bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Mechanism of Recording in Pro‐ and Eukaryotes
Authors: Poole Elizabeth S. , Major Louise L. , Cridge Andrew G. , Tate Warren P. 
Published: March 2008

AbstractOriginally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1The sections in this article areIntroductionMaintaining Decoding Accuracy and the Reading FrameThe Use of a Stop Signal for both Elongation and Termination of Protein SynthesisThe Mechanism for Sec Incorporation at UGA Sites in Bacterial mRNAsThe Gene ProductsThe Mechanism of Sec IncorporationThe Competition between Sec Incorporation and Canonical Decoding of UGA by RF2Mechanism for Sec Incorporation at UGA Sites in Eukaryotic and Archaeal mRNAsThe Gene ProductsThe Mechanism of Sec Incorporation at Specific UGA Stop CodonsWhy does Recoding Occur at Stop Signals?The Stop Signal of Prokaryotic Genomes — Engineered for High Efficiency Decoding?The Stop Signal of Eukaryotic Genomes – Diversity Contributes to RecodingReadthrough of a Stop Signal: Decoding Stop as SenseBypassing of a Stop Codon: ‘Free‐wheeling’ on the mRNAFrameshifting Around Stop or Sense CodonsForward Frameshifting: the +1 EventProgramed −1 Frameshifting: A Common Mechanism used by Many Viruses During Gene ExpressionConclusion
Structure of the Ribosome
Authors: Blaha Gregor , Ivanov Pavel 
Published: March 2008

AbstractOriginally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1The sections in this article areIntroductionGeneral Features of the Ribosome and Ribosomal SubunitsA Special Feature of the 50S Subunit: The TunnelFeatures of the Ribosomal Subunits at Atomic ResolutionThe Domain Structure of the Ribosomal SubunitsInteractions of RNA with RNA or Struts and Bolts in the Three‐dimensional Fold of rRNA: Coaxial Stacking and A‐minor MotifsCoaxial StackingA‐minor MotifsRibose Zippers and Patches of A‐minor MotifsCanonical Ribose ZipperSingle‐base Ribose ZipperProgress and New Developments in Understanding rRNA StructuresK‐turnLonepair TriloopClassification of Lonepair TriloopsSystemizing Base PairsSystemizing RNA Structural ElementsRNA–protein InteractionsProblem of RNA RecognitionChemistry of RNA–protein InteractionsrRNA–protein Interaction
Assembly of The Prokaryotic Ribosome
Authors: Nierhaus Knud H. 
Published: March 2008

Abstract
Originally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1
The sections in this article are

Introduction

Processing of rRNAs

Precursor Particles and Reconstitution Intermediates

Assembly‐initiator Proteins

Proteins Essential for the Early Assembly: The Assembly Gradient

Late‐assembly Components

Proteins Solely Involved in Assembly

Assembly Maps
Assembly of the Eukaryotic Ribosome
Authors: Lafontaine Denis L. 
Published: March 2008

AbstractOriginally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1The sections in this article areIntroductionWhy so manyRRPs?(Pre‐)ribosome Assembly, the Proteomic EraRibosomalRNAProcessing, Getting there…RibosomalRNAModification: A Solved Issue?Ribose Methylation, Pseudouridines Formation and the snoRNAsThe Emergence of the snoRNAsNon‐ribosomalRNASubstrates for the snoRNAsPossible Function(s) ofRNAModificationsBase MethylationU3 snoRNP, the ‘SSUProcessome’, and the Central PseudoknotSnoRNASynthesis and Intranuclear TraffickingSnoRNAs SynthesisNon‐core snoRNPProteins Required for snoRNAAccumulationInteractions between Cleavage Factors and Core snoRNPProteinsSnoRNAs TraffickingCB/NBare Conserved Sites of SmallRNPSynthesisRibosome Intranuclear Movements and Ribosome ExportThe Cytoplasmic Phase of Ribosome MaturationRegulatory Mechanisms, all alongOutlookConclusionsUsefulWWWlinksAcknowledgements
Genetic Code Organization and Protein Structure
Authors: Budisa Nediljko 
Published: March 2008

AbstractOriginally published in: Engineering the Genetic Code. By Nediljko Budisa. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31243‐6The sections in this article areBasic Features and Adaptive Nature of the Universal Genetic CodeMetabolism and Intracellular Uptake of Canonical Amino AcidsPhysicochemical Properties of Canonical Amino AcidsReasons for the Occurrence of Only 20 Amino Acids in the Genetic CodeWhat Properties of Amino Acids are Best Preserved by the Genetic Code?Evolutionary Legacy: Dual Nature of Conserved Code and Finite Number of Protein FoldsNatural Variations in Assignment of Codons of the Universal Genetic CodeNucleoside Modifications and Codon ReassignmentsCodon Reassignment Concepts Possibly Relevant to Code EngineeringGenome Size, Composition, Complexity and Codon ReassignmentsStop Codon Takeover, Codon Capture and Codon Ambiguity
The Cellular Translation Apparatus
Authors: Budisa Nediljko 
Published: March 2008

AbstractOriginally published in: Engineering the Genetic Code. By Nediljko Budisa. Copyright © 2006 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐31243‐6The sections in this article areNatural Laws, Genetic Information and the “Central Dogma” of Molecular BiologyCellular Investments in Ribosome‐mediated Protein SynthesisMolecular Architecture ofAARSStructure and Function of thetRNAMoleculeAminoacylation ReactionAARS:tRNAInteractions – Identity SetsTranslational ProofreadingRibosomal Decoding – A Brief OverviewCodon Bias and the Fidelity of Protein SynthesisPreprogrammed Context‐dependent Recoding: fMet, Sec, Pyl, etcBeyond Basic Coding – Posttranslational Modifications
The Ribosomal Elongation Cycle
Authors: Nierhaus Knud H. 
Published: March 2008

AbstractOriginally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1The sections in this article areIntroductionModels of the Elongation CycleThe Hybrid‐site Model for ElongationThe Allosteric Three‐site Model (α–ɛ Model; Reciprocal Coupling between the A‐ and E‐sites)Decoding and A‐site OccupationSome General Remarks about ProofreadingDiscrimination against Noncognate aa‐tRNAsDecoding of an aa‐tRNA (Cognate versus Near‐cognate aa‐tRNAs)Roles of EF‐TuMimicry at the Ribosomal A‐siteTranslational ErrorsThe PTF ReactionA Short Intermission: Two Enzymatic Principles of PTF ActivityChemical Concept: A Transient Covalent Bond between Active Center and Substrate(s)Physical Concept: The Template ModelData from the Crystal StructuresWhy both the Physical and Chemical Concepts for Peptide‐bond Formation?The Translocation ReactionConservation in the Elongation Factor‐G Binding SiteDynamics within the Ribosome
Gene Expression: Basic Concepts
Authors: Cullen Paul , Lorkowski Stefan , Kratz Mario , Werner Michel , Marschall Christoph , Klein Hanns‐Georg , Goodlett David , Aebersold Ruedi , Wenner Claudia 
Published: March 2008

Abstract
Originally published in: Analysing Gene Expression. Edited by Stefan Lorkowski, Paul Cullen, Copyright © 2003 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30448‐2
The sections in this article are

Introduction

Basics of Transcription and Translation in the cell

Introduction

Transcription

Translation

Summary

Regulation of transcription

Introduction

m
RNA
expression profiles – the transcriptome

Protein expression profiles — the proteome

Interaction between genes and proteins – the interactome

The transcription machinery and core promoters

Regulatory promoters

Enhancers

Locus control regions

Matrix attachment regions

Insulators

RIDGEs
– Regions of increased gene expression

Enhanceosomes

Chromatin

Silencer elements

Transcription factors, repressors and co‐repressors

Epigenetics

Conclusions
Anger and assaultiveness of male forensic patients with developmental disabilities: links to volatile parents
Authors: Novaco Raymond W. , Taylor John L. 
Published: March 2008

AbstractThis study with 107 male forensic patients with developmental disabilities investigated whether exposure to parental anger and aggression was related to anger and assaultiveness in a hospital, controlling for background variables. Patient anger and aggression were assessed by self‐report, staff‐ratings, and archival records. Exposure to parental anger/aggression, assessed by a clinical interview, was significantly related to patient self‐reported anger, staff‐rated anger and aggression, and physical assaults in hospital, controlling for age, intelligence quotient, length of hospital stay, violent offense history, and childhood physical abuse. Results are consonant with previous findings concerning detrimental effects of witnessing parental violence and with the theory on acquisition of cognitive scripts for aggression. Implications for clinical assessment and cognitive restructuring in anger treatment are discussed. Aggr. Behav. 34:380–393, 2008. © 2008 Wiley‐Liss, Inc.
Repeated partial eyewitness questioning causes confidence inflation but not retrieval‐induced forgetting
Authors: Odinot Geralda , Wolters Gezinus , Lavender Tristan 
Published: March 2008

AbstractDuring a crime investigation eyewitnesses are often interviewed more than once. Repeated post‐event questioning offers an opportunity for retrieval practice. Practicing retrieval of a subset of memories may suppress access to related memories, a phenomenon known as retrieval‐induced forgetting. In this short report we investigated the generalization of retrieval‐induced forgetting to episodic eyewitness memory of a complex event. The results indicated that repeated retrieval improves future recall of practiced information, but does not induce forgetting of related information. Retrieval practice, however, did result in higher confidence ratings, both for correct and incorrect answers. The practical consequence of this study is that repeated questioning should be avoided if possible. Not because it may induce retrieval‐induced forgetting, but because it may lead to confidence inflation. Copyright © 2008 John Wiley & Sons, Ltd.
Engineering motility as a phenotypic response to LuxI/R‐dependent quorum sensing in Escherichia coli
Authors: Weiss Lucien E. , Badalamenti Jonathan P. , Weaver Lane J. , Tascone Anthony R. , Weiss Paul S. , Richard Tom L. , Cirino Patrick C. 
Published: March 2008

AbstractThe repertoire of functional outputs interfaced with the LuxI/LuxR quorum sensing system in engineered Escherichia coli has been expanded to include motility via inducible expression of motB. Appropriate choice of ribosome binding site controlling MotB translation was crucial to achieving control over motility. Biotechnol. Biotechnol. Bioeng. 2008;100: 1251–1255. © 2008 Wiley Periodicals, Inc.
Distinctive microbial ecology and biokinetics of autotrophic ammonia and nitrite oxidation in a partial nitrification bioreactor
Authors: Ahn Joon Ho , Yu Ran , Chandran Kartik 
Published: March 2008

AbstractBiological nitrogen removal (BNR) based on partial nitrification and denitrification via nitrite is a cost‐effective alternate to conventional nitrification and denitrification (via nitrate). The goal of this study was to investigate the microbial ecology, biokinetics, and stability of partial nitrification. Stable long‐term partial nitrification resulting in 82.1 ± 17.2% ammonia oxidation, primarily to nitrite (77.3 ± 19.5% of the ammonia oxidized) was achieved in a lab‐scale bioreactor by operation at a pH, dissolved oxygen and solids retention time of 7.5 ± 0.1, 1.54 ± 0.87 mg O2/L, and 3.0 days, respectively. Bioreactor ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) populations were most closely related to Nitrosomonas europaea and Nitrobacter spp., respectively. The AOB population fraction varied in the range 61 ± 45% and was much higher than the NOB fraction, 0.71 ± 1.1%. Using direct measures of bacterial concentrations in conjunction with independent activity measures and mass balances, the maximum specific growth rate (µmax), specific decay (b) and observed biomass yield coefficients (Yobs) for AOB were 1.08 ± 1.03 day−1, 0.32 ± 0.34 day−1, and 0.15 ± 0.06 mg biomass COD/mg N oxidized, respectively. Corresponding µmax, b, and Yobs values for NOB were 2.6 ± 2.05 day−1, 1.7 ± 1.9 day−1, and 0.04 ± 0.02 mg biomass COD/mg N oxidized, respectively. The results of this study demonstrate that the highly selective partial nitrification operating conditions enriched for a narrow diversity of rapidly growing AOB and NOB populations unlike conventional BNR reactors, which host a broader diversity of nitrifying bacteria. Further, direct measures of microbial abundance enabled not only elucidation of mixed community microbial ecology but also estimation of key engineering parameters describing bioreactor systems supporting these communities. Biotechnol. Bioeng. 2008;100: 1078–1087. © 2008 Wiley Periodicals, Inc.
Inhibitory effects of the macrolide antimicrobial tylosin on anaerobic treatment
Authors: Shimada Toshio , Zilles Julie L. , Morgenroth Eberhard , Raskin Lutgarde 
Published: March 2008

AbstractA laboratory‐scale anaerobic sequencing batch reactor (ASBR) was operated using a glucose‐based synthetic wastewater to study the effects of tylosin, a macrolide antimicrobial commonly used in swine production, on treatment performance. The experimental period was divided into three consecutive phases with different influent tylosin concentrations (0, 1.67, and 167 mg/L). The addition of 1.67 mg/L tylosin to the reactor had negligible effects on the overall treatment performance, that is, total methane production and effluent chemical oxygen demand did not change significantly (P < 0.05), yet analyses of individual ASBR cycles revealed a decrease in the rates of both methane production and propionate uptake after tylosin was added. The addition of 167 mg/L tylosin to the reactor resulted in a gradual decrease in methane production and the accumulation of propionate and acetate. Subsequent inhibition of methanogenesis was attributed to a decrease in the pH of the reactor. After the addition of 167 mg/L tylosin to the reactor, an initial decrease in the rate of glucose uptake during the ASBR cycle followed by a gradual recovery was observed. In batch tests, the specific biogas production with the substrate butyrate was completely inhibited in the presence of tylosin. This study indicated that tylosin inhibited propionate‐ and butyrate‐oxidizing syntrophic bacteria and fermenting bacteria resulting in unfavorable effects on methanogenesis. Biotechnol. Biotechnol. Bioeng. 2008;101: 73–82. © 2008 Wiley Periodicals, Inc.
On the calculation of the elastic modulus of a biofilm streamer
Authors: Aravas N. , Laspidou C.S. 
Published: March 2008

AbstractBiofilm mechanical properties are essential in quantifying the rate of microbial detachment, a key process in determining the function and structure of biofilm systems. Although properties such as biofilm elastic moduli, yield stress and cohesive strength have been studied before, a wide range of values for the biofilm Young's modulus that differ by several orders of magnitude are reported in the literature. In this article, we use experimental data reported in Stoodley et al. [Stoodley et al., Biotechnol Bioeng (1999): 65(1):83–92] and present a methodology for the calculation of Young's modulus, which partially explains the large difference between the values reported in the literature. Biotechnol. Biotechnol. Bioeng. 2008;101: 196–200. © 2008 Wiley Periodicals, Inc.
Ionic liquids as alternative co‐solvents for laccase: Study of enzyme activity and stability
Authors: Tavares Ana Paula Mora , Rodriguez Oscar , Macedo Eugénia A. 
Published: March 2008

AbstractThe activity and stability of commercial laccase (DeniLite base) in three different water soluble ionic liquids (ILs) (1‐ethyl‐3‐methylimidazolium 2‐(2‐methoxyethoxy) ethylsulfate, [emim][MDEGSO4], 1‐ethyl‐3‐methylimidazolium ethylsulfate, [emim][EtSO4], and 1‐ethyl‐3‐methylimidazolium methanesulfonate, [emim][MeSO3]) have been studied and compared to that in two organic solvents (acetonitrile and dimethyl sulfoxide). Initial enzyme activities were similar among the ILs if the same conditions were used. A high reduction on initial enzyme activity was found with acidic pH (5.0). The effect of pH and solvent concentration on enzyme stability were investigated in more detail for 1 week. The enzyme maintained a high stability at pH 9.0 for all ILs tested. [emim][MDEGSO4] was the most promising IL for laccase with an activity loss of about 10% after 7 days of incubation. The kinetic studies in the presence of ABTS as substrate allowed to calculate the Michaelis– Menten parameters. Good agreement was found between experimental data and calculated values using the Michaelis–Menten mechanism, with a total average relative deviation of 2.1%. Biotechnol. Biotechnol. Bioeng. 2008;101: 201–207. © 2008 Wiley Periodicals, Inc.
Mechanistic kinetic model for symmetric carboligations using benzaldehyde lyase
Authors: Zavrel Michael , Schmidt Thomas , Michalik Claas , Ansorge‐Schumacher Marion , Marquardt Wolfgang , Büchs Jochen , Spiess Antje C. 
Published: March 2008

AbstractFor reactions using thiamine diphosphate (ThDP)‐dependent enzymes many empirically‐derived kinetic models exist. However, there is a lack of mechanistic kinetic models. This is especially true for the synthesis of symmetric 2‐hydroxy ketones from two identical aldehydes, with one substrate acting as the donor and the other as the acceptor. In this contribution, a systematic approach for deriving such a kinetic model for thiamine diphosphate (ThDP)‐dependent enzymes is presented. The derived mechanistic kinetic model takes this donor–acceptor principle into account by containing two Km‐values even for identical substrate molecules. As example the stereoselective carbon–carbon coupling of two 3,5‐dimethoxy‐benzaldehyde molecules to (R)‐3,3′,5,5′‐tetramethoxy‐benzoin using benzaldehyde lyase (EC 4.1.2.38) from Pseudomonas fluorescens is studied. The model is derived using a model‐based experimental analysis method which includes parameter estimation, model analysis, optimal experimental design, in silico experiments, sensitivity analysis and model revision. It is shown that this approach leads to a robust kinetic model with accurate parameter estimates and an excellent prediction capability. Biotechnol. Biotechnol. Bioeng. 2008;101: 27–38. © 2008 Wiley Periodicals, Inc.
Amphiphilic conetworks as activating carriers for the enhancement of enzymatic activity in supercritical CO2
Authors: Bruns Nico , Bannwarth Willi , Tiller Joerg C. 
Published: March 2008

AbstractEnzymatic reactions in supercritical carbon dioxide (scCO2) represent a way of combining the advantages of biocatalysis with the environmental benign nature of scCO2 as a solvent. Here we demonstrate that activities of enzymes in scCO2 can be greatly enhanced by incorporating them into amphiphilic conetworks (APCNs), a novel type of enzyme support. Two sets of hydrophilic/scCO2‐philic APCNs, poly(2‐hydroxyethyl acrylate)‐linked by‐poly(dimethyl siloxane) (PHEA‐l‐PDMS) and poly(2‐hydroxyethyl acrylate)‐linked by‐perfluoropolyether (PHEA‐l‐PFPE), were prepared and loaded with the synthetically relevant lipase from Rhizomucor miehei. The effect of the APCNs' composition on the amount of the absorbed lipase was studied. It is observed that both sets of lipase‐loaded APCNs enhance the catalytic activity of the enzyme in scCO2. The chemical nature of the scCO2‐philic phase as well as the conetworks composition greatly influences the activity of the lipase in the conetworks. Activities obtained with PFPE‐based APCNS were up to 10‐fold higher than those obtained with PDMS‐based conetworks. The highest specific activity measured corresponds to a 2,000‐fold activation compared to the lyophilized enzyme powder. This activity is 10 times higher than the specific activity of the lipase immobilized on an optimized commercial carrier. Biotechnol. Biotechnol. Bioeng. 2008;101: 19–26. © 2008 Wiley Periodicals, Inc.
Matrix notation for efficient development of first‐principles models within PAT applications: Integrated modeling of antibiotic production with Streptomyces coelicolor
Authors: Sin Gürkan , Ödman Peter , Petersen Nanna , Lantz Anna Eliasson , Gernaey Krist V. 
Published: March 2008

AbstractA matrix notation coupled to macroscopic principles is introduced as a means to develop first‐ principles models in an efficient and structured way within PAT applications. The notation was evaluated for developing an integrated biological, chemical (pH modeling) and physical (gas–liquid exchange) model for describing antibiotic production with Streptomyces coelicolor in batch fermentations. The model provided statistically adequate fits to all the monitored macroscopic biological, chemical and physical data of the process, except the phosphate uptake dynamics. This phosphate discrepancy is hypothesized to result from the internal storage of phosphate as polyphosphate prior to the exponential growth phase. The antibiotic production was associated with the stationary phase and its kinetics was adequately described using a modified Luedeking–Piret equation. Further, the maintenance was best described by employing a combination of Pirt and Herbert models, a result that was supported by a model‐based hypothesis testing. Overall the process knowledge currently incorporated in the model is believed to be useful both for process optimization purposes and for further testing of hypotheses aiming at improving the mechanistic understanding of antibiotic production with S. coelicolor. Last but not least, the matrix notation is believed to be a promising supporting tool for efficient development and communication of complex dynamic models within a PAT framework. Biotechnol. Biotechnol. Bioeng. 2008;101: 153–171. © 2008 Wiley Periodicals, Inc.
Metabolic flux model for an anchorage‐dependent MDCK cell line: Characteristic growth phases and minimum substrate consumption flux distribution
Authors: Wahl Aljoscha , Sidorenko Yury , Dauner Michael , Genzel Yvonne , Reichl Udo 
Published: March 2008

AbstractUp to now cell‐culture based vaccine production processes only reach low productivities. The reasons are: (i) slow cell growth and (ii) low cell concentrations. To address these shortcomings, a quantitative analysis of the process conditions, especially the cell growth and the metabolic capabilities of the host cell line is required. For this purpose a MDCK cell based influenza vaccine production process was investigated. With a segregated growth model four distinct cell growth phases are distinguished in the batch process. In the first phase the cells attach to the surface of the microcarriers and show low metabolic activity. The second phase is characterized by exponential cell growth. In the third phase, preceded by a change in oxygen consumption, contact inhibition leads to a decrease in cell growth. Finally, the last phase before infection shows no further increase in cell numbers. To gain insight into the metabolic activity during these phases, a detailed metabolic model of MDCK cell was developed based on genome information and experimental analysis. The MDCK model was also used to calculate a theoretical flux distribution representing an optimized cell that only consumes a minimum of carbon sources. Comparing this minimum substrate consumption flux distribution to the fluxes estimated from experiments unveiled high overflow metabolism under the applied process conditions. Biotechnol. Biotechnol. Bioeng. 2008;101: 135–152. © 2008 Wiley Periodicals, Inc.