acid by catalytic thermometric titration, has been achieved by using nitromethane or acetic anhydride as solvent. Catalytic thermometric titrations were also performed by coulometric generation of hydrogen ions for the determination of micro amounts of weak bases in a mixture of acetic anhyride and acetic acid.

How the RNA isolation method can affect microRNA microarray results

DEFF Research Database (Denmark)

Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

2011-01-01

RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...
Petroleum Refineries (Catalytic Cracking, Catalytic Reforming and Sulfur Recovery Units): National Emission Standards for Hazardous Air Pollutants (NESHAP)

Science.gov (United States)

learn more about the NESHAP for catalytic cracking and reforming units, as well as sulfur recovery units in petroleum refineries by reading the rule history, rule summary, background information documents, and compliance information
The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.

Science.gov (United States)

Wang, Na; Wang, Ruoqing; Wang, Renkai; Tian, Yongsheng; Shao, Changwei; Jia, Xiaodong; Chen, Songlin

2017-01-01

Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish
Human liver phosphatase 2A: cDNA and amino acid sequence of two catalytic subunit isotypes

International Nuclear Information System (INIS)

Arino, J.; Woon, Chee Wai; Brautigan, D.L.; Miller, T.B. Jr.; Johnson, G.L.

1988-01-01

Two cDNA clones were isolated from a human liver library that encode two phosphatase 2A catalytic subunits. The two cDNAs differed in eight amino acids (97% identity) with three nonconservative substitutions. All of the amino acid substitutions were clustered in the amino-terminal domain of the protein. Amino acid sequence of one human liver clone (HL-14) was identical to the rabbit skeletal muscle phosphatase 2A cDNA (with 97% nucleotide identity). The second human liver clone (HL-1) is encoded by a separate gene, and RNA gel blot analysis indicates that both mRNAs are expressed similarly in several human clonal cell lines. Sequence comparison with phosphatase 1 and 2A indicates highly divergent amino acid sequences at the amino and carboxyl termini of the proteins and identifies six highly conserved regions between the two proteins that are predicted to be important for phosphatase enzymatic activity
Switching off small RNA regulation with trap-mRNA

DEFF Research Database (Denmark)

Overgaard, Martin; Johansen, Jesper; Møller-Jensen, Jakob

2009-01-01

to operate at the level of transcription initiation. By employing a highly sensitive genetic screen we uncovered a novel RNA-based regulatory principle in which induction of a trap-mRNA leads to selective degradation of a small regulatory RNA molecule, thereby abolishing the sRNA-based silencing of its...
Overexpression, crystallization and preliminary X-ray crystallographic analysis of the RNA polymerase domain of primase from Streptococcus mutans strain UA159

International Nuclear Information System (INIS)

Im, Dong-Won; Kim, Tae-O; Jung, Ha Yun; Oh, Ji Eun; Lee, Se Jin; Heo, Yong-Seok

2011-01-01

The RNA polymerase domain of primase from S. mutans strain UA159 was cloned, overexpressed, purified and crystallized. X-ray diffraction data were collected to a resolution of 1.60 Å. Primase is the enzyme that synthesizes RNA primers on single-stranded DNA during normal DNA replication. In this study, the catalytic core domain of primase from Streptococcus mutans UA159 was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 1.60 Å resolution using a synchrotron-radiation source. The crystal belonged to space group P4 1 or P4 3 , with unit-cell parameters a = b = 52.63, c = 110.31 Å. The asymmetric unit is likely to contain one molecule, with a corresponding V M of 1.77 Å 3 Da −1 and a solvent content of 30.7%
Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene.

Science.gov (United States)

Schneider, Mary D; Bains, Anupinder K; Rajendra, T K; Dominski, Zbigniew; Matera, A Gregory; Simmonds, Andrew J

2010-11-01

MRP RNA is a noncoding RNA component of RNase mitochondrial RNA processing (MRP), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal RNA processing, mitochondrial DNA replication, and cell cycle regulation. A recent study predicted a potential Drosophila ortholog of MRP RNA (CR33682) by computer-based genome analysis. We have confirmed the expression of this gene and characterized the phenotype associated with this locus. Flies with mutations that specifically affect MRP RNA show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. We present several lines of evidence demonstrating a role for Drosophila MRP RNA in rRNA processing. The nuclear fraction of Drosophila MRP RNA localizes to the nucleolus. Further, a mutant strain shows defects in rRNA processing that include a defect in 5.8S rRNA processing, typical of MRP RNA mutants in other species, as well as defects in early stages of rRNA processing.
Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine

International Nuclear Information System (INIS)

Kim, Moon-Jung; Lee, Byung Cheon; Hwang, Kwang Yeon; Gladyshev, Vadim N.; Kim, Hwa-Young

2015-01-01

Thioredoxin (Trx) is a major thiol-disulfide reductase that plays a role in many biological processes, including DNA replication and redox signaling. Although selenocysteine (Sec)-containing Trxs have been identified in certain bacteria, their enzymatic properties have not been characterized. In this study, we expressed a selenoprotein Trx from Treponema denticola, an oral spirochete, in Escherichia coli and characterized this selenoenzyme and its natural cysteine (Cys) homologue using E. coli Trx1 as a positive control. 75 Se metabolic labeling and mutation analyses showed that the SECIS (Sec insertion sequence) of T. denticola selenoprotein Trx is functional in the E. coli Sec insertion system with specific selenium incorporation into the Sec residue. The selenoprotein Trx exhibited approximately 10-fold higher catalytic activity than the Sec-to-Cys version and natural Cys homologue and E. coli Trx1, suggesting that Sec confers higher catalytic activity on this thiol-disulfide reductase. Kinetic analysis also showed that the selenoprotein Trx had a 30-fold higher K m than Cys-containing homologues, suggesting that this selenoenzyme is adapted to work efficiently with high concentrations of substrate. Collectively, the results of this study support the hypothesis that selenium utilization in oxidoreductase systems is primarily due to the catalytic advantage provided by the rare amino acid, Sec. - Highlights: • The first characterization of a selenoprotein Trx is presented. • The selenoenzyme Trx exhibits 10-fold higher catalytic activity than Cys homologues. • Se utilization in Trx is primarily due to the catalytic advantage provided by Sec residue
Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine

Energy Technology Data Exchange (ETDEWEB)

Kim, Moon-Jung [Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717 (Korea, Republic of); Lee, Byung Cheon [Division of Genetics, Department of Medicine, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA 02115 (United States); Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Hwang, Kwang Yeon [Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Gladyshev, Vadim N. [Division of Genetics, Department of Medicine, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA 02115 (United States); Kim, Hwa-Young, E-mail: hykim@ynu.ac.kr [Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717 (Korea, Republic of)

2015-06-12

Thioredoxin (Trx) is a major thiol-disulfide reductase that plays a role in many biological processes, including DNA replication and redox signaling. Although selenocysteine (Sec)-containing Trxs have been identified in certain bacteria, their enzymatic properties have not been characterized. In this study, we expressed a selenoprotein Trx from Treponema denticola, an oral spirochete, in Escherichia coli and characterized this selenoenzyme and its natural cysteine (Cys) homologue using E. coli Trx1 as a positive control. {sup 75}Se metabolic labeling and mutation analyses showed that the SECIS (Sec insertion sequence) of T. denticola selenoprotein Trx is functional in the E. coli Sec insertion system with specific selenium incorporation into the Sec residue. The selenoprotein Trx exhibited approximately 10-fold higher catalytic activity than the Sec-to-Cys version and natural Cys homologue and E. coli Trx1, suggesting that Sec confers higher catalytic activity on this thiol-disulfide reductase. Kinetic analysis also showed that the selenoprotein Trx had a 30-fold higher K{sub m} than Cys-containing homologues, suggesting that this selenoenzyme is adapted to work efficiently with high concentrations of substrate. Collectively, the results of this study support the hypothesis that selenium utilization in oxidoreductase systems is primarily due to the catalytic advantage provided by the rare amino acid, Sec. - Highlights: • The first characterization of a selenoprotein Trx is presented. • The selenoenzyme Trx exhibits 10-fold higher catalytic activity than Cys homologues. • Se utilization in Trx is primarily due to the catalytic advantage provided by Sec residue.
Development of a catalytically assisted combustor for a gas turbine

Energy Technology Data Exchange (ETDEWEB)

Ozawa, Yasushi; Fujii, Tomoharu; Sato, Mikio [Central Research Institute of Electric Power Industry, 2-6-1 Nagasaka, Yokosuka, Kanagawa 240-01 (Japan); Kanazawa, Takaaki; Inoue, Hitoshi [Kansai Electric Power Company, Inc., 3-11-20 Nakoji, Amagasaki, Hyoho 661 (Japan)

1999-01-01

A catalytically assisted low NO{sub x} combustor has been developed which has the advantage of catalyst durability. This combustor is composed of a burner section and a premixed combustion section behind the burner section. The burner system consists of six catalytic combustor segments and six premixing nozzles, which are arranged alternately and in parallel. Fuel flow rate for the catalysts and the premixing nozzles are controlled independently. The catalytic combustion temperature is maintained under 1000C, additional premixed gas is injected from the premixing nozzles into the catalytic combustion gas, and lean premixed combustion at 1300C is carried out in the premixed combustion section. This system was designed to avoid catalytic deactivation at high temperature and thermal or mechanical shock fracture of the honeycomb monolith. In order to maintain the catalyst temperature under 1000C, the combustion characteristics of catalysts at high pressure were investigated using a bench scale reactor and an improved catalyst was selected for the combustor test. A combustor for a 20MW class multi-can type gas turbine was designed and tested under high pressure conditions using LNG fuel. Measurements of NO{sub x}, CO and unburned hydrocarbon were made and other measurements were made to evaluate combustor performance under various combustion temperatures and pressures. As a result of the tests, it was proved that NO{sub x} emission was lower than 10ppm converted at 16% O{sub 2}, combustion efficiency was almost 100% at 1300C of combustor outlet temperature and 13.5ata of combustor inlet pressure
Synthesis and Catalytic Hydrogen Transfer Reaction of Ruthenium(II) Complex

Energy Technology Data Exchange (ETDEWEB)

Son, Jung Ik; Kim, Aram; Noh, Hui Bog; Lee, Hyun Ju; Shim, Yoon Bo; Park, Kang Hyun [Pusan National University, Busan (Korea, Republic of)

2012-01-15

The ruthenium(II) complex [Ru(bpy){sub 2}-(PhenTPy)] was synthesized, and used for the transfer hydrogenation of ketones and the desired products were obtained in good yield. Based on the presented results, transition-metal complexes can be used as catalysts for a wide range of organic transformations. The relationship between the electro-reduction current density and temperature are being examined in this laboratory. Attempts to improve the catalytic activity and determine the transfer hydrogenation mechanism are currently in progress. The catalytic hydrogenation of a ketone is a basic and critical process for making many types of alcohols used as the final products and precursors in the pharmaceutical, agrochemical, flavor, fragrance, materials, and fine chemicals industries. The catalytic hydrogenation process developed by Noyori is a very attractive process. Formic acid and 2-propanol have been used extensively as hydrogenation sources. The advantage of using 2-propanol as a hydrogen source is that the only side product will be acetone, which can be removed easily during the workup process. Hydrogen transfer (HT) catalysis, which generates alcohols through the reduction of ketones, is an attractive protocol that is used widely. Ruthenium(II) complexes are the most useful catalysts for the hydrogen transfer (HT) of ketones. In this method, a highly active catalytic system employs a transition metal as a catalyst to synthesize alcohols, and is a replacement for the hydrogen-using hydrogenation process. The most active system is based on Ru, Rh and Ir, which includes a nitrogen ligand that facilitates the formation of a catalytically active hydride and phosphorus.
Synthesis and Catalytic Hydrogen Transfer Reaction of Ruthenium(II) Complex

International Nuclear Information System (INIS)

Son, Jung Ik; Kim, Aram; Noh, Hui Bog; Lee, Hyun Ju; Shim, Yoon Bo; Park, Kang Hyun

2012-01-01

The ruthenium(II) complex [Ru(bpy) 2 -(PhenTPy)] was synthesized, and used for the transfer hydrogenation of ketones and the desired products were obtained in good yield. Based on the presented results, transition-metal complexes can be used as catalysts for a wide range of organic transformations. The relationship between the electro-reduction current density and temperature are being examined in this laboratory. Attempts to improve the catalytic activity and determine the transfer hydrogenation mechanism are currently in progress. The catalytic hydrogenation of a ketone is a basic and critical process for making many types of alcohols used as the final products and precursors in the pharmaceutical, agrochemical, flavor, fragrance, materials, and fine chemicals industries. The catalytic hydrogenation process developed by Noyori is a very attractive process. Formic acid and 2-propanol have been used extensively as hydrogenation sources. The advantage of using 2-propanol as a hydrogen source is that the only side product will be acetone, which can be removed easily during the workup process. Hydrogen transfer (HT) catalysis, which generates alcohols through the reduction of ketones, is an attractive protocol that is used widely. Ruthenium(II) complexes are the most useful catalysts for the hydrogen transfer (HT) of ketones. In this method, a highly active catalytic system employs a transition metal as a catalyst to synthesize alcohols, and is a replacement for the hydrogen-using hydrogenation process. The most active system is based on Ru, Rh and Ir, which includes a nitrogen ligand that facilitates the formation of a catalytically active hydride and phosphorus
Modulation of catalytic activity in multi-domain protein tyrosine phosphatases.

Directory of Open Access Journals (Sweden)

Lalima L Madan

Full Text Available Signaling mechanisms involving protein tyrosine phosphatases govern several cellular and developmental processes. These enzymes are regulated by several mechanisms which include variation in the catalytic turnover rate based on redox stimuli, subcellular localization or protein-protein interactions. In the case of Receptor Protein Tyrosine Phosphatases (RPTPs containing two PTP domains, phosphatase activity is localized in their membrane-proximal (D1 domains, while the membrane-distal (D2 domain is believed to play a modulatory role. Here we report our analysis of the influence of the D2 domain on the catalytic activity and substrate specificity of the D1 domain using two Drosophila melanogaster RPTPs as a model system. Biochemical studies reveal contrasting roles for the D2 domain of Drosophila Leukocyte antigen Related (DLAR and Protein Tyrosine Phosphatase on Drosophila chromosome band 99A (PTP99A. While D2 lowers the catalytic activity of the D1 domain in DLAR, the D2 domain of PTP99A leads to an increase in the catalytic activity of its D1 domain. Substrate specificity, on the other hand, is cumulative, whereby the individual specificities of the D1 and D2 domains contribute to the substrate specificity of these two-domain enzymes. Molecular dynamics simulations on structural models of DLAR and PTP99A reveal a conformational rationale for the experimental observations. These studies reveal that concerted structural changes mediate inter-domain communication resulting in either inhibitory or activating effects of the membrane distal PTP domain on the catalytic activity of the membrane proximal PTP domain.
Effect of radioactive radiation on catalytic properties of solid materials

Energy Technology Data Exchange (ETDEWEB)

Sokol' skii, D V; Kuzembaev, K K; Kel' man, I V [AN Kazakhskoj SSR, Alma-Ata. Inst. Organicheskogo Kataliza i Ehlektrokhimii

1977-05-01

General survey is made of the problem of radiation modification of the action of solid catalysts with respect to the various types of heterogeneous catalytic reactions. Consideration is given to the key mechanisms responsible for radiation damage in the interaction of high-energy radiation with a solid body. The effect of ionizing radiation on the adsorption capacity and catalytic activity of solid bodies is discussed.
A new approach to inertise the containments during catalytic removal of hydrogen

International Nuclear Information System (INIS)

Chakraborty, A.K.; Markandeya, S.G.

1994-01-01

Use of catalytic recombiners for the removal of hydrogen during a severe accident has been recommended by the German Reactor Safety Commission (RSK) due to numerous successful demonstrations of their performances. At the early stages of the accident, a huge quantity of hydrogen is expected to be released in some compartments requiring supplementary measures to ensure that the excess hydrogen concentration wouldn't pose a threat of deflagration /1/. In this presentation a new idea based on catalytic removal of hydrogen with simultaneous passive inertisation of the atmosphere is proposed for large dry containments particularly for those compartments where high H 2 -concentrations are expected. During the catalytic oxidation of hydrogen, the large exothermic heat of reaction causes strong heating of the catalytic plates as well as a continuous energy input in the containment. This can be limited if this large heat energy is efficiently used for heating some chemical compounds to release inert gases such as steam and/or CO 2 by dissociation at moderate temperatures. Such compounds can be arranged in the form of thin slabs in good thermal contact with the catalytic plates. Several such compounds have been identified which are capable of releasing steam and CO 2 equivalent to about 40 - 75% of their mass. Preliminary calculations have been carded out to demonstrate the effectiveness of the proposed concept for the case of two such selected chemicals placed adjacent to the catalytic plate type recombiners. The calculations performed show promising results. (author)
Catalytic Decoupling of Quantum Information

DEFF Research Database (Denmark)

Majenz, Christian; Berta, Mario; Dupuis, Frédéric

2017-01-01

The decoupling technique is a fundamental tool in quantum information theory with applications ranging from quantum thermodynamics to quantum many body physics to the study of black hole radiation. In this work we introduce the notion of catalytic decoupling, that is, decoupling in the presence...... and quantum state merging, and leads to a resource theory of decoupling....
Toward a catalytic site in DNA

DEFF Research Database (Denmark)

Jakobsen, Ulla; Rohr, Katja; Vogel, Stefan

2007-01-01

A number of functionalized polyaza crown ether building blocks have been incorporated into DNA-conjugates as catalytic Cu(2+) binding sites. The effect of the DNA-conjugate catalyst on the stereochemical outcome of a Cu(2+)-catalyzed Diels-Alder reaction will be presented....
Dynamical community structure of populations evolving on genotype networks

International Nuclear Information System (INIS)

Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

2015-01-01

Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics
Cytoplasmic Z-RNA

International Nuclear Information System (INIS)

Zarling, D.A.; Calhoun, C.J.; Hardin, C.C.; Zarling, A.H.

1987-01-01

Specific immunochemical probes for Z-RNA were generated and characterized to search for possible Z-RNA-like double helices in cells. Z-RNA was detected in the cytoplasm of fixed protozoan cells by immunofluorescence microscopy using these anti-Z-RNA IgCs. In contrast, autoimmune or experimentally elicited anti-DNA antibodies, specifically reactive with B-DNA or Z-DNA, stained the nuclei. Pre-or nonimmune IgGs did not bind to the cells. RNase A or T1 digestion eliminated anti-Z-RNA IgG binding to cytoplasmic determinants; however, DNase I or mung bean nuclease had no effect. Doxorubicin and ethidium bromide prevented anti-Z-RNA antibody binding; however, actinomycin D, which does not bind double-stranded RNA, did not. Anti-Z-RNA immunofluorescence was specifically blocked in competition assays by synthetic Z-RNA but not Z-DNA, A-RNA, or single-stranded RNAs. Thus, some cytoplasmic sequences in fixed cells exist in the left-handed Z-RNA conformation
Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.

Science.gov (United States)

Beckers, Matthew; Mohorianu, Irina; Stocks, Matthew; Applegate, Christopher; Dalmay, Tamas; Moulton, Vincent

2017-06-01

Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a H. sapiens data set; additional examples on a B. terrestris data set and on an A. thaliana data set are described in the Supplemental Information A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis and how the new pipeline may be used to do this. © 2017 Beckers et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Investigation of polypyrrole/polyvinyl alcohol–titanium dioxide composite films for photo-catalytic applications

Energy Technology Data Exchange (ETDEWEB)

Cao, Shaoqiang; Zhang, Hongyang; Song, Yuanqing; Zhang, Jianling; Yang, Haigang; Jiang, Long, E-mail: jianglong@scu.edu.cn; Dan, Yi, E-mail: danyichenweiwei@163.com

2015-07-01

Graphical abstract: - Highlights: • The study provides an easy and convenient method to fabricate films, which will give guidance for the preparation of three-dimensional materials. • The PPy/PVA–TiO{sub 2} films can keep better photo-catalytic activities both under UV and visible light irradiation when compared with TiO{sub 2} film. • There exist electron transfers between PPy/PVA and TiO{sub 2}. - Abstract: Polypyrrole/polyvinyl alcohol–titanium dioxide (PPy/PVA–TiO{sub 2}) composite films used as photo-catalysts were fabricated by combining TiO{sub 2} sol with PPy/PVA solution in which PPy was synthesized by in situ polymerization of pyrrole (Py) in polyvinyl alcohol (PVA) matrix and loaded on glass. The prepared photo-catalysts were investigated by X-ray diffraction (XRD), ultraviolet–visible diffuse reflection spectroscopy (UV–vis DRS), scanning electron microscopy (SEM), Fourier transform infrared (FT-IR) spectra and photoluminescence (PL). The results indicate that the composites have same crystal structure as the TiO{sub 2} and extend the optic absorption from UV region to visible light region. By detecting the variation ratio, detected by ultraviolet–vis spectroscopy, of model pollutant rhodamine B (RhB) solution in the presence of the composite films under both UV and visible light irradiation, the photo-catalytic performance of the composite films was investigated. The results show that the PPy/PVA–TiO{sub 2} composite films show better photo-catalytic properties than TiO{sub 2} film both under UV and visible light irradiation, and the photo-catalytic degradation of RhB follows the first-order kinetics. The effects of the composition of composite films and the concentration of RhB on the photo-catalytic performance, as well as the possible photo-catalytic mechanism, were also discussed. By photo-catalytic recycle experiments, the structure stability of the PPy/PVA–TiO{sub 2} composite film was investigated and the results show that
Critical mutation rate has an exponential dependence on population size in haploid and diploid populations.

Directory of Open Access Journals (Sweden)

Elizabeth Aston

Full Text Available Understanding the effect of population size on the key parameters of evolution is particularly important for populations nearing extinction. There are evolutionary pressures to evolve sequences that are both fit and robust. At high mutation rates, individuals with greater mutational robustness can outcompete those with higher fitness. This is survival-of-the-flattest, and has been observed in digital organisms, theoretically, in simulated RNA evolution, and in RNA viruses. We introduce an algorithmic method capable of determining the relationship between population size, the critical mutation rate at which individuals with greater robustness to mutation are favoured over individuals with greater fitness, and the error threshold. Verification for this method is provided against analytical models for the error threshold. We show that the critical mutation rate for increasing haploid population sizes can be approximated by an exponential function, with much lower mutation rates tolerated by small populations. This is in contrast to previous studies which identified that critical mutation rate was independent of population size. The algorithm is extended to diploid populations in a system modelled on the biological process of meiosis. The results confirm that the relationship remains exponential, but show that both the critical mutation rate and error threshold are lower for diploids, rather than higher as might have been expected. Analyzing the transition from critical mutation rate to error threshold provides an improved definition of critical mutation rate. Natural populations with their numbers in decline can be expected to lose genetic material in line with the exponential model, accelerating and potentially irreversibly advancing their decline, and this could potentially affect extinction, recovery and population management strategy. The effect of population size is particularly strong in small populations with 100 individuals or less; the
RNA Interference - Towards RNA becoming a Medicine -42 ...

Indian Academy of Sciences (India)

research. A brief history of the development ofRNAi is shown in. Box 2. Mechanism of ... new RNA strand using target RNA as the template and thereby converting it ... thought to excise precursor stRNA from their -70 nt stem loop precursor to ...
Correction: Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges.

Science.gov (United States)

Martínez-Araya, Jorge Ignacio; Grand, André; Glossman-Mitnik, Daniel

2016-01-28

Correction for 'Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges' by Jorge Ignacio Martínez-Araya et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c5cp03822g.
Role of RNase MRP in viral RNA degradation and RNA recombination.

Science.gov (United States)

Jaag, Hannah M; Lu, Qiasheng; Schmitt, Mark E; Nagy, Peter D

2011-01-01

RNA degradation, together with RNA synthesis, controls the steady-state level of viral RNAs in infected cells. The endoribonucleolytic cleavage of viral RNA is important not only for viral RNA degradation but for RNA recombination as well, due to the participation of some RNA degradation products in the RNA recombination process. To identify host endoribonucleases involved in degradation of Tomato bushy stunt virus (TBSV) in a Saccharomyces cerevisiae model host, we tested eight known endoribonucleases. Here we report that downregulation of SNM1, encoding a component of the RNase MRP, and a temperature-sensitive mutation in the NME1 gene, coding for the RNA component of RNase MRP, lead to reduced production of the endoribonucleolytically cleaved TBSV RNA in yeast. We also show that the highly purified yeast RNase MRP cleaves the TBSV RNA in vitro, resulting in TBSV RNA degradation products similar in size to those observed in yeast cells. Knocking down the NME1 homolog in Nicotiana benthamiana also led to decreased production of the cleaved TBSV RNA, suggesting that in plants, RNase MRP is involved in TBSV RNA degradation. Altogether, this work suggests a role for the host endoribonuclease RNase MRP in viral RNA degradation and recombination.
Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges.

Science.gov (United States)

Ignacio Martínez-Araya, Jorge; Grand, André; Glossman-Mitnik, Daniel

2015-11-28

By means of the Spin-Polarized Conceptual Density Functional Theory (SP-CDFT), three 2,6-bis(imino)pyridine catalysts based on iron(II), used for polymerization of ethylene, were studied. The catalysts differed by the substituent group, bearing either -H, -NO2 or -OCH3. To date, catalytic activity, a purely experimental parameter measuring the mass of polyethylene produced per millimole of iron per time and pressure unit at a fixed temperature, has not been explained in terms of local hyper-softness. The latter is a purely theoretical parameter designed for quantifying electronic effects; it is measured using the metal atom responsible for the coordination process with the monomer (ethylene). Because steric effects are not relevant in these kinds of catalysts and only electronic effects drive the catalytic process, an interesting link is found between catalytic activity and the local hyper-softness condensed on the iron atom by means of four functionals (B3LYP, BP86, B97D, and VSXC). This work demonstrates that the use of local hyper-softness, predicted by the SP-CDFT, is a suitable parameter for explaining order relationships among catalytic activity values, thus quantifying the electronic influence of the substituent group inducing this difference; the use of only net electric charges does not lead to clear conclusions. This finding can aid in estimating catalytic activities leading to a more rational design of new catalysts via computational chemistry.
MEMS-based fuel cells with integrated catalytic fuel processor and method thereof

Science.gov (United States)

Jankowski, Alan F [Livermore, CA; Morse, Jeffrey D [Martinez, CA; Upadhye, Ravindra S [Pleasanton, CA; Havstad, Mark A [Davis, CA

2011-08-09

Described herein is a means to incorporate catalytic materials into the fuel flow field structures of MEMS-based fuel cells, which enable catalytic reforming of a hydrocarbon based fuel, such as methane, methanol, or butane. Methods of fabrication are also disclosed.
RNA-dependent RNA polymerase: Addressing Zika outbreak by a phylogeny-based drug target study.

Science.gov (United States)

Stephen, Preyesh; Lin, Sheng-Xiang

2018-01-01

Since the first major outbreak of Zika virus (ZIKV) in 2007, ZIKV is spreading explosively through South and Central America, and recent reports in highly populated developing countries alarm the possibility of a more catastrophic outbreak. ZIKV infection in pregnant women leads to embryonic microcephaly and Guillain-Barré syndrome in adults. At present, there is limited understanding of the infectious mechanism, and no approved therapy has been reported. Despite the withdrawal of public health emergency, the WHO still considers the ZIKV as a highly significant and long-term public health challenge that the situation has to be addressed rapidly. Non-structural protein 5 is essential for capping and replication of viral RNA and comprises a methyltransferase and RNA-dependent RNA polymerase (RdRp) domain. We used molecular modeling to obtain the structure of ZIKV RdRp, and by molecular docking and phylogeny analysis, we here demonstrate the potential sites for drug screening. Two metal binding sites and an NS3-interacting region in ZIKV RdRp are demonstrated as potential drug screening sites. The docked structures reveal a remarkable degree of conservation at the substrate binding site and the potential drug screening sites. A phylogeny-based approach is provided for an emergency preparedness, where similar class of ligands could target phylogenetically related proteins. © 2017 John Wiley & Sons A/S.
Simulations de dynamique moléculaires d'ARN – Structures et environnements

OpenAIRE

Auffinger , Pascal

2004-01-01

RNA's, the only type of biomolecules that are at the same time informative and catalytic, play a role at all levels of cellular life. For some RNA's, the function is inscribed in their sequence. For others like transfer RNA's, the function resides in the formation and maintenance of their compact three-dimensional folds. These last RNA's, called structured RNA's, need Mg2+ cations to maintain their tertiary structure and participate to catalytic functions. In Eric WESTHOF's team, numerous thr...
Protein kinase A-alpha directly phosphorylates FoxO1 in vascular endothelial cells to regulate expression of vascular cellular adhesion molecule-1 mRNA.

Science.gov (United States)

Lee, Ji-Won; Chen, Hui; Pullikotil, Philomena; Quon, Michael J

2011-02-25

FoxO1, a forkhead box O class transcription factor, is abundant in insulin-responsive tissues. Akt, downstream from phosphatidylinositol 3-kinase in insulin signaling, phosphorylates FoxO1 at Thr(24), Ser(256), and Ser(319), negatively regulating its function. We previously reported that dehydroepiandrosterone-stimulated phosphorylation of FoxO1 in endothelial cells requires cAMP-dependent protein kinase α (PKA-α). Therefore, we hypothesized that FoxO1 is a novel direct substrate for PKA-α. Using an immune complex kinase assay with [γ-(32)P]ATP, purified PKA-α directly phosphorylated wild-type FoxO1 but not FoxO1-AAA (mutant with alanine substitutions at known Akt phosphorylation sites). Phosphorylation of wild-type FoxO1 (but not FoxO1-AAA) was detectable using phospho-specific antibodies. Similar results were obtained using purified GST-FoxO1 protein as the substrate. Thus, FoxO1 is a direct substrate for PKA-α in vitro. In bovine aortic endothelial cells, interaction between endogenous PKA-α and endogenous FoxO1 was detected by co-immunoprecipitation. In human aortic endothelial cells (HAEC), pretreatment with H89 (PKA inhibitor) or siRNA knockdown of PKA-α decreased forskolin- or prostaglandin E(2)-stimulated phosphorylation of FoxO1. In HAEC transfected with a FoxO-promoter luciferase reporter, co-expression of the catalytic domain of PKA-α, catalytically inactive mutant PKA-α, or siRNA against PKA-α caused corresponding increases or decreases in transactivation of the FoxO promoter. Expression of vascular cellular adhesion molecule-1 mRNA, up-regulated by FoxO1 in endothelial cells, was enhanced by siRNA knockdown of PKA-α or treatment of HAEC with the PKA inhibitor H89. Adhesion of monocytes to endothelial cells was enhanced by H89 treatment or overexpression of FoxO1-AAA, similar to effects of TNF-α treatment. We conclude that FoxO1 is a novel physiological substrate for PKA-α in vascular endothelial cells.
Evidence for X-chromosomal schizophrenia associated with microRNA alterations.

Directory of Open Access Journals (Sweden)

Jinong Feng

2009-07-01

Full Text Available Schizophrenia is a severe disabling brain disease affecting about 1% of the population. Individual microRNAs (miRNAs affect moderate downregulation of gene expression. In addition, components required for miRNA processing and/or function have also been implicated in X-linked mental retardation, neurological and neoplastic diseases, pointing to the wide ranging involvement of miRNAs in disease.To explore the role of miRNAs in schizophrenia, 59 microRNA genes on the X-chromosome were amplified and sequenced in males with (193 and without (191 schizophrenia spectrum disorders to test the hypothesis that ultra-rare mutations in microRNA collectively contribute to the risk of schizophrenia. Here we provide the first association of microRNA gene dysfunction with schizophrenia. Eight ultra-rare variants in the precursor or mature miRNA were identified in eight distinct miRNA genes in 4% of analyzed males with schizophrenia. One ultra-rare variant was identified in a control sample (with a history of depression (8/193 versus 1/191, p = 0.02 by one-sided Fisher's exact test, odds ratio = 8.2. These variants were not found in an additional 7,197 control X-chromosomes.Functional analyses of ectopically expressed copies of the variant miRNA precursors demonstrate loss of function, gain of function or altered expression levels. While confirmation is required, this study suggests that microRNA mutations can contribute to schizophrenia.
Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.

Science.gov (United States)

Bjelic, Sinisa; Kipnis, Yakov; Wang, Ling; Pianowski, Zbigniew; Vorobiev, Sergey; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Kornhaber, Gregory; Hunt, John F; Tong, Liang; Hilvert, Donald; Baker, David

2014-01-09

Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (>10(-3)s(-1)) and kcat/KM (11-25M(-1)s(-1)) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the >10(5)-fold rate accelerations that were achieved are within 1-3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat=10(6) to 10(8)) and an extensively evolved computational design (kcat/kuncat>10(7)). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches. © 2013.
Repression of multiple CYP2D genes in mouse primary hepatocytes with a single siRNA construct.

Science.gov (United States)

Elraghy, Omaima; Baldwin, William S

2015-01-01

The Cyp2d subfamily is the second most abun-dant subfamily of hepatic drug-metabolizing CYPs. In mice, there are nine Cyp2d members that are believed to have redundant catalytic activity. We are testing and optimizing the ability of one short interfering RNA (siRNA) construct to knockdown the expression of multiple mouse Cyp2ds in primary hepatocytes. Expression of Cyp2d10, Cyp2d11, Cyp2d22, and Cyp2d26 was observed in the primary male mouse hepatocytes. Cyp2d9, which is male-specific and growth hormone-dependent, was not expressed in male primary hepatocytes, potentially because of its dependence on pulsatile growth hormone release from the anterior pituitary. Several different siRNAs at different concentrations and with different reagents were used to knockdown Cyp2d expression. siRNA constructs designed to repress only one construct often mildly repressed several Cyp2d isoforms. A construct designed to knockdown every Cyp2d isoform provided the best results, especially when incubated with transfection reagents designed specifically for primary cell culture. Interestingly, a construct designed to knockdown all Cyp2d isoforms, except Cyp2d10, caused a 2.5× increase in Cyp2d10 expression, presumably because of a compensatory response. However, while RNA expression is repressed 24 h after siRNA treatment, associated changes in Cyp2d-mediated metabolism are tenuous. Overall, this study provides data on the expression of murine Cyp2ds in primary cell lines, valuable information on designing siRNAs for silencing multiple murine CYPs, and potential pros and cons of using siRNA as a tool for repressing Cyp2d and estimating Cyp2d's role in murine xenobiotic metabolism.
Studies of Catalytic Properties of Inorganic Rock Matrices in Redox Reactions

Directory of Open Access Journals (Sweden)

Nikolay M. Dobrynkin

2017-09-01

Full Text Available Intrinsic catalytic properties of mineral matrices of various kinds (basalts, clays, sandstones were studied, which are of interest for in-situ heavy oil upgrading (i.e., underground to create advanced technologies for enhanced oil recovery. The elemental, surface and phase composition and matrix particle morphology, surface and acidic properties were studied using elemental analysis, X-ray diffraction, adsorption and desorption of nitrogen and ammonia. The data on the catalytic activity of inorganic matrices in ammonium nitrate decomposition (reaction with a large gassing, oxidation of hydrocarbons and carbon monoxide, and hydrocracking of asphaltenes into maltenes (the conversion of heavy hydrocarbons into more valuable light hydrocarbons were discussed. In order to check their applicability for the asphaltenes hydrocracking catalytic systems development, basalt and clay matrices were used as supports for iron/basalt, nickel/basalt and iron/clay catalysts. The catalytic activity of the matrices in the reactions of the decomposition of ammonium nitrate, oxidation of hydrocarbons and carbon monoxide, and hydrocracking of asphaltens was observed for the first time.
Investigation on CO catalytic oxidation reaction kinetics of faceted perovskite nanostructures loaded with Pt

KAUST Repository

Yin, S. M.

2017-01-18

Perovskite lead titanate nanostructures with specific {111}, {100} and {001} facets exposed, have been employed as supports to investigate the crystal facet effect on the growth and CO catalytic activity of Pt nanoparticles. The size, distribution and surface chemical states of Pt on the perovskite supports have been significantly modified, leading to a tailored conversion temperature and catalytic kinetics towards CO catalytic oxidation.
Investigation on CO catalytic oxidation reaction kinetics of faceted perovskite nanostructures loaded with Pt

KAUST Repository

Yin, S. M.; Duanmu, J. J.; Zhu, Yihan; Yuan, Y. F.; Guo, S. Y.; Yang, J. L.; Ren, Z. H.; Han, G. R.

2017-01-01

Perovskite lead titanate nanostructures with specific {111}, {100} and {001} facets exposed, have been employed as supports to investigate the crystal facet effect on the growth and CO catalytic activity of Pt nanoparticles. The size, distribution and surface chemical states of Pt on the perovskite supports have been significantly modified, leading to a tailored conversion temperature and catalytic kinetics towards CO catalytic oxidation.
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.
Liquid-phase chemical hydrogen storage: catalytic hydrogen generation under ambient conditions.

Science.gov (United States)

Jiang, Hai-Long; Singh, Sanjay Kumar; Yan, Jun-Min; Zhang, Xin-Bo; Xu, Qiang

2010-05-25

There is a demand for a sufficient and sustainable energy supply. Hence, the search for applicable hydrogen storage materials is extremely important owing to the diversified merits of hydrogen energy. Lithium and sodium borohydride, ammonia borane, hydrazine, and formic acid have been extensively investigated as promising hydrogen storage materials based on their relatively high hydrogen content. Significant advances, such as hydrogen generation temperatures and reaction kinetics, have been made in the catalytic hydrolysis of aqueous lithium and sodium borohydride and ammonia borane as well as in the catalytic decomposition of hydrous hydrazine and formic acid. In this Minireview we briefly survey the research progresses in catalytic hydrogen generation from these liquid-phase chemical hydrogen storage materials.
Procedure for the preparation of catalysts for application in catalytic gas phase reactions

International Nuclear Information System (INIS)

1976-01-01

The invention describes the preparation of catalysts to be used in catalytic reactions in the gaseous phase. The catalytic material is disposed at the surface of a ceramic or carbon substrate (av. particle size 0.1 μ - 0.5 cm, surface area smaller than 20 m 2 /g) by bombardment of the catalytic material (Pt, Rh, Pd, Ru, Os, Ir) with energetic ions (Ne, Ar, Kr, Xe) in the vicinity of the substrate in medium vacuum

A kinetic study on non-catalytic reactions in hydroprocessing Boscan crude oil

Energy Technology Data Exchange (ETDEWEB)

A. Marafi; E. Kam; A. Stanislaus [Kuwait Institute for Scientific Research, Safat (Kuwait). Petroleum Refining Department, Petroleum Research and Studies Center

2008-08-15

Non-catalytic hydrothermal cracking reactions are known to associate with catalytic hydrocracking reactions. In a recent study on hydroprocessing of Boscan crude over a specific catalyst system containing three distinct catalysts, it was found that hydrodesulfurization (HDS) and hydrodemetallation (HDM) reactions continued even when the catalyst is severely deactivated. Since the reactor was packed with considerable amount of inert material besides the three catalysts, it will be advantage to determine if the inert materials can also facilitate hydroprocessing reactions. A series of kinetic experiments for the inert particles was undertaken under different space velocity and temperature conditions. The extent of catalytic and non-catalytic hydroprocessing reactions was assessed. Through statistical analysis, the initial reaction rate constant, reaction order and activation energy for various hydroprocessing reactions were then determined. The absolute average deviations (AAD) of the kinetics values obtained for inert materials are less than 10%. 25 refs., 7 figs., 4 tabs.
Cyanide Containing Wastewater Treatment by Ozone Enhanced Catalytic Oxidation over Diatomite Catalysts

Directory of Open Access Journals (Sweden)

Lin Mingguo

2018-01-01

Full Text Available Cyanide containing wastewater that discharged from gold mining process creates environmental problems due to the toxicity of cyanide. As one of the promising advanced oxidation process, catalytic oxidation with ozone is considered to be effective on the purification of cyanide. Diatomite, a natural mineral, was used as catalyst in this study. The effect of O3 dosage, salinity, initial cyanide concentration and initial pH condition were investigated. It was observed that the removal rate of cyanide was much higher in the catalytic oxidation with ozone process than the one in zone alone process. Alkaline condition was especially favorable for cyanide in catalytic oxidation with ozone. The ozone and catalytic oxidation with ozone were simulated by pseudo-first-order kinetics model. The apparent first-order rate constant contribution of the diatomite catalyst was 0.0757 min-1, and the contribution percentage was 65.77%.
Structural/surface characterization and catalytic evaluation of rare-earth (Y, Sm and La) doped ceria composite oxides for CH{sub 3}SH catalytic decomposition

Energy Technology Data Exchange (ETDEWEB)

He, Dedong; Chen, Dingkai; Hao, Husheng; Yu, Jie; Liu, Jiangping; Lu, Jichang; Liu, Feng [Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500 (China); Wan, Gengping [Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500 (China); Research Center for Analysis and Measurement, Hainan University, Haikou, 570228 (China); He, Sufang [Research Center for Analysis and Measurement, Kunming University of Science and Technology, Kunming, 650093 (China); Luo, Yongming, E-mail: environcatalysis222@yahoo.com [Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500 (China)

2016-12-30

Highlights: • Ce{sub 0.75}RE{sub 0.25}O{sub 2-δ} (RE = Y, Sm and La) were synthesized by citrate complexation method. • Ce{sub 0.75}Y{sub 0.25}O{sub 2-δ} exhibited the best stability for the decomposition of CH{sub 3}SH. • Cation radius played a key role in determining structure and surface characteristics. • Catalytic behavior depended on synergistic role of oxygen vacancies and basic sites. • Ce{sub 2}S{sub 3} accumulation on the surface was responsible for the deactivation of catalyst. - Abstract: A series of rare earth (Y, Sm and La) doped ceria composite oxides and pure CeO{sub 2} were synthesized and evaluated by conducting CH{sub 3}SH catalytic decomposition test. Several characterization studies, including XRD, BET, Raman, H{sub 2}-TPR, XPS, FT-IR, CO{sub 2}-TPD and CH{sub 3}SH-TPD, were undertaken to correlate structural and surface properties of the obtained ceria-based catalysts with their catalytic performance for CH{sub 3}SH decomposition. More oxygen vacancies and increased basic sites exhibited in the rare earth doped ceria catalysts. Y doped ceria sample (Ce{sub 0.75}Y{sub 0.25}O{sub 2-δ}), with a moderate increase in basic sites, contained more oxygen vacancies. More structural defects and active sites could be provided, and a relatively small amount of sulfur would accumulate, which resulted in better catalytic performance. The developed catalyst presented good catalytic behavior with stability very similar to that of typical zeolite-based catalysts reported previously. However, La doped ceria catalyst (Ce{sub 0.75}La{sub 0.25}O{sub 2-δ}) with the highest alkalinity was not the most active one. More sulfur species would be adsorbed and a large amount of cerium sulfide species (Ce{sub 2}S{sub 3}) would accumulate, which caused deactivation of the catalysts. The combined effect of increased oxygen vacancies and alkalinity led to the catalytic stability of Ce{sub 0.75}Sm{sub 0.25}O{sub 2-δ} sample was comparable to that of pure Ce
Catalytic combustion of gasified waste - Experimental part. Final report

Energy Technology Data Exchange (ETDEWEB)

Jaeraas, Sven; Kusar, Henrik [Royal Institute of Technology, Stockholm (Sweden). Chemical Engineering and Technology

2003-08-01

This final report covers the work that has been performed within the project P 10547-2, 'Catalytic combustion of gasified waste - system analysis ORWARE'. This project is part of the research programme 'Energy from Waste' financed by the Swedish National Energy Administration. The project has been carried out at the division of Industrial Ecology and at the division of Chemical Technology at Royal Inst. of Technology. The aim of the project has been to study the potentials for catalytic combustion of gasified waste. The supposed end user of the technique is a smaller community in Sweden with 15,000-20,000 inhabitants. The project contains of two sub projects: an experimental part carried out at Chemical Technology and a system analysis carried out at Industrial Ecology. This report covers the experimental part of the project carried out at Chemical Technology. The aim for the experimental part has been to develop and test catalysts with long life-time and a high performance, to reduce the thermal-NO{sub x} below 5 ppm and to significantly reduce NO{sub x} formed from fuel-bound nitrogen. Different experimental studies have been carried out within the project: a set-up of catalytic materials have been tested over a synthetic mixture of the gasified waste, the influence of sulfur present in the gas stream, NO{sub x} formation from fuel bound nitrogen, kinetic studies of CO and H{sub 2} with and without the presence of water and the effects of adding a co-metal to palladium catalysts Furthermore a novel annular reactor design has been used to carry out experiments for kinetic measurements. Real gasification tests of waste pellets directly coupled to catalytic combustion have successfully been performed. The results obtained from the experiments, both the catalytic combustion and from the gasification, have been possible to use in the system analysis. The aim of the system analysis of catalytic combustion of gasified waste takes into consideration
Catalytic properties of niobium compounds

International Nuclear Information System (INIS)

Tanabe, K.; Iizuka, T.

1983-04-01

The catalytic activity and selectivity of niobium compounds including oxides, salts, organometallic compounds and others are outlined. The application of these compounds as catalysts to diversified reactions is reported. The nature and action of niobium catalysts are characteristic and sometimes anomalous, suggesting the necessity of basic research and the potential use as catalysts for important processes in the chemical industry. (Author) [pt
Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins.

OpenAIRE

ARCURI, P.B.; THONNEY, M.L.; SCHOFIELD, P.; PELL, A.N.

2003-01-01

In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA) probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG) and polyvinylpirrolidone (PVP) on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/...
Efficient fully controlled up-to-date equipment for catalytic treatment of waste gases

International Nuclear Information System (INIS)

Dvorak, Radek; Stulir, Roman; Cagas, Pavel

2007-01-01

This paper describes research and development of a new unit for catalytic destruction of waste gases polluted mainly by volatile organic compounds (VOC), halogenated organic compounds (HOC) or carbon monoxide. Novel equipment has considerable advantages compared with commonly used arrangement (combustion chamber (catalytic reactor)-pipeline-heat exchanger). It is very compact and light and has the combustion chamber, catalytic reactor and heat exchanger integrated into one unit. Maximum utilizing heat losses in the combustion chamber and catalytic reactor is achieved. During the development of this unit experience from tests of previously developed equipment used for thermal treatment of waste gases was used, as well as from experimental studies of catalytic disposal of various VOC carried out in the newly built experimental unit. During the development calculation methods were created allowing design modifications of this unit for real industrial applications. The newly developed unit can be used in various branches of industry such as paint shops, refining plants, sewage treatment plants, food processing industry, pharmaceutical industry, but also in companies processing and transporting crude-oil or natural gas, etc
Microwave-induced carbon nanotubes catalytic degradation of organic pollutants in aqueous solution

Energy Technology Data Exchange (ETDEWEB)

Chen, Jing; Xue, Shuang; Song, Youtao; Shen, Manli [School of Environment Science, Liaoning University, Shenyang 110036 (China); Zhang, Zhaohong, E-mail: lnuhjhx@163.com [School of Environment Science, Liaoning University, Shenyang 110036 (China); Yuan, Tianxin; Tian, Fangyuan [School of Environment Science, Liaoning University, Shenyang 110036 (China); Dionysiou, Dionysios D., E-mail: dionysios.d.dionysiou@uc.edu [Environmental Engineering and Science Program, University of Cincinnati, Cincinnati, OH 45221-0012 (United States)

2016-06-05

Highlights: • Microwave-induced CNTs-based catalytic degradation technology is developed. • Microwave catalytic activities of CNTs with different diameters are compared. • Organic pollutants with different structure can be degraded in MW/CNTs system. • The 10–20 nm CNTs shows the higher catalytic activity under MW irradiation. - Abstract: In this study, a new catalytic degradation technology using microwave induced carbon nanotubes (MW/CNTs) was proposed and applied in the treatment of organic pollutants in aqueous solution. The catalytic activity of three CNTs of 10–20 nm, 20–40 nm, and 40–60 nm diameters were compared. The results showed that organic pollutants such as methyl orange (MO), methyl parathion (MP), sodium dodecyl benzene sulfonate (SDBS), bisphenol A (BPA), and methylene blue (MB) in aqueous solution could be degraded effectively and rapidly in MW/CNTs system. CNTs with diameter of 10–20 nm exhibited the highest catalytic activity of the three CNTs under MW irradiation. Further, complete degradation was obtained using 10–20 nm CNTs within 7.0 min irradiation when 25 mL MO solution (25 mg/L), 1.2 g/L catalyst dose, 450 W, 2450 MHz, and pH = 6.0 were applied. The rate constants (k) for the degradation of SDBS, MB, MP, MO and BPA using 10–20 nm CNTs/MW system were 0.726, 0.679, 0.463, 0.334 and 0.168 min{sup −1}, respectively. Therefore, this technology may have potential application for the treatment of targeted organic pollutants in wastewaters.
Microwave-induced carbon nanotubes catalytic degradation of organic pollutants in aqueous solution

International Nuclear Information System (INIS)

Chen, Jing; Xue, Shuang; Song, Youtao; Shen, Manli; Zhang, Zhaohong; Yuan, Tianxin; Tian, Fangyuan; Dionysiou, Dionysios D.

2016-01-01

Highlights: • Microwave-induced CNTs-based catalytic degradation technology is developed. • Microwave catalytic activities of CNTs with different diameters are compared. • Organic pollutants with different structure can be degraded in MW/CNTs system. • The 10–20 nm CNTs shows the higher catalytic activity under MW irradiation. - Abstract: In this study, a new catalytic degradation technology using microwave induced carbon nanotubes (MW/CNTs) was proposed and applied in the treatment of organic pollutants in aqueous solution. The catalytic activity of three CNTs of 10–20 nm, 20–40 nm, and 40–60 nm diameters were compared. The results showed that organic pollutants such as methyl orange (MO), methyl parathion (MP), sodium dodecyl benzene sulfonate (SDBS), bisphenol A (BPA), and methylene blue (MB) in aqueous solution could be degraded effectively and rapidly in MW/CNTs system. CNTs with diameter of 10–20 nm exhibited the highest catalytic activity of the three CNTs under MW irradiation. Further, complete degradation was obtained using 10–20 nm CNTs within 7.0 min irradiation when 25 mL MO solution (25 mg/L), 1.2 g/L catalyst dose, 450 W, 2450 MHz, and pH = 6.0 were applied. The rate constants (k) for the degradation of SDBS, MB, MP, MO and BPA using 10–20 nm CNTs/MW system were 0.726, 0.679, 0.463, 0.334 and 0.168 min"−"1, respectively. Therefore, this technology may have potential application for the treatment of targeted organic pollutants in wastewaters.
Dimension meditated optic and catalytic performance over vanadium pentoxides

International Nuclear Information System (INIS)

Su, Dezhi; Zhao, Yongjie; Zhang, Ruibo; Ning, Mingqiang; Zhao, Yuzhen; Zhou, Heping; Li, Jingbo; Jin, Haibo

2016-01-01

Highlights: • V_2O_5 with diverse dimensional morphologies were synthesized. • The optic properties of diverse dimensional V_2O_5 were investigated in detail. • The catalytic properties of diverse dimensional V_2O_5 on the thermal decomposition of ammonium perchlorate were analyzed. - Abstract: Morphologies and sizes of V_2O_5 had crucial effect on their optic and catalytic performance. Diverse dimensional V_2O_5 were successfully synthesized by the combination of a hydrothermal and post heat treatment method. The as-obtained samples were characterized by X-ray power diffraction, scanning electron microscopy, transmission electron microscopy and Raman spectra. Moreover, the optic properties of diverse dimensional V_2O_5 were examined by Fourier transform imaging spectrometer and UV–vis-spectrophotometer. It showed that the IR transmittance of nanowire (at 1019 cm"−"1 is 85%) and UV absorbance of microflowers (at 480 nm) were high. Furthermore, the catalytic properties of diverse dimensional V_2O_5 on the thermal decomposition of ammonium perchlorate were evaluated and compared by Thermo-Gravimetric Analysis and Differential Scanning Calorimetry. Moreover, the best catalytic performance was obtained with the morphology of nanowire. It showed the thermal decomposition temperatures of AP with nanowire, microflowers and microsphere were reduced to 373 °C, 382 °C and 376 °C (decreased by 52 °C, 43 °C and 49 °C).
Dimension meditated optic and catalytic performance over vanadium pentoxides

Energy Technology Data Exchange (ETDEWEB)

Su, Dezhi [Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081 (China); Zhao, Yongjie, E-mail: zhaoyjpeace@gmail.com [Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081 (China); Zhang, Ruibo; Ning, Mingqiang [Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081 (China); Zhao, Yuzhen; Zhou, Heping [State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Li, Jingbo; Jin, Haibo [Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081 (China)

2016-12-15

Highlights: • V{sub 2}O{sub 5} with diverse dimensional morphologies were synthesized. • The optic properties of diverse dimensional V{sub 2}O{sub 5} were investigated in detail. • The catalytic properties of diverse dimensional V{sub 2}O{sub 5} on the thermal decomposition of ammonium perchlorate were analyzed. - Abstract: Morphologies and sizes of V{sub 2}O{sub 5} had crucial effect on their optic and catalytic performance. Diverse dimensional V{sub 2}O{sub 5} were successfully synthesized by the combination of a hydrothermal and post heat treatment method. The as-obtained samples were characterized by X-ray power diffraction, scanning electron microscopy, transmission electron microscopy and Raman spectra. Moreover, the optic properties of diverse dimensional V{sub 2}O{sub 5} were examined by Fourier transform imaging spectrometer and UV–vis-spectrophotometer. It showed that the IR transmittance of nanowire (at 1019 cm{sup −1} is 85%) and UV absorbance of microflowers (at 480 nm) were high. Furthermore, the catalytic properties of diverse dimensional V{sub 2}O{sub 5} on the thermal decomposition of ammonium perchlorate were evaluated and compared by Thermo-Gravimetric Analysis and Differential Scanning Calorimetry. Moreover, the best catalytic performance was obtained with the morphology of nanowire. It showed the thermal decomposition temperatures of AP with nanowire, microflowers and microsphere were reduced to 373 °C, 382 °C and 376 °C (decreased by 52 °C, 43 °C and 49 °C).
Catalytic flash pyrolysis of oil-impregnated-wood and jatropha cake using sodium based catalysts

KAUST Repository

Imran, Ali

2015-11-24

Catalytic pyrolysis of wood with impregnated vegetable oil was investigated and compared with catalytic pyrolysis of jatropha cake making use of sodium based catalysts to produce a high quality bio-oil. The catalytic pyrolysis was carried out in two modes: in-situ catalytic pyrolysis and post treatment of the pyrolysis vapors. The in-situ catalytic pyrolysis was carried out in an entrained flow reactor system using a premixed feedstock of Na2CO3 and biomass and post treatment of biomass pyrolysis vapor was conducted in a downstream fixed bed reactor of Na2CO3/γ-Al2O3. Results have shown that both Na2CO3 and Na2CO3/γ-Al2O3 can be used for the production of a high quality bio-oil from catalytic pyrolysis of oil-impregnated-wood and jatropha cake. The catalytic bio-oil had very low oxygen content, water content as low as 1wt.%, a neutral pH, and a high calorific value upto 41.8MJ/kg. The bio-oil consisted of high value chemical compounds mainly hydrocarbons and undesired compounds in the bio-oil were either completely removed or considerably reduced. Increasing the triglycerides content (vegetable oil) in the wood enhanced the formation of hydrocarbons in the bio-oil. Post treatment of the pyrolysis vapor over a fixed bed of Na2CO3/γ-Al2O3 produced superior quality bio-oil compared to in-situ catalytic pyrolysis with Na2CO3. This high quality bio-oil may be used as a precursor in a fractionating process for the production of alternative fuels. © 2015 Elsevier B.V.
High-efficiency plasma catalytic removal of dilute benzene from air

International Nuclear Information System (INIS)

Fan, Hong-Yu; Shi, Chuan; Li, Xiao-Song; Zhao, De-Zhi; Xu, Yong; Zhu, Ai-Min

2009-01-01

Achieving complete oxidation, good humidity tolerance and low energy cost is the key issue that needs to be addressed in plasma catalytic volatile organic compounds removal from air. For this purpose, Ag/HZSM-5 catalyst-packed dielectric barrier discharge using a cycled system composed of a storage stage and a discharge stage was studied. For dilute benzene removal from simulated air, Ag/HZSM-5 catalysts exhibit not only preferential adsorption of benzene in humid air at the storage stage but also almost complete oxidation of adsorbed benzene at the discharge stage. Five 'storage-discharge' cycles were examined, which suggests that Ag/HZSM-5 catalysts are very stable during the cycled 'storage-discharge' (CSD) plasma catalytic process. High oxidation rate of absorbed benzene as well as low energy cost can be achieved at a moderate discharge power. In an example of the CSD plasma catalytic remedy of simulated air containing 4.7 ppm benzene with 50% RH and 600 ml min -1 flow rate, the energy cost was as low as 3.7 x 10 -3 kWh m -3 air. This extremely low energy cost to remove low-concentration pollutants from air undoubtedly makes the environmental applications of the plasma catalytic technique practical.
Physical chemistry of catalytic reduction of nitroarenes using various nanocatalytic systems: past, present, and future

International Nuclear Information System (INIS)

Begum, Robina; Rehan, Rida; Farooqi, Zahoor H.; Butt, Zonarah; Ashraf, Sania

2016-01-01

The catalytic reduction of nitroarenes under various catalytic systems has been widely reported in the flood of publications during last twenty years. This reaction has become a benchmark for testing catalytic activity of inorganic nanoparticles stabilized in various systems. This tutorial review presents design and classification of inorganic nanocatalysts along with their stabilizing agents used for catalytic reduction of nitroarenes. The techniques used for characterization of catalysts have been highlighted in this review. The mechanism of catalytic reduction has been described in a tutorial way. Factors affecting the rate of reduction of nitroarenes in the presence of metal nanoparticles stabilized in polyelectrolyte brushes, polyionic liquids, micelles, dendrimers, and microgels have been discussed for further development in this area.Graphical abstract
Physical chemistry of catalytic reduction of nitroarenes using various nanocatalytic systems: past, present, and future

Energy Technology Data Exchange (ETDEWEB)

Begum, Robina [University of the Punjab, Centre for Undergraduate Studies (Pakistan); Rehan, Rida; Farooqi, Zahoor H., E-mail: zhfarooqi@gmail.com; Butt, Zonarah; Ashraf, Sania [University of the Punjab, Institute of Chemistry (Pakistan)

2016-08-15

The catalytic reduction of nitroarenes under various catalytic systems has been widely reported in the flood of publications during last twenty years. This reaction has become a benchmark for testing catalytic activity of inorganic nanoparticles stabilized in various systems. This tutorial review presents design and classification of inorganic nanocatalysts along with their stabilizing agents used for catalytic reduction of nitroarenes. The techniques used for characterization of catalysts have been highlighted in this review. The mechanism of catalytic reduction has been described in a tutorial way. Factors affecting the rate of reduction of nitroarenes in the presence of metal nanoparticles stabilized in polyelectrolyte brushes, polyionic liquids, micelles, dendrimers, and microgels have been discussed for further development in this area.Graphical abstract.
Catalytic oxidation of soot over alkaline niobates

International Nuclear Information System (INIS)

Pecchi, G.; Cabrera, B.; Buljan, A.; Delgado, E.J.; Gordon, A.L.; Jimenez, R.

2013-01-01

Highlights: ► No previous reported studies about alkaline niobates as catalysts for soot oxidation. ► NaNbO 3 and KNbO 3 perovskite-type oxides show lower activation energy than other lanthanoid perovskite-type oxides. ► The alkaline niobate does not show deactivation by metal loss. - Abstract: The lack of studies in the current literature about the assessment of alkaline niobates as catalysts for soot oxidation has motivated this research. In this study, the synthesis, characterization and assessment of alkaline metal niobates as catalysts for soot combustion are reported. The solids MNbO 3 (M = Li, Na, K, Rb) are synthesized by a citrate method, calcined at 450 °C, 550 °C, 650 °C, 750 °C, and characterized by AAS, N 2 adsorption, XRD, O 2 -TPD, FTIR and SEM. All the alkaline niobates show catalytic activity for soot combustion, and the activity depends basically on the nature of the alkaline metal and the calcination temperature. The highest catalytic activity, expressed as the temperature at which combustion of carbon black occurs at the maximum rate, is shown by KNbO 3 calcined at 650 °C. At this calcination temperature, the catalytic activity follows an order dependent on the atomic number, namely: KNbO 3 > NaNbO 3 > LiNbO 3 . The RbNbO 3 solid do not follow this trend presumably due to the perovskite structure was not reached. The highest catalytic activity shown by of KNbO 3 , despite the lower apparent activation energy of NaNbO 3 , stress the importance of the metal nature and suggests the hypothesis that K + ions are the active sites for soot combustion. It must be pointed out that alkaline niobate subjected to consecutive soot combustion cycles does not show deactivation by metal loss, due to the stabilization of the alkaline metal inside the perovskite structure.
RNA-dependent RNA polymerases from cowpea mosaic virus-infected cowpea leaves

NARCIS (Netherlands)

Dorssers, L.

1983-01-01

The aim of the research described in this thesis was the purification and identification of the RNA-dependent RNA polymerase engaged in replicating viral RNA in cowpea mosaic virus (CPMV)- infected cowpea leaves.
Previously, an RNA-dependent RNA polymerase produced upon infection of
RNA interference of NADPH-cytochrome P450 reductase results in reduced insecticide resistance in the bed bug, Cimex lectularius.

Science.gov (United States)

Zhu, Fang; Sams, Sarah; Moural, Tim; Haynes, Kenneth F; Potter, Michael F; Palli, Subba R

2012-01-01

NADPH-cytochrome P450 reductase (CPR) plays a central role in cytochrome P450 action. The genes coding for P450s are not yet fully identified in the bed bug, Cimex lectularius. Hence, we decided to clone cDNA and knockdown the expression of the gene coding for CPR which is suggested to be required for the function of all P450s to determine whether or not P450s are involved in resistance of bed bugs to insecticides. The full length Cimex lectularius CPR (ClCPR) cDNA was isolated from a deltamethrin resistant bed bug population (CIN-1) using a combined PCR strategy. Bioinformatics and in silico modeling were employed to identify three conserved binding domains (FMN, FAD, NADP), a FAD binding motif, and the catalytic residues. The critical amino acids involved in FMN, FAD, NADP binding and their putative functions were also analyzed. No signal peptide but a membrane anchor domain with 21 amino acids which facilitates the localization of ClCPR on the endoplasmic reticulum was identified in ClCPR protein. Phylogenetic analysis showed that ClCPR is closer to the CPR from the body louse, Pediculus humanus corporis than to the CPRs from the other insect species studied. The ClCPR gene was ubiquitously expressed in all tissues tested but showed an increase in expression as immature stages develop into adults. We exploited the traumatic insemination mechanism of bed bugs to inject dsRNA and successfully knockdown the expression of the gene coding for ClCPR. Suppression of the ClCPR expression increased susceptibility to deltamethrin in resistant populations but not in the susceptible population of bed bugs. These data suggest that P450-mediated metabolic detoxification may serve as one of the resistance mechanisms in bed bugs.
Validation of the catalytic properties of Cu-Os/13X using single fixed bed reactor in selective catalytic reduction of NO

International Nuclear Information System (INIS)

Oh, Kwang Seok; Woo, Seong Ihl

2007-01-01

Catalytic decomposition of NO over Cu-Os/13X has been carried out in a tubular fixed bed reactor at atmospheric pressure and the results were compared with literature data performed by high-throughput screening (HTS). The activity and durability of Cu-Os/13X prepared by conventional ion-exchange method have been investigated in the presence of H 2 O and SO 2 . It was found that Cu-Os/13X prepared by ion-exchange shows a high activity in a wide temperature range in selective catalytic reduction (SCR) of NO with C 3 H 6 compared to Cu/13X, proving the existence of more NO adsorption site on Cu-Os/13X. However, Cu-Os/13X exhibited low activity in the presence of water, and was quite different from the result reported in literature. SO 2 resistance is also low and does not recover its original activity when the SO 2 was blocked in the feed gas stream. This result suggested that catalytic activity between combinatorial screening and conventional testing should be compared to confirm the validity of high-throughput screening
Novel RNA viruses within plant parasitic cyst nematodes.

Science.gov (United States)

Ruark, Casey L; Gardner, Michael; Mitchum, Melissa G; Davis, Eric L; Sit, Tim L

2018-01-01

The study of invertebrate-and particularly nematode-viruses is emerging with the advancement of transcriptome sequencing. Five single-stranded RNA viruses have now been confirmed within the economically important soybean cyst nematode (SCN; Heterodera glycines). From previous research, we know these viruses to be widespread in greenhouse and field populations of SCN. Several of the SCN viruses were also confirmed within clover (H. trifolii) and beet (H. schachtii) cyst nematodes. In the presented study, we sequenced the transcriptomes of several inbred SCN populations and identified two previously undiscovered viral-like genomes. Both of these proposed viruses are negative-sense RNA viruses and have been named SCN nyami-like virus (NLV) and SCN bunya-like virus (BLV). Finally, we analyzed publicly available transcriptome data of two potato cyst nematode (PCN) species, Globodera pallida and G. rostochiensis. From these data, a third potential virus was discovered and called PCN picorna-like virus (PLV). PCN PLV is a positive-sense RNA virus, and to the best of our knowledge, is the first virus described within PCN. The presence of these novel viruses was confirmed via qRT-PCR, endpoint PCR, and Sanger sequencing with the exception of PCN PLV due to quarantine restrictions on the nematode host. While much work needs to be done to understand the biological and evolutionary significance of these viruses, they offer insight into nematode ecology and the possibility of novel nematode management strategies.

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