bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comparative Analysis of the Structural Architecture of ssDNA Viruses
Authors: Bennett Antonette , McKenna Robert , Agbandje-McKenna Mavis
Published: July 2008

Virus assembly, utilizing a limited number of viral coat protein (CP or VP) building blocks, is an excellent example of a directed macromolecular interaction occurring in nature. Two basic principles govern the assembly of spherical (icosahedral) viruses: (i) Genetic Economy – the encapsidated genome encodes a single or few CPs that assemble a protective shell (the viral capsid); and (ii) specificity – the CPs have to fold to recognize each other and form exact CP–CP interfacial interactions during the assembly pathway. Using a variety of biophysical techniques, including X‐ray crystallography and cryo‐electron microscopy, combined with homology model building, biochemistry and molecular biology, the nature of the interactions between protein–protein subunits and protein–nucleic acid that facilitate viral capsid assembly have been studied. This review discusses both the similarities and differences that have been elucidated for ssDNA Microviridae, Geminiviridae, and Parvoviridae virus families. The Microviridae represent a family of bacteriophages that utilize several CPs and scaffold proteins to assemble a TT=1 icosahedral capsid, the Geminiviridae plant viruses assemble a unique twinned quasi‐isometric (geminate) pseudo T = 1 virion assembled from a single CP and the Parvoviridae represent animal viruses whose T = 1 capsids are formed from the common overlapping region of two to four VPs that have unique N‐terminal extensions. A survey of the three‐dimensional (3D) data available for these viruses shows that they utilize structural commonalities, facilitated by disparate CP/VP amino acid sequences for the successful assembly of mature infectious virions.
Dynamics of Icosahedral Viruses: What Does Viral Tiling Theory Teach Us?
Authors: Peeters Kasper , Taormina Anne
Published: July 2008

We present a top‐down approach to the study of the dynamics of icosahedral virus capsids, in which each protein is approximated by a point mass. Although this represents a rather crude coarse‐graining, we argue that it highlights several generic features of vibrational spectra which have been overlooked so far. We furthermore discuss the consequences of approximate inversion symmetry as well as the role played by viral tiling theory in the study of virus capsid vibrations.
SV40 Assembly In Vivo and In Vitro
Authors: Oppenheim Ariella , Ben-nun-Shaul O. , Mukherjee S. , Abd-El-Latif M.
Published: July 2008

The Simian virus 40 (SV40) capsid is a T = 7d icosahedral lattice ∼45 nm in diameter surrounding the ∼5 kb circular minichromosome. The outer shell is composed of 360 monomers of the major capsid protein VP1, tightly bound in 72 pentamers. VP1 is a jellyroll β‐barrel, with extending N‐ and C‐terminal arms. The N‐terminal arms bind DNA and face the interior of the capsid. The flexible C‐arms tie together the 72 pentamers in three distinct kinds of interactions, thus facilitating the formation of a T = 7 icosahedron from identical pentameric building blocks. Assembly in vivo was shown to occur by addition of capsomers around the DNA. We apply a combination of biochemical and genetic approaches to study SV40 assembly. Our in vivo and in vitro studies suggest the following model: one or two capsomers bind at a high affinity to ses, the viral DNA encapsidation signal, forming the nucleation centre for assembly. Next, multiple capsomers attach concomitantly, at lower affinity, around the minichromosome. This increases their local concentration facilitating rapid, cooperative assembly reaction. Formation of the icosahedron proceeds either by gradual addition of single pentamers to the growing shell or by concerted assembly of pentamer clusters.
Pathway Complexity of Model Virus Capsid Assembly Systems
Authors: Misra Navodit , Lees Daniel , Zhang Tiequan , Schwartz Russell
Published: July 2008

As computational and mathematical studies become increasingly central to studies of complicated reaction systems, it will become ever more important to identify the assumptions our models must make and determine when those assumptions are valid. Here, we examine that question with respect to viral capsid assembly by studying the ‘pathway complexity’ of model capsid assembly systems, which we informally define as the number of reaction pathways and intermediates one must consider to accurately describe a given system. We use two model types for this study: ordinary differential equation models, which allow us to precisely and deterministically compare the accuracy of capsid models under different degrees of simplification, and stochastic discrete event simulations, which allow us to sample use of reaction intermediates across a wide parameter space allowing for an extremely large number of possible reaction pathways. The models provide complementary information in support of a common conclusion that the ability of simple pathway models to adequately explain capsid assembly kinetics varies considerably across the space of biologically meaningful assembly parameters. These studies provide grounds for caution regarding our ability to reliably represent real systems with simple models and to extrapolate results from one set of assembly conditions to another. In addition, the analysis tools developed for this study are likely to have broader use in the analysis and efficient simulation of large reaction systems.
The Influence of Symmetry on the Probability of Assembly Pathways for Icosahedral Viral Shells
Authors: Bóna Miklós , Sitharam Meera
Published: July 2008

This paper motivates and sets up the mathematical framework for a new program of investigation: to isolate and clarify the precise influence of symmetry on the probability space of assembly pathways that successfully lead to icosahedral viral shells. Several tractable open questions are posed. Besides its virology motivation, the topic is of independent mathematical interest for studying constructions of symmetric polyhedra. Preliminary results are presented: a natural, structural classification of subsets of facets of T = 1 polyhedra, based on their stabilizing subgroups of the icosahedral group; and a theorem that uses symmetry to formalize why increasing depth increases the numeracy (and hence probability) of an assembly pathway type (or symmetry class) for a T = 1 viral shell.
Conformational Changes in the Connector Protein Complex of the Bacteriophage φ29 DNA Packaging Motor
Authors: Tolley Arron C. , Stonehouse Nicola J.
Published: July 2008

DNA packaging in the bacteriophage φ29 involves a molecular motor. It is proposed that dsDNA is packaged through a channel in a connector located at the 5‐fold vertex of a preformed prolate icosahedral capsid. The packaging motor also consists of virally‐encoded RNA molecules (pRNA) coupled to ATPases. Data obtained from studies using surface plasmon resonance, fluorescence quenching and circular dichroism are presented to demonstrate the importance of the N‐termini of the connector protein subunits in pRNA interaction and in conformational change. Based on our findings, we propose a model of DNA packaging based on connector conformational change.
RNA Packaging Motor: From Structure to Quantum Mechanical Modelling and Sequential‐Stochastic Mechanism
Authors: Telenius Jelena , Wallin Anders E. , Straka Michal , Zhang Hongbo , Mancini Erika J. , Tuma Roman
Published: July 2008

The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA‐like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate, i.e. the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum‐chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work.
A Centralcasting Postmortem and a News-Share Projection: Using Market Theory to Assess Alternative Local Television News Strategies
Authors: Daniels George L.
Published: July 2008

In the wake of decisions by two television station groups in 2006 to end centralcasting experiments, the author of this paper employed market theory to compare both centralcasting and contracted newscast products with traditional newscast products. Twenty-two newscasts that aired between 2004 and 2005 were recorded and analyzed in three southern markets. Results showed in the 2,583 stories analyzed there were more similarities than differences between the traditionally staffed local news operations and the operations produced with alternative staffing. News programs produced in a news share agreement or with a centralized news operation showed no less commitment than the “fully” staffed operations to stories related to state and local politics or government. The results of this study were consistent with data in the State of the News Media 2006 report that found a heavy emphasis on crime and accidents in local news.
Entertainment Tonight? The Value of Informative TV News Among U.S. Viewers
Authors: Southwell Brian G. , Boudewyns Vanessa , Hwang Yoori , Yzer Marco
Published: July 2008

Local television news professionals face audience declines and a rapidly changing information environment. Faced with such circumstances, many have suggested that sensational and entertaining fare might offer a way to bolster viewership. Our data from a national survey of local TV news viewers in the United States (n = 2,728) suggest that view might be incomplete. Although a variety of beliefs about TV news, including those related to how exciting or entertaining the news is, predicted general attitude toward TV news viewing, the most important predictor of such attitude was the extent to which a person found programming to be informative. TV professionals might be wrong about the need to chase audiences with dramatic and entertaining fare, sacrificing substantive reporting in the process.
The Battle of Ideological Images: CNN vs. FOX in Visual Framing of the Invasion of Iraq
Authors: Silcock B. William
Published: July 2008

In their coverage of the invasion of Iraq, CNN and FNC broadcast two distinct ideological news cultures. An in-depth interview with Aaron Brown reveals the CNN news routine of skepticism. Using visual content analysis methodology, Fox's pro-administration news culture was found clearly different from CNN's, as evidenced by graphic selections, lead story framing, the time allotted to sound bites by U.S. cabinet and military officials, and the visual framing of two iconic stories. An in-depth interview with a key gatekeeper at FNC reveals their intent was not to create an editorial bias but to be seen as a global news player on par with CNN and the American networks. The Fox's newsroom team focus was on achieving respectability by completing the rite of passage into becoming a credible source of war coverage.
Quantum Hypercomputation—Hype or Computation?
Authors: Hagar Amit , Korolev Alex
Published: July 2008

A recent attempt to compute a (recursion-theoretic) noncomputable function using the quantum adiabatic algorithm is criticized and found wanting. Quantum algorithms may outperform classical algorithms in some cases, but so far they retain the classical (recursion-theoretic) notion of computability. A speculation is then offered as to where the putative power of quantum computers may come from.
Defining Dysfunction: Natural Selection, Design, and Drawing a Line
Authors: Schwartz Peter H.
Published: July 2008

Accounts of the concepts of function and dysfunction have not adequately explained what factors determine the line between low-normal function and dysfunction. I call the challenge of doing so theline-drawing problem. Previous approaches emphasize facts involving the action of natural selection (Wakefield 1992a, 1999a, 1999b) or the statistical distribution of levels of functioning in the current population (Boorse 1977, 1997). I point out limitations of these two approaches and present a solution to the line-drawing problem that builds on the second one.
Scientific Understanding after the Ingold Revolution in Organic Chemistry
Authors: Goodwin William
Published: July 2008

This paper characterizes the increase in ‘scientific understanding’ that resulted from the Ingold Revolution in organic chemistry. By describing both the sorts of explanations facilitated by Ingold's Revolution and the sense in which organic chemistry was ‘unified’ by adopting these approaches to explanation, one can appreciate how this revolution led to a dramatic qualitative improvement in organic chemists’ understanding of the phenomena that they study. The explanatory unification responsible for this transformation in organic chemistry is contrasted with contemporary philosophical accounts of unification and its relationship to both scientific understanding and explanation.
Computing the Perfect Model: Why Do Economists Shun Simulation?
Authors: Lehtinen Aki , Kuorikoski Jaakko
Published: July 2008

Like other mathematically intensive sciences, economics is becoming increasingly computerized. Despite the extent of the computation, however, there is very little true simulation. Simple computation is a form of theory articulation, whereas true simulation is analogous to an experimental procedure. Successful computation is faithful to an underlying mathematical model, whereas successful simulation directly mimics a process or a system. The computer is seen as a legitimate tool in economics only when traditional analytical solutions cannot be derived, i.e., only as a purely computational aid. We argue that true simulation is seldom practiced because it does not fit the conception of understanding inherent in mainstream economics. According to this conception, understanding is constituted by analytical derivation from a set of fundamental economic axioms. We articulate this conception using the concept of economists' perfect model. Since the deductive links between the assumptions and the consequences are not transparent in ‘bottom-up’ generative microsimulations, microsimulations cannot correspond to the perfect model and economists do not therefore consider them viable candidates for generating theories that enhance economic understanding.
Dependence of heat transport on toroidal rotation in conventional H-modes in JT-60U
Authors: Urano H. , Takenaga H. , Fujita T. , Kamada Y. , Koide Y. , Oyama N. , Yoshida M.
Published: July 2008

The relation between heat transport in the plasma core and the toroidal rotation profile was examined in conventional ELMy H-mode plasmas in JT-60U. Heat transport in the plasma core is not strongly influenced locally by toroidal rotation. The large increase in heat conduction imposes a resilient profile of ion temperature, under which the local effect of the toroidal rotation profile on scale length of the ion temperature gradient is very weak. Energy confinement improvement is observed with toroidal rotation which increases in the co-direction with respect to the plasma current. In this case, the increase in the ion temperature in both the plasma core and the pedestal region is observed. However, heat transport in the plasma core varies while maintaining self-similar temperature profiles as the toroidal rotation profile is varied. Pressure at the H-mode pedestal becomes slightly larger with the toroidal rotation in the co-direction. Thus, energy confinement enhanced with co-toroidal rotation is determined by increased pedestal height and reduced transport brought on by profile resilience. When pedestal temperature was fixed between the cases of co- and counter-NBI by adjusting the plasma density, identical temperature profiles were obtained in spite of totally different toroidal rotation profiles.
Divertor power and particle fluxes between and during type-I ELMs in the ASDEX Upgrade
Authors: Kallenbach A. , Dux R. , Eich T. , Fischer R. , Giannone L. , Harhausen J. , Herrmann A. , Müller H.W. , Pautasso G. , Wischmeier M.
Published: July 2008

Particle, electric charge and power fluxes for type-I ELMy H-modes are measured in the divertor of the ASDEX Upgrade tokamak by triple Langmuir probes, shunts, infrared (IR) thermography and spectroscopy. The discharges are in the medium to high density range, resulting in predominantly convective edge localized modes (ELMs) with moderate fractional stored energy losses of 2% or below. Time resolved data over ELM cycles are obtained by coherent averaging of typically one hundred similar ELMs, spatial profiles from the flush-mounted Langmuir probes are obtained by strike point sweeps. The application of simple physics models is used to compare different diagnostics and to make consistency checks, e.g. the standard sheath model applied to the Langmuir probes yields power fluxes which are compared with the thermographic measurements. In between ELMs, Langmuir probe and thermography power loads appear consistent in the outer divertor, taking into account additional load due to radiation and charge exchange neutrals measured by thermography. The inner divertor is completely detached and no significant power flow by charged particles is measured. During ELMs, quite similar power flux profiles are found in the outer divertor by thermography and probes, albeit larger uncertainties in Langmuir probe evaluation during ELMs have to be taken into account. In the inner divertor, ELM power fluxes from thermography are a factor 10 larger than those derived from probes using the standard sheath model. This deviation is too large to be caused by deficiencies of probe analysis. The total ELM energy deposition from IR is about a factor 2 higher in the inner divertor compared with the outer divertor. Spectroscopic measurements suggest a quite moderate contribution of radiation to the target power load. Shunt measurements reveal a significant positive charge flow into the inner target during ELMs. The net number of elementary charges correlates well with the total core particle loss obtained from highly resolved density profiles. As a consequence, the discrepancy between probe and IR measurements is attributed to the ion power channel via a high mean impact energy of the ions at the inner target. The dominant contributing mechanism is proposed to be the directed loss of ions from the pedestal region into the inner divertor.
hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework
Authors: Abo Ryan , Knight Stacey , Wong Jathine , Cox Angela , Camp Nicola J.
Published: July 2008

Summary: Haplotypes carry important information that can direct investigators towards underlying susceptibility variants, and hence multiple tagging single nucleotide polymorphisms (tSNPs) are usually studied in candidate gene association studies. However, it is often unknown which SNPs should be included in haplotype analyses, or which tests should be performed for maximum power. We have developed a program, hapConstructor, which automatically builds multi-locus SNP sets to test for association in a case-control framework. The multi-SNP sets considered need not be contiguous; they are built based on significance. An important feature is that the missing data imputation is carried out based on the full data, for maximal information and consistency. HapConstructor is implemented in a Monte Carlo framework and naturally extends to allow for significance testing and false discovery rates that account for the construction process and to related individuals. HapConstructor is a useful tool for exploring multi-locus associations in candidate genes and regions.

Availability: http://www-genepi.med.utah.edu/Genie

Contact:  ryan.abo@hsc.utah.edu
An integrated approach for automating validation of extracted ion chromatographic peaks
Authors: Nelson William D. , Viele Kert , Lynn Bert C.
Published: July 2008

Summary: Accurate determination of extracted ion chromatographic peak areas in isotope-labeled quantitative proteomics is difficult to automate. Manual validation of identified peaks is typically required. We have integrated a peak confidence scoring algorithm into existing tools which are compatible with analysis pipelines based on the standards from the Institute for Systems Biology. This algorithm automatically excludes incorrectly identified peaks, improving the accuracy of the final protein expression ratio calculation.

Contact:  wnels2@uky.edu

Source and Supplementary Information:  http://www.chem.uky.edu/research/lynn/Nelson.pdf
Development and application of seasonal indices of coastal-zone eutrophication
Authors: Ryan Scott A. , Roff John C. , Yeats Philip A.
Published: July 2008

Ryan, S. A., Roff, J. C., and Yeats, P. A. 2008. Development and application of seasonal indices of coastal-zone eutrophication. – ICES Journal of Marine Science, 65: 1469–1474. Indices of coastal-zone eutrophication were developed based on combined values of nitrogen, phosphorus, and phytoplankton biomass (measured as Chl a). Measurements of nitrate, ammonia, phosphate, Chl a, and total phosphorous were taken at a series of inlets (bays and estuaries) along the Atlantic coast of Nova Scotia and the north shore of Prince Edward Island in summer 2006. Reference data from offshore sites and measured data are displayed on a N (nitrogen):P (phosphorus) nutrient–space diagram, which clearly indicates thresholds between impacted and unimpacted inlets. The problem of seasonal variability in nutrient levels and phytoplankton concentrations is accounted for by using an amalgamation of the Redfield nutrient ratios and the coastal carbon–Chl a ratio and allowing for sedimentary losses. This amalgamated ratio allows for the inverse seasonal relationship between labile nutrient levels and Chl a, permitting the collection, comparison, and interpretation of seasonally variable data. Measured concentrations of phosphate were adjusted from measured Chl a and were compared with measured levels of total phosphorous for the Nova Scotian sites to assess the accuracy of conversions. Given regional calibration, these indices should be applicable to all coastal waters.
Evaluating potential indicators for an ecosystem approach to fishery management in European waters
Authors: Piet Gerjan J. , Jansen Henrice M. , Rochet Marie-Joëlle
Published: July 2008

Piet, G. J., Jansen, H. M., and Rochet, M-J. 2008. Evaluating potential indicators for an ecosystem approach to fishery management in European waters. – ICES Journal of Marine Science, 65: 1449–1455. This study describes the process of evaluating potential indicators for an ecosystem approach to fishery management in European waters by evaluating these indicators against existing criteria using questionnaires completed by experts. We (i) compare the use of a longer list of simple criteria with a shorter list of elaborate ones; (ii) compare evaluation results when screening criteria are applied to specific indicators vs. high-level headline indicators; and (iii) examine whether detailed questionnaires, with elaborate indicators and elaborate criteria, result in ranked scores that are less influenced by familiarity with the indicators. The results show that the ranked scores of indicators are affected by the level of detail, both in terms of criteria and indicators, provided in the questionnaires. It appears that adding detail to the questionnaires makes the scoring process more transparent and provides better founded scores; at a certain point, however, more-detailed indicators and/or more-detailed criteria result in decreased performance of the scoring process, reflecting mostly factors that do not determine the suitability of the indicator (e.g. the level of familiarity), while giving the false impression of a more thorough analysis.
A subcellular model of glucose-stimulated pancreatic insulin secretion
Authors: Pedersen Morten Gram , Corradin Alberto , Toffolo Gianna M , Cobelli Claudio
Published: July 2008

When glucose is raised from a basal to stimulating level, the pancreatic islets respond with a typical biphasic insulin secretion pattern. Moreover, the pancreas is able to recognize the rate of change of the glucose concentration. We present a relatively simple model of insulin secretion from pancreatic β-cells, yet founded on solid physiological grounds and capable of reproducing a series of secretion patterns from perfused pancreases as well as from stimulated islets. The model includes the notion of distinct pools of granules as well as mechanisms such as mobilization, priming, exocytosis and kiss-and-run. Based on experimental data, we suggest that the individual β-cells activate at different glucose concentrations. The model reproduces most of the data it was tested against very well, and can therefore serve as a general model of glucose-stimulated insulin secretion. Simulations predict that the effect of an increased frequency of kiss-and-run exocytotic events is a reduction in insulin secretion without modification of the qualitative pattern. Our model also appears to be the first physiology-based one to reproduce the staircase experiment, which underlies ‘derivative control’, i.e. the pancreatic capacity of measuring the rate of change of the glucose concentration.
Neurobiological mechanisms for opponent motivational processes in addiction
Authors: Koob George F , Le Moal Michel
Published: July 2008

The conceptualization of drug addiction as a compulsive disorder with excessive drug intake and loss of control over intake requires motivational mechanisms. Opponent process as a motivational theory for the negative reinforcement of drug dependence has long required a neurobiological explanation. Key neurochemical elements involved in reward and stress within basal forebrain structures involving the ventral striatum and extended amygdala are hypothesized to be dysregulated in addiction to convey the opponent motivational processes that drive dependence. Specific neurochemical elements in these structures include not only decreases in reward neurotransmission such as dopamine and opioid peptides in the ventral striatum, but also recruitment of brain stress systems such as corticotropin-releasing factor (CRF), noradrenaline and dynorphin in the extended amygdala. Acute withdrawal from all major drugs of abuse produces increases in reward thresholds, anxiety-like responses and extracellular levels of CRF in the central nucleus of the amygdala. CRF receptor antagonists block excessive drug intake produced by dependence. A brain stress response system is hypothesized to be activated by acute excessive drug intake, to be sensitized during repeated withdrawal, to persist into protracted abstinence and to contribute to stress-induced relapse. The combination of loss of reward function and recruitment of brain stress systems provides a powerful neurochemical basis for the long hypothesized opponent motivational processes responsible for the negative reinforcement driving addiction.
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
Authors: Merrihew Gennifer E. , Davis Colleen , Ewing Brent , Williams Gary , Käll Lukas , Frewen Barbara E. , Noble William Stafford , Green Phil , Thomas James H. , MacCoss Michael J.
Published: July 2008

We describe a general mass spectrometry-based approach for gene annotation of any organism and demonstrate its effectiveness using the nematode Caenorhabditis elegans. We detected 6779 C. elegans proteins (67,047 peptides), including 384 that, although annotated in WormBase WS150, lacked cDNA or other prior experimental support. We also identified 429 new coding sequences that were unannotated in WS150. Nearly half (192/429) of the new coding sequences were confirmed with RT-PCR data. Thirty-three (∼8%) of the new coding sequences had been predicted to be pseudogenes, 151 (∼35%) reveal apparent errors in gene models, and 245 (57%) appear to be novel genes. In addition, we verified 6010 exon–exon splice junctions within existing WormBase gene models. Our work confirms that mass spectrometry is a powerful experimental tool for annotating sequenced genomes. In addition, the collection of identified peptides should facilitate future proteomics experiments targeted at specific proteins of interest.
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
Authors: Moxon Simon , Jing Runchun , Szittya Gyorgy , Schwach Frank , Rusholme Pilcher Rachel L. , Moulton Vincent , Dalmay Tamas
Published: July 2008

In plants there are several classes of 21–24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato fruit and leaf. Several conserved miRNAs showed tissue-specific expression, which, combined with target gene validation results, suggests that miRNAs may play a role in fleshy fruit development. We also identified four new nonconserved miRNAs. One of the validated targets of a novel miRNA is a member of the CTR family involved in fruit ripening. However, 62 predicted targets showing near perfect complementarity to potential new miRNAs did not validate experimentally. This suggests that target prediction of plant short RNAs could have a high false-positive rate and must therefore be validated experimentally. We also found short RNAs from a Solanaceae-specific foldback transposon, which showed a miRNA/miRNA*-like distribution, suggesting that this element may function as a miRNA gene progenitor. The other Solanaceae-specific class of short RNA was derived from an endogenous pararetrovirus sequence inserted into the tomato chromosomes. This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation.
TonB induces conformational changes in surface‐exposed loops of FhuA, outer membrane receptor of Escherichia coli
Authors: James Karron J. , Hancock Mark A. , Moreau Violaine , Molina Franck , Coulton James W.
Published: July 2008

FhuA, outer membrane receptor of Escherichia coli, transports hydroxamate‐type siderophores into the periplasm. Cytoplasmic membrane–anchored TonB transduces energy to FhuA to facilitate siderophore transport. Because the N‐terminal cork domain of FhuA occludes the C‐terminal β‐barrel lumen, conformational changes must occur to enable siderophore passage. To localize conformational changes at an early stage of the siderophore transport cycle, four anti‐FhuA monoclonal antibodies (mAbs) were purified to homogeneity, and the epitopes that they recognize were determined by phage display. We mapped continuous and discontinuous epitopes to outer surface‐exposed loops 3, 4, and 5 and to β‐barrel strand 14. To probe for conformational changes of FhuA, surface plasmon resonance measured mAb binding to FhuA in its apo‐ and siderophore‐bound states. Changes in binding kinetics were observed for mAbs whose epitopes were mapped to outer surface‐exposed loops. Further, we measured mAb binding in the absence and presence of TonB. After forming immobilized FhuA–TonB complexes, changes in kinetics of mAb binding to FhuA were even more pronounced compared with kinetics of binding in the absence of TonB. Measurement of extrinsic fluorescence of the dye MDCC conjugated to residue 336 in outer surface‐exposed loop 4 revealed 33% fluorescence quenching upon ferricrocin binding and up to 56% quenching upon TonB binding. Binding of mAbs to apo‐ and ferricrocin‐bound FhuA complemented by fluorescence spectroscopy studies showed that their cognate epitopes on loops 3, 4, and 5 undergo conformational changes upon siderophore binding. Further, our data demonstrate that TonB binding promotes conformational changes in outer surface‐exposed loops of FhuA.
Estimating density of Kirk’s dik‐dik (Madoqua kirkiiGünther), impala (Aepyceros melampusLichtenstein) and common zebra (Equus burchelliGray) at Mpala, Laikipia District, Kenya
Authors: Shorrocks Bryan , Cristescu Bogdan , Magane Samiro
Published: July 2008

This study compares two methods of estimating the density of three ungulate species: Kirk’s dik‐dik, impala and common zebra, in a dry savannah ecosystem. Fixed strip width and distance sampling involving direct animal counts were used in parallel, and tested for bias and precision in two habitats. Distance sampling was the method that achieved a better balance between accuracy and precision. The differences in sightability of ungulates, according to body size, colour and habitat characteristics, are taken into account by the distance sampling method, but not by the strip method, which produced, what we suspect are, underestimates of animal density.
Diet selection and density estimates of forest buffalo in Campo‐Ma’an National Park, Cameroon
Authors: Bekhuis Patricia D. B. M. , De Jong Christine B. , Prins Herbert H. T.
Published: July 2008

We studied diet selection and density of forest buffalo in the Campo Ma’an National Park of southern Cameroon. The buffalo’s diet in this rainforest comprised 43% grass, including 15%Leptochloa caerulecens. Other species eaten were non‐graminoid monocots (21.3%), mainly Commelinaceae (18.2%), including Palisota spp. and dicotyledons (32.7%), mainly leaves (26.5%). This diet revealed that buffalo collect their food on road verges, logging tracks and along large rivers. This agrees well with the distribution of buffalo tracks in the study area. Mean buffalo density in the forest was only 0.01 buffalo km−2, whereas the density on the road together with its direct surroundings was 0.4 buffalo per km of road. We estimated the total number of buffalo in the 650 km2 southern part of National Park Campo‐Ma’an of only twenty individuals. We suggest that the buffalo’s ancestral niche was not a primeval type of rainforest, as suggested by Kingdon, but an interface between savanna and rainforest. The Campo‐Ma’an buffalo most likely depend to a very large extent on anthropogenic vegetation types. Maintaining some grass cover by annual clear‐cutting along roads and on logging tracks might be necessary for the survival of the buffalo population within the National Park.
The microbiological and chemical composition of silage over the course of fermentation in round bales relative to that of silage made from unchopped and precision‐chopped herbage in laboratory silos
Authors: McEniry J. , O’Kiely P. , Clipson N. J. W. , Forristal P. D. , Doyle E. M.
Published: July 2008

The composition of baled silage frequently differs from that of comparable conventional silage. A factorial experiment was conducted with three wilting treatments (0, 24 or 48 h) × three ensiling systems [unchopped grass in bales, unchopped grass in laboratory silos (LS), precision‐chopped grass in LS] × six stages of ensiling to (i) confirm that the fermentation of unchopped grass in LS could be used as an adequate model for baled silage fermentation, (ii) quantify the differences between baled silage and silage made from precision‐chopped herbage across a range of dry‐matter contents and (c) quantify the fermentation dynamics within the various treatments. The onset of fermentation as evidenced by the accumulation of fermentation products and the decline in pH were slower (P < 0·05) in baled silage compared with silage made from precision‐chopped herbage. Furthermore the pH (P < 0·001) and overall concentration of fermentation acids (P < 0·01) were lower while ammonia‐N concentration was generally higher in baled silage, making it more conducive to the activities of Clostridia, Enterobacteria and yeast. Numbers of Enterobacteria were higher (P < 0·001) in baled silage in the early stages of ensilage and persisted in baled silage at the end of the storage period. The implications of a slower onset of fermentation in baled herbage are greater in farm practice, as the fermentation would be further restricted by a more extensive wilting of the herbage prior to ensiling.
Intake, rumen fermentation, degradability and digestion kinetics in beef cattle offered autumn grass herbage differing in regrowth interval
Authors: Owens D. , McGee M. , Boland T.
Published: July 2008

The effects of a 10‐d increase in regrowth interval (35 and 45 d) of a predominantly perennial ryegrass sward harvested in two periods in the autumn in Ireland on feed intake, rumen fermentation, in situ degradability and rumen digesta kinetics was examined using six ruminally cannulated Holstein–Friesian steers in three replicates of a 2 × 2 crossover design. The longer regrowth interval had a higher grass dry‐matter (DM) yield of herbage by 615 kg DM ha−1 and a lower crude protein (CP) concentration of herbage by 27 g kg−1 DM. There was no effect of regrowth interval on DM intake, rumen pH, total volatile fatty acid concentration or the molar proportions of acetate, propionate or butyrate in the rumen but the concentration of rumen ammonia (NH3‐N) was lower on the longer regrowth interval. The longer regrowth interval had a lower apparent total tract digestibility of DM, organic matter (OM), N and neutral‐detergent fibre (NDF). There was no effect of regrowth interval on the in situ degradability of DM, OM, N or NDF. The passage rates (kp) of DM and OM were higher while the rate of digestion (kd) of DM and NDF was lower with the longer regrowth interval. The results indicated that, although increasing the regrowth interval by 10 d in autumn reduced the apparent digestibility of the grass herbage, there was no adverse effect on DM intake, rumen fermentation pattern or in situ rumen degradability. The reduction in rumen NH3‐N concentrations, reflecting the lower herbage CP concentration in herbage for the longer regrowth interval, may potentially reduce nitrogen excretion to the environment.
Quality and textural behaviour of par‐baked and rebaked cake during prolonged storage
Authors: Karaoğlu Mehmet Murat , Kotancilar Halis Gürbüz
Published: July 2008

The effect of par‐baking and refrigerator storage on the quality of cake was investigated. Quality evaluation of rebaked cakes was performed by using physical, chemical and instrumental texture profile analysis. Cakes were par‐baked for 15, 20 and 25 min at 175 °C and then they were stored at refrigerator temperature (4 °C) for 30, 60 and 90 days, wrapped with two polyethylene bags. After storage, par‐baked cakes were rebaked at 175 °C and were subjected to analysis. Par‐baking and intermediate storage time had a significant effect on baking loss, crumb moisture content, colour, symmetry index and textural properties of cake. The increase in the par‐baking time led to a decrease in the baking loss and an increase in the moisture content of cake. Specific volume, moisture content, L colour value and symmetry index significantly decreased with increasing intermediate storage time, while baking loss significantly increased. However, regarding the crumb hardness, cohesiveness, springiness, gumminess and chewiness, the results indicated that the best result was obtained when cakes were baked for 15 min at the par‐baking stage. Overall, the cakes became firmer, less cohesive and less dry crumb as the intermediate storage time increased, whereas springiness increased.
Inhibition of toxicogenic Bacillus licheniformis 553/1 in Nigerian Wara soft cheese by nisin‐producing Lactococcus lactis LAC309
Authors: Raheem Dele , Saris Per E. J.
Published: July 2008

Wara soft cheese is a traditionally produced cheese in Nigeria. The production of this cheese includes a heating step for killing vegetative cells. Therefore, mainly spore‐forming bacteria surviving the process may function as the first spoilers resulting in lowered shelf‐life and safety of the product. In this study, we investigated if the addition of a nisin‐producing Lactococcus lactis LAC309 starter after the high temperature treatment could result in nisin production and inhibition of the toxicogenic Bacillus licheniformis 553/1 strain spiked into the cheese. The results showed that L. lactis LAC309 could produce nisin in Wara cheese and that the strain inhibited (3 log reduction) B. licheniformis 553/1 in Wara cheese. Food technologists developing industrialised Wara cheese should therefore consider including a nisin‐producing starter strain in the cheese‐making process.
Starch‐lipid composites in plain set yogurt
Authors: Singh Mukti , Byars Jeffrey A.
Published: July 2008

Starch‐lipid composites (SLC) were used to replace milk solids in yogurt mixes. The effects of the SLC on the yogurt fermentations and rheology were studied. The rate of fermentation was evaluated by the change of pH during the fermentation of yogurt. The syneresis of yogurt was observed over 3 weeks of storage. Small amplitude oscillatory shear flow measurements of the storage modulus, the loss modulus, and the loss tangent were obtained using a vane geometry. Yogurt mixes with milk solids partially replaced by SLC fermented at a similar rate than as with no milk solids replaced. Initial viscosity was higher for yogurt mixes with higher levels of SLC. The higher initial viscosity did not affect the gel structure. The addition of SLC above a level of 3% strengthened the gel and resulted in no syneresis for yogurt samples stored for 3 weeks at 4 °C.
Process optimisation and physicochemical characterisation of potato powder
Authors: Carillo Petronia , Cacace Domenico , De Rosa Maria , De Martino Ermanno , Cozzolino Concettina , Nacca Francesco , D’Antonio Rosaria , Fuggi Amodio
Published: July 2008

Samples of two potato cultivars (Agria and Merit), cultivated either conventionally or organically, were analysed to evaluate their suitability to transformation into powder. Agria cultivar potatoes from the conventional farming were selected as the most suitable for drying process both for their high‐dry matter and good nutritional value. Blanching resulted in the most effective treatment to prevent potato browning. The potato powder was obtained by means of a drum dryer using different process parameters (temperature, time and product thickness) to minimise thermal damage on the final product. The effects of these different processes were evaluated by analysing some quality indicators, as final moisture, nutrients (carbohydrates, proteins and amino acids) and colour of the powder, and rheological properties of the rehydrated puree. The results of such analyses showed that the lower the process temperature, the better the powder quality.
Physicochemical characteristics of soybean oil, palm kernel olein, and their binary blends
Authors: Nor Hayati Ibrahim , Che Man Yaakob B. , Tan Chin Ping , Nor Aini Idris
Published: July 2008

Soybean oil (SBO), palm kernel olein (PKO) and their binary blends (containing 5–40% PKO) were studied for their physicochemical characteristics. Decreases in band absorbencies of the resultant Fourier transform infrared spectra were observed in regions attributable to vibrations of the functional groups of unsaturated fatty acids, mainly the =C–H cis stretching at 3009 cm−1and –C=C cis stretching at 1657 cm−1. The solid fat content was measurable in the blends containing 15–40% PKO at 5 and 10 °C, ranging within 4–20% and 2–13%, respectively. The differential scanning calorimetry melting curve for SBO exhibited more complex transition peaks, suggesting a polymorphic transformation when compared with PKO with a simpler . Blending of SBO with PKO reduced the complexity caused by the polymorphic transformation, featuring the endotherms that only related to the β′ fat crystals.
Effect of oil content and processing conditions on the thermal behaviour and physicochemical stability of oil‐in‐water emulsions
Authors: Tippetts Megan , Martini Silvana
Published: July 2008

The destabilisation mechanism of oil‐in‐water (o/w) emulsions was studied as a function of oil content (20% and 40% o/w), homogenisation conditions and crystallisation temperatures (10, 5, 0, −5 and −10 °C). A mixture of anhydrous milk fat and soya bean oil was used as the lipid phase and whey protein isolate (2 wt%) as emulsifier. Crystallisation and melting behaviours were analysed using differential scanning calorimetry. Physicochemical stability was measured with a vertical scan macroscopic analyser. Emulsions with 20% oil were found to be less stable than those with 40% oil. For 20% o/w emulsions, the crystallisation was delayed and inhibited in emulsions with smaller droplets and promoted in emulsions with larger droplets when compared with 40% o/w emulsions. Depending on the droplet sizes in the emulsion, the formation of lipid crystals (in combination with the emulsifier) either stabilises (small droplets) or destabilises (big droplets) the emulsion.
Historical biogeography of New World emballonurid bats (tribe Diclidurini): taxon pulse diversification
Authors: Lim Burton K.
Published: July 2008

Aim  To reconstruct the biogeographical history of New World emballonurid bats (tribe Diclidurini). Although bats are the second most species‐rich order of mammals, they have not contributed substantially to our understanding of the historical biogeography of mammals in the Neotropics because of a poor fossil record. In addition, being the only group of mammals that fly, bats typically have large distributions with relatively few species endemic to restricted areas that are amenable to vicariant biogeographical approaches.

Location  Central and South America.

Methods  Phylogenetic analysis for comparing trees (PACT) is a new algorithm that incorporates all spatial information from taxon area cladograms into a general area cladogram. There were nine biogeographical areas identified in Central and South America for New World emballonurid bats. Molecular dating was used to incorporate the temporal aspect of historical biogeography. This method was compared with dispersal–vicariance analysis (DIVA), which assumes vicariance as the default mode of speciation.

Results  Of the 45 speciation events in a fully resolved phylogeny, eight that were hypothesized by DIVA as vicariance were considered by PACT as two peripheral isolations and six within‐area events. DIVA was less parsimonious because it required six more post‐speciation dispersal events in addition to the 73 hypothesized by PACT. DIVA reconstructed a widely distributed ancestor, suggesting that most dispersal events occurred earlier, whereas the ancestral area for PACT based on character optimization was the Northern Amazon, suggesting that dispersal events were more recent phenomena.

Main conclusions  The general area cladogram from PACT indicated that within‐area events, and not vicariance, provide the major mode of speciation for New World emballonurid bats. There was no biological evidence supporting or rejecting sympatric speciation in New World emballonurid bats. However, the geological history, combined with fluctuations in temperature and sea level, suggested within‐area speciation in a changing and heterogeneous environment in the Northern Amazon during the Miocene. This scenario is similar to the taxon‐pulse hypothesis of biotic diversification, which posits repeated episodes of range expansions and contractions from a stable core area such as the Guiana Shield within the Northern Amazon.