bluuebunny/crossref_metadata_2025 huggingface dataset:
The academic life: small worlds, different worlds
Authors: Locke William
Published: October 2010

The Academic Life: Small Worlds, Different Worlds represented an impressive investigation of the largest and most complex national academic community in the world, which seriously attempted a detailed representation of the variations in its form. Its ethnographic orientation
to understanding the internal academic life through exploratory interviews with individual faculty in different types of institution and a range of disciplines provided subtle and complex insights. The strength of its subsequent influence on scholars in this field, however, may have restricted
analysis of broader transformations in higher education and society and the related restructuring of academic work and careers.
The entrepreneurial university: an idea for its time
Authors: Shattock Michael
Published: October 2010

This article explores the context, contents and impact of Burton Clark's two books devoted to the concept of 'the entrepreneurial university'. It describes the widespread influence of the entrepreneurial idea particularly in Europe and discusses its relevance a decade or so after its
first formulation. It argues that Creating Entrepreneurial Universities had a major impact on the way European universities thought about the appropriate balance between institutional autonomy and state control and it released energies in many countries and a concern for self-management
which had hitherto lain dormant. It also raised the important question of the relationship between the organisational framework necessary to assist institutional self-reliance and the conduct of academic work.
Burton Clark's half century: selected writings 1956–2006
Authors: Scott Peter
Published: October 2010

The work of Burton Clark extended over more than half a century – and also from its original base in sociology to embrace wider inter-disciplinary studies. His identification of the major research themes in higher education continues to be valid, despite the substantial changes
that have taken place in the scale, structure and values of the system. Although his work continued to evolve taking in new topics such as the entrepreneurial university, it continued to be reflect the 'sociological imagination' which had been his starting point – and which explained
its conceptual clarity and methodological integrity.
Association between Objects and Body Parts Mediated by Function
Authors: Bonfiglioli Claudia
Published: October 2010

Recent accounts of conceptual knowledge suggest that the specific gestures/actions that should be performed in order to use an object for its intended function are an integral part of its mental representation. If this is true, then the information regarding which body part needs activating to interact with the object should also be part of such representation. Starting from the assumption that not only artefacts (i.e., tools), but also natural objects (i.e., fruits and vegetables) have a function, the present study investigates the existence of a link between a specific object and the effector involved in its use. The Implicit Association Test (IAT) paradigm was adopted to test for an association between natural objects and mouth, and between artefacts and hand (Experiment 1) or foot (Experiment 2). Results showed selective links between objects and effectors, based on which body part is needed to carry out the object's function.
Mapping Temporal Constructs: Actions Reveal that Time is a Place
Authors: Miles Lynden K. , Betka Ewa , Pendry Louise F. , Macrae C. Neil
Published: October 2010

Many languages employ metaphors that associate temporal constructs with locations in space (e.g., back in the old days). However, whether such space–time mappings extend beyond the linguistic domain has received little empirical attention. Noting that motor action represents a pathway through which the integration of spatial and temporal information can be revealed, the current work examined the dynamics of hand movements during a time-classification task. Results revealed that when participants were instructed to process information pertaining to the past (or future), their movements were drawn towards the left (or right). This affirms that spatiotemporal processing is grounded in the sensory-motor systems that regulate human movement.
A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes
Authors: Zhan Haimao , Chen Xin , Xu Shizhong
Published: October 2010

Motivation: Most biological traits may be correlated with the underlying gene expression patterns that are partially determined by DNA sequence variation. The correlations between gene expressions and quantitative traits are essential for understanding the functions of genes and dissecting gene regulatory networks.

Results: In the present study, we adopted a novel statistical method, called the stochastic expectation and maximization (SEM) algorithm, to analyze the associations between gene expression levels and quantitative trait values and identify genetic loci controlling the gene expression variations. In the first step, gene expression levels measured from microarray experiments were assigned to two different clusters based on the strengths of their association with the phenotypes of a quantitative trait under investigation. In the second step, genes associated with the trait were mapped to genetic loci of the genome. Because gene expressions are quantitative, the genetic loci controlling the expression traits are called expression quantitative trait loci. We applied the same SEM algorithm to a real dataset collected from a barley genetic experiment with both quantitative traits and gene expression traits. For the first time, we identified genes associated with eight agronomy traits of barley. These genes were then mapped to seven chromosomes of the barley genome. The SEM algorithm and the result of the barley data analysis are useful to scientists in the areas of bioinformatics and plant breeding.

Availability and implementation: The R program for the SEM algorithm can be downloaded from our website: http://www.statgen.ucr.edu

Contact:  shizhong.xu@ucr.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bayesian sampling of genomic rearrangement scenarios via double cut and join
Authors: Miklós István , Tannier Eric
Published: October 2010

Motivation: When comparing the organization of two genomes, it is important not to draw conclusions on their modes of evolution from a single most parsimonious scenario explaining their differences. Better estimations can be obtained by sampling many different genomic rearrangement scenarios. For this problem, the Double Cut and Join (DCJ) model, while less relevant, is computationally easier than the Hannenhalli–Pevzner (HP) model. Indeed, in some special cases, the total number of DCJ sorting scenarios can be analytically calculated, and uniformly distributed random DCJ scenarios can be drawn in polynomial running time, while the complexity of counting the number of HP scenarios and sampling from the uniform distribution of their space is unknown, and conjectured to be #P-complete. Statistical methods, like Markov chain Monte Carlo (MCMC) for sampling from the uniform distribution of the most parsimonious or the Bayesian distribution of all possible HP scenarios are required.

Results: We use the computational facilities of the DCJ model to draw a sampling of HP scenarios. It is based on a parallel MCMC method that cools down DCJ scenarios to HP scenarios. We introduce two theorems underlying the theoretical mixing properties of this parallel MCMC method. The method was tested on yeast and mammalian genomic data, and allowed us to provide estimates of the different modes of evolution in diverse lineages.

Availability: The program implemented in Java 1.5 programming language is available from http://www.renyi.hu/~miklosi/DCJ2HP/.

Contact:  miklosi@renyi.hu
Identification of human-specific transcript variants induced by DNA insertions in the human genome
Authors: Kim Dong Seon , Hahn Yoonsoo
Published: October 2010

Motivation: Many genes in the human genome produce a wide variety of transcript variants resulting from alternative exon splicing, differential promoter usage, or altered polyadenylation site utilization that may function differently in human cells. Here, we present a bioinformatics method for the systematic identification of human-specific novel transcript variants that might have arisen after the human–chimpanzee divergence.

Results: The procedure involved collecting genomic insertions that are unique to the human genome when compared with orthologous chimpanzee and rhesus macaque genomic regions, and that are expressed in the transcriptome as exons evidenced by mRNAs and/or expressed sequence tags (ESTs). Using this procedure, we identified 112 transcript variants that are specific to humans; 74 were associated with known genes and the remaining transcripts were located in unannotated genomic loci. The original source of inserts was mostly transposable elements including L1, Alu, SVA, and human endogenous retroviruses (HERVs). Interestingly, some non-repetitive genomic segments were also involved in the generation of novel transcript variants. Insert contributions to the transcripts included promoters, terminal exons and insertions in exons, splice donors and acceptors and complete exon cassettes. Comparison of personal genomes revealed that at least seven loci were polymorphic in humans. The exaptation of human-specific genomic inserts as novel transcript variants may have increased human gene versatility or affected gene regulation.

Contact:  hahny@cau.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Graphene nanoribbons in criss-crossed electric and magnetic fields
Authors: Roslyak Oleksiy , Gumbs Godfrey , Huang Danhong
Published: November 2010

Graphene nanoribbons (GNRs) in mutually perpendicular electric and magnetic fields are shown to exhibit dramatic changes in their band structure and electron-transport properties. A strong electric field across the ribbon induces multiple chiral Dirac points, closing the semiconducting gap in armchair GNRs. A perpendicular magnetic field induces partially formed Landau levels as well as dispersive surface-bound states. Each of the applied fields on its own preserves the even symmetry
E

k

=
E

−
k

of the sub-band dispersion. When applied together, they reverse the dispersion parity to be odd, which gives
E

e,
k

=−
E

h,−
k

, and mix the electron and hole sub-bands within the energy range corresponding to the change in potential across the ribbon. This leads to oscillations of the ballistic conductance within this energy range. The broken time-reversal symmetry provides dichroism in the absorption of the circularly polarized light. As a consequence, one can observe electrically enhanced Faraday rotation, since the edges of the ribbon provide formation of the substantial density of states.
Electron–electron and electron–hole pairing in graphene structures
Authors: Lozovik Yu. E. , Ogarkov S. L. , Sokolik A. A.
Published: November 2010

The superconducting pairing of electrons in doped graphene owing to in-plane and out-of-plane phonons is considered. It is shown that the structure of the order parameter in the valley space substantially affects conditions of the pairing. Electron–hole pairing in a graphene bilayer in the strong coupling regime is also considered. Taking into account retardation of the screened Coulomb pairing potential shows a significant competition between the electron–hole direct attraction and their repulsion owing to virtual plasmons and single-particle excitations.
Historical linguistics in Australia: trees, networks and their implications
Authors: Bowern Claire
Published: November 2010

This paper presents an overview of the current state of historical linguistics in Australian languages. Australian languages have been important in theoretical debates about the nature of language change and the possibilities for reconstruction and classification in areas of intensive diffusion. Here are summarized the most important outstanding questions for Australian linguistic prehistory; I also present a case study of the Karnic subgroup of Pama–Nyungan, which illustrates the problems for classification in Australian languages and potential approaches using phylogenetic methods.
The Antarctic Nematode Plectus murrayi: An Emerging Model to Study Multiple Stress Survival
Authors: Adhikari Bishwo N. , Tomasel Cecilia M. , Li Grace , Wall Diana H. , Adams Byron J.
Published: November 2010

INTRODUCTION

The genus Plectus is one of the most widely distributed and common nematode taxa of freshwater and terrestrial habitats in the world, and is of particular interest because of its phylogenetic position relative to the origin of the Secernentean radiation. Plectus murrayi, a bacteria-feeding nematode, inhabits both semi-aquatic and terrestrial biotopes in the Antarctic McMurdo Dry Valleys (MCM), where its distribution is limited by organic carbon and soil moisture. Plectus nematodes from the MCM can survive extreme desiccation, freezing conditions, and other types of stress. Ongoing investigations of the physiological and molecular aspects of the stress biology of P. murrayi, along with the availability of genomic resources, will likely establish this nematode as an excellent invertebrate model system for studies of extreme environmental survival, and may provide a valuable source of genomic resources for comparative studies in other organisms. Moreover, because P. murrayi and Caenorhabditis elegans share a most recent common ancestor with the rest of the Secernentea, and given the ability of P. murrayi to be cultured at lower temperatures compared to C. elegans, P. murrayi could also be an emerging model system for the study of the evolution of environment-sensitive (stress response) alleles in nematodes.
Isolation of Plant DNA for PCR and Genotyping Using Organic Extraction and CTAB
Authors: Springer Nathan M.
Published: November 2010

INTRODUCTION

A general difficulty in isolation of DNA from plant cells is the presence of a cell wall. It is necessary to degrade plant cell walls, either physically or enzymatically, in order to effectively isolate plant DNA. Additionally, some tissues (such as endosperm) or some species contain high levels of starches or phenolic compounds that can complicate DNA isolation. A number of plant DNA isolation protocols are designed to overcome species-specific difficulties. This is a relatively simple protocol that uses an extraction buffer containing cetyltrimethylammonium bromide (CTAB); it can be used for many plant species. It provides a substantial amount of high-quality DNA that is suitable for polymerase chain reaction (PCR) procedures and is stable for long periods of time. The cost per sample is very low. In addition, this protocol is relatively robust and can be performed by individuals who have had relatively little training. A typical undergraduate student can perform ~200-300 isolations in a day using this protocol. The disadvantages are that it requires a freeze-dryer and a mill or paint-shaker-like device and that it utilizes an organic extraction step, requiring the use of a fume hood.
Transcriptomic and Phenotypic Analyses Identify Coregulated, Overlapping Regulons among PrfA, CtsR, HrcA, and the Alternative Sigma Factors σ
B
, σ
C
, σ
H
, and σ
L
in
Listeria monocytogenes
Authors: Chaturongakul Soraya , Raengpradub Sarita , Palmer M. Elizabeth , Bergholz Teresa M. , Orsi Renato H. , Hu Yuewei , Ollinger Juliane , Wiedmann Martin , Boor Kathryn J.
Published: October 2010

A set of seven
Listeria monocytogenes
10403S mutant strains, each bearing an in-frame null mutation in a gene encoding a key regulatory protein, was used to characterize transcriptional networks in
L. monocytogenes
; the seven regulatory proteins addressed include all four
L. monocytogenes
alternative sigma factors (σ
B
, σ
C
, σ
H
, and σ
L
), the virulence gene regulator PrfA, and the heat shock-related negative regulators CtsR and HrcA. Whole-genome microarray analyses, used to identify regulons for each of these 7 transcriptional regulators, showed considerable overlap among regulons. Among 188 genes controlled by more than one regulator, 176 were coregulated by σ
B
, including 92 genes regulated by both σ
B
and σ
H
(with 18 of these genes coregulated by σ
B
, σ
H
, and at least one additional regulator) and 31 genes regulated by both σ
B
and σ
L
(with 10 of these genes coregulated by σ
B
, σ
L
, and at least one additional regulator). Comparative phenotypic characterization measuring acid resistance, heat resistance, intracellular growth in J774 cells, invasion into Caco-2 epithelial cells, and virulence in the guinea pig model indicated contributions of (i) σ
B
to acid resistance, (ii) CtsR to heat resistance, and (iii) PrfA, σ
B
, and CtsR to virulence-associated characteristics. Loss of the remaining transcriptional regulators (i.e.,
sigH
,
sigL
, or
sigC
) resulted in limited phenotypic consequences associated with stress survival and virulence. Identification of overlaps among the regulons provides strong evidence supporting the existence of complex regulatory networks that appear to provide the cell with regulatory redundancies, along with the ability to fine-tune gene expression in response to rapidly changing environmental conditions.
Prevalence and Genetic Diversity of
Bartonella
Species Detected in Different Tissues of Small Mammals in Nepal
Authors: Gundi Vijay A. K. B. , Kosoy Michael Y. , Myint Khin S. A. , Shrestha Sanjaya K. , Shrestha Mrigendra P. , Pavlin Julie A. , Gibbons Robert V.
Published: October 2010

Bartonellae were detected in a total of 152 (23.7%) of 642 tissues from 108 (48.4%) of 223 small mammals trapped in several urban areas of Nepal. Based on
rpoB
and
gltA
sequence analyses, genotypes belonging to seven known
Bartonella
species and five genotypes not belonging to previously known species were identified in these animals.
Nuclear Targeting of a Bacterial Integrase That Mediates Site-Specific Recombination between Bacterial and Human Target Sequences
Authors: Agúndez Leticia , Machón Cristina , César Carolina Elvira , Rosa-Garrido Manuel , Delgado M. Dolores , Llosa Matxalen
Published: October 2010

TrwC is a bacterial protein involved in conjugative transfer of plasmid R388. It is transferred together with the DNA strand into the recipient bacterial cell, where it can integrate the conjugatively transferred DNA strand into its target sequence present in the recipient cell. Considering that bacterial conjugation can occur between bacteria and eukaryotic cells, this protein has great biotechnological potential as a site-specific integrase. We have searched for possible TrwC target sequences in the human genome. Recombination assays showed that TrwC efficiently catalyzes recombination between its natural target sequence and a discrete number of sequences, located in noncoding sites of the human genome, which resemble this target. We have determined the cellular localization of TrwC and derivatives in human cells by immunofluorescence and also by an indirect yeast-based assay to detect both nuclear import and export signals. The results indicate that the recombinase domain of TrwC (N600) has nuclear localization, but full-length TrwC locates in the cytoplasm, apparently due to the presence of a nuclear export signal in its C-terminal domain. The recombinase domain of TrwC can be transported to recipient cells by conjugation in the presence of the helicase domain of TrwC, but with very low efficiency. We mutagenized the
trwC
gene and selected for mutants with nuclear localization. We obtained one such mutant with a point A904T mutation and an extra peptide at its C terminus, which maintained its functionality in conjugation and recombination. This TrwC mutant could be useful for future TrwC-mediated site-specific integration assays in mammalian cells.
Longitudinal Molecular Epidemiological Study of Thermophilic Campylobacters on One Conventional Broiler Chicken Farm
Authors: Ridley Anne M. , Morris Victoria K. , Cawthraw Shaun A. , Ellis-Iversen Johanne , Harris Jillian A. , Kennedy Emma M. , Newell Diane G. , Allen Vivien M.
Published: October 2010

Improved understanding of the ecology and epidemiology of
Campylobacter
in the poultry farm environment is key to developing appropriate farm-based strategies for preventing flock colonization. The sources of
Campylobacter
causing broiler flock colonization were investigated on one poultry farm and its environment, from which samples were obtained on three occasions during each of 15 crop cycles. The farm was adjacent to a dairy farm, with which there was a shared concreted area and secondary entrance. There was considerable variation in the
Campylobacter
status of flocks at the various sampling times, at median ages of 20, 26, and 35 days, with 3 of the 15 flocks remaining negative at slaughter. Campylobacters were recoverable from various locations around the farm, even while the flock was
Campylobacter
negative, but the degree of environmental contamination increased substantially once the flock was positive. Molecular typing showed that strains from house surroundings and the dairy farm were similar to those subsequently detected in the flock and that several strains intermittently persisted through multiple crop cycles. The longitudinal nature of the study suggested that bovine fecal
Campylobacter
strains, initially recovered from the dairy yard, may subsequently colonize poultry. One such strain, despite being repeatedly recovered from the dairy areas, failed to colonize the concomitant flock during later crop cycles. The possibility of host adaptation of this strain was investigated with 16-day-old chickens experimentally exposed to this strain naturally present in, or spiked into, bovine feces. Although the birds became colonized by this infection model, the strain may preferentially infect cattle. The presence of
Campylobacter
genotypes in the external environment of the poultry farm, prior to their detection in broiler chickens, confirms the horizontal transmission of these bacteria into the flock and highlights the risk from multispecies farms.
Ethanolamine Utilization Contributes to Proliferation of
Salmonella enterica
Serovar Typhimurium in Food and in Nematodes
Authors: Srikumar Shabarinath , Fuchs Thilo M.
Published: October 2010

Only three pathogenic bacterial species,
Salmonella enterica
,
Clostridium perfringens
, and
Listeria monocytogenes
, are able to utilize both ethanolamine and 1,2-propanediol as a sole carbon source. Degradation of these substrates, abundant in food and the gut, depends on cobalamin, which is synthesized
de novo
only under anaerobic conditions. Although the
eut
,
pdu
, and
cob
-
cbi
gene clusters comprise 40 kb, the conditions under which they confer a selection advantage on these food-borne pathogens remain largely unknown. Here we used the luciferase reporter system to determine the response of the
Salmonella enterica
serovar Typhimurium promoters P

eutS

, P

pocR

, P

pduF

, and P

pduA

to a set of carbon sources, to egg yolk, to whole milk, and to milk protein or fat fractions. Depending on the supplements, specific inductions up to 3 orders of magnitude were observed for P

eutS

and P

pduA

, which drive the expression of most
eut
and
pdu
genes. To correlate these significant expression data with growth properties, nonpolar deletions of
pocR
, regulating the
pdu
and
cob
-
cbi
genes, and of
eutR
, involved in
eut
gene activation, were constructed in
S
. Typhimurium strain 14028. During exponential growth of the mutants 14028Δ
pocR
and 14028Δ
eutR
, 2- to 3-fold-reduced proliferation in milk and egg yolk was observed. Using the
Caenorhabditis elegans
infection model, we could also demonstrate that the proliferation of
S
. Typhimurium in the nematode is supported by an active ethanolamine degradation pathway. Taking these findings together, this study quantifies the differential expression of
eut
and
pdu
genes under distinct conditions and provides experimental evidence that the ethanolamine utilization pathway allows salmonellae to occupy specific metabolic niches within food environments and within their host organisms.
Verotoxins in Bovine and Meat Verotoxin-Producing
Escherichia coli
Isolates: Type, Number of Variants, and Relationship to Cytotoxicity
Authors: Krüger Alejandra , Lucchesi Paula M. A. , Parma Alberto E.
Published: October 2010

In this study, we determined
vt
subtypes and evaluated verotoxicity in basal as well as induced conditions of verotoxin-producing
Escherichia coli
(VTEC) strains isolated from cattle and meat products. Most (87%) of the 186 isolates carried a
vt
2
gene. Moreover, the
vt
2
subtype, which is associated with serious disease, was present in 42% of our VTEC collection. The other
vt
subtypes detected were
vt
1
,
vt
1d
,
vt
2vha
,
vt
2vhb
,
vt
2O118
,
vt
2d
(mucus activatable), and
vt
2g
. A total of 41 (22%) of the isolates possessed more than one
vt
subtype in its genome, and among them the most frequent combination was
vt
1
/
vt
2
, but we also observed multiple combinations among
vt
2
subtypes. Differences in verotoxicity titers were found among a selection of 54 isolates. Among isolates with a single
vt
2
variant, those carrying the
vt
2
subtype had high titers under both uninduced and induced conditions. However, the highest increase in cytotoxicity under mitomycin C treatment was detected among the strains carrying
vt
2vha
or
vt
2hb
variants. Notably, the isolates carrying the
vt
1
subtype showed a lesser increase than that of most of the
vt
2
-positive VTEC strains. Furthermore, the presence of more than one
vt
gene variant in the same isolate was not reflected in higher titers, and generally the titers were lower than those for strains with only one gene variant. The main observation was that both basal and induced cytotoxic effects seemed to be associated with the type and number of
vt
variants more than with the serotype or origin of the isolate.
Raman Spectroscopy of Xylitol Uptake and Metabolism in Gram-Positive and Gram-Negative Bacteria
Authors: Palchaudhuri Sunil , Rehse Steven J. , Hamasha Khozima , Syed Talha , Kurtovic Eldar , Kurtovic Emir , Stenger James
Published: October 2010

Visible-wavelength Raman spectroscopy was used to investigate the uptake and metabolism of the five-carbon sugar alcohol xylitol by Gram-positive viridans group streptococcus and the two extensively used strains of Gram-negative
Escherichia coli
,
E. coli
C and
E. coli
K-12.
E. coli
C, but not
E. coli
K-12, contains a complete xylitol operon, and the viridans group streptococcus contains an incomplete xylitol operon used to metabolize the xylitol. Raman spectra from xylitol-exposed viridans group streptococcus exhibited significant changes that persisted even in progeny grown from the xylitol-exposed mother cells in a xylitol-free medium for 24 h. This behavior was not observed in the
E. coli
K-12. In both viridans group streptococcus and the
E. coli
C derivative HF4714, the metabolic intermediates are stably formed to create an anomaly in bacterial normal survival. The uptake of xylitol by Gram-positive and Gram-negative pathogens occurs even in the presence of other high-calorie sugars, and its stable integration within the bacterial cell wall may discontinue bacterial multiplication. This could be a contributing factor for the known efficacy of xylitol when taken as a prophylactic measure to prevent or reduce occurrences of persistent infection. Specifically, these bacteria are causative agents for several important diseases of children such as pneumonia, otitis media, meningitis, and dental caries. If properly explored, such an inexpensive and harmless sugar-alcohol, alone or used in conjunction with fluoride, would pave the way to an alternative preventive therapy for these childhood diseases when the causative pathogens have become resistant to modern medicines such as antibiotics and vaccine immunotherapy.
Binding of Virus-Like Particles of Norwalk Virus to Romaine Lettuce Veins
Authors: Gandhi Kamal M. , Mandrell Robert E. , Tian Peng
Published: October 2010

Noroviruses (NoV) annually cause millions of cases of gastrointestinal disease in the United States. NoV are associated with raw shellfish outbreaks, particularly oysters, which are thought to bioaccumulate NoV particles during the filter-feeding process. NoV outbreaks, however, have also been known to occur from other common-source food-borne vehicles, such as lettuce, frozen raspberries, and salad. In this study, we evaluated romaine lettuce as a potential vehicle for NoV transmission by testing the binding and distribution of NoV to the surface of romaine. Recombinant Norwalk virus-like particles (rNVLP) applied to the surface of romaine lettuce localized as large clusters primarily on the leaf veins. An extract of romaine lettuce leaves in phosphate-buffered saline (PBS) (romaine extract [RE]) bound rNVLP in a dose-dependent manner. RE did not bind rNVLP by histo-blood group antigens (HBGA), nor was RE competitive with rNVLP binding to porcine gastric mucin. These results suggested that non-HBGA molecules in RE bind rNVLP by a binding site(s) that is different from the defined binding pocket on the virion. Extracts of cilantro, iceberg lettuce, spinach, and celery also bound rNVLP. Samples of each of the vegetables spiked with rNVLP and tested with anti-NVLP antibody revealed by confocal microscopy the presence of rNVLP not only on the veins of cilantro but also throughout the surface of iceberg lettuce.
Development of a Fatty Acid and RNA Stable Isotope Probing-Based Method for Tracking Protist Grazing on Bacteria in Wastewater
Authors: Kuppardt Steffen , Chatzinotas Antonis , Kästner Matthias
Published: October 2010

Removal of potential pathogenic bacteria, for example, during wastewater treatment, is effected by sorption, filtration, natural die-off, lysis by viruses, and grazing by protists, but the actual contribution of grazing has never been assessed quantitatively. A methodical approach for analyzing the grazing of protists on
13
C-labeled prey bacteria was developed which enables mass balances of the carbon turnover to be drawn, including yield estimation. Model experiments for validating the approach were performed in closed microcosms with the ciliate
Uronema
sp. and
13
C-labeled
Escherichia coli
as model prey. The transfer of bacterial
13
C into grazing protist biomass was investigated by fatty acid (FA) and RNA stable isotope probing (SIP).
Uronema
sp. showed ingestion rates of ∼390 bacteria protist
−1
h
−1
, and the temporal patterns of
13
C assimilation from the prey bacteria to the protist FA were identified. Nine fatty acids specific for
Uronema
sp. were found (20:0, i20:0, 22:0, 24:0, 20:1ω9c, 20:1ω9t, 22:1ω9c, 22:1ω9t, and 24:1). Four of these fatty acids (22:0, 20:1ω9t, 22:1ω9c, and 22:1ω9t) were enriched very rapidly after 3 h, indicating grazing on bacteria without concomitant cell division. Other fatty acids (20:0, i20:0, and 20:1ω9c) were found to be indicative of growth with cell division. The fatty acids were found to be labeled with a percentage of labeled carbon (atoms percent [atom%]) up to 50. Eighteen percent of the
E. coli
-derived
13
C was incorporated into
Uronema
biomass, whereas 11% was mineralized. Around 5 mol bacterial carbon was necessary in order to produce 1 mol protist carbon (

y
x

/

s

≈ 0.2), and the temporal pattern of
13
C labeling of protist rRNA was also shown. A consumption of around 1,000 prey bacteria (∼98 atom%
13
C) per protist cell appears to be sufficient to provide detectable amounts of label in the protist RNA. The large shift in the buoyant density fraction of
13
C-labeled protist RNA demonstrated a high incorporation of
13
C, and reverse transcription-real-time PCR (RT-qPCR) confirmed that protist rRNA increasingly dominated in the heavy RNA fraction.
Podospora anserina
Hemicellulases Potentiate the
Trichoderma reesei
Secretome for Saccharification of Lignocellulosic Biomass
Authors: Couturier Marie , Haon Mireille , Coutinho Pedro M. , Henrissat Bernard , Lesage-Meessen Laurence , Berrin Jean-Guy
Published: October 2010

To improve the enzymatic hydrolysis (saccharification) of lignocellulosic biomass by
Trichoderma reesei
, a set of genes encoding putative polysaccharide-degrading enzymes were selected from the coprophilic fungus
Podospora anserina
using comparative genomics. Five hemicellulase-encoding genes were successfully cloned and expressed as secreted functional proteins in the yeast
Pichia pastoris
. These novel fungal CAZymes belonging to different glycoside hydrolase families (
Pa
Man5A and
Pa
Man26A mannanases,
Pa
Xyn11A xylanase, and
Pa
Abf51A and
Pa
Abf62A arabinofuranosidases) were able to break down their predicted cognate substrates. Although
Pa
Man5A and
Pa
Man26A displayed similar specificities toward a range of mannan substrates, they differed in their end products, suggesting differences in substrate binding. The N-terminal CBM35 module of
Pa
Man26A displayed dual binding specificity toward xylan and mannan.
Pa
Xyn11A harboring a C-terminal CBM1 module efficiently degraded wheat arabinoxylan, releasing mainly xylobiose as end product.
Pa
Abf51A and
Pa
Abf62A arabinose-debranching enzymes exhibited differences in activity toward arabinose-containing substrates. Further investigation of the contribution made by each
P. anserina
auxiliary enzyme to the saccharification of wheat straw and spruce demonstrated that the endo-acting hemicellulases (
Pa
Xyn11A,
Pa
Man5A, and
Pa
Man26A) individually supplemented the secretome of the industrial
T. reesei
CL847 strain. The most striking effect was obtained with
Pa
Man5A that improved the release of total sugars by 28% and of glucose by 18%, using spruce as lignocellulosic substrate.
Same-Day Detection ofEscherichia coliO157:H7 from Spinach by Using Electrochemiluminescent and Cytometric Bead Array Biosensors
Authors: Leach Kelly M. , Stroot Joyce M. , Lim Daniel V.
Published: October 2010

Contamination of fresh produce withEscherichia coliO157:H7 and other pathogens commonly causes food-borne illness and disease outbreaks. Thus, screening for pathogens is warranted, but improved testing procedures are needed to allow reproducible same-day detection of low initial contamination levels on perishable foods, and methods for detecting numerous pathogens in a single test are desired. Experimental procedures were developed to enable rapid screening of spinach forE. coliO157:H7 by using multiplex-capable immunological assays that are analyzed using biosensors. Detection was achieved using an automated electrochemiluminescent (ECL) assay system and a fluorescence-based cytometric bead array. Using the ECL system, less than 0.1 CFU ofE. coliO157:H7 per gram of spinach was detected after 5 h of enrichment, corresponding to 6.5 h of total assay time. Using the cytometric bead array, less than 0.1 CFU/g was detected after 7 h of enrichment, with a total time to detection of less than 10 h. These results illustrate that both biosensor assays are useful for rapid detection ofE. coliO157:H7 on produce in time frames that are comparable to or better than those of other testing formats. Both methods may be useful for multiplexed pathogen detection in the food industry and other testing situations.
Production of Glutaconic Acid in a RecombinantEscherichia coliStrain
Authors: Djurdjevic Ivana , Zelder Oskar , Buckel Wolfgang
Published: October 2010

The assembly of six genes that encode enzymes from glutamate-fermenting bacteria convertedEscherichia coliinto a glutaconate producer when grown anaerobically on a complex medium. The new anaerobic pathway starts with 2-oxoglutarate from general metabolism and proceeds via (R)-2-hydroxyglutarate, (R)-2-hydroxyglutaryl-coenzyme A (CoA), and (E)-glutaconyl-CoA to yield 2.7 ± 0.2 mM (E)-glutaconate in the medium.
Preclinical Class 1 Integron with a Complete Tn
402
-Like Transposition Module
Authors: Sajjad Ammara , Holley Marita P. , Labbate Maurizio , Stokes H. W. , Gillings Michael R.
Published: October 2010

The presence of integrons was assessed in gut bacteria isolated from wild-caught prawns. A pseudomonad was recovered that contained a Tn
402
-like class 1 integron with a complete transposition module and two gene cassettes. One cassette was identical to a previously described cassette from a chromosomal class 3 integron in
Delftia
tsuruhatensis
.
Diffusion of Nanoparticles in Biofilms Is Altered by Bacterial Cell Wall Hydrophobicity
Authors: Habimana Olivier , Steenkeste Karine , Fontaine-Aupart Marie-Pierre , Bellon-Fontaine Marie-Noëlle , Kulakauskas Saulius , Briandet Romain
Published: October 2010

Diffusion of entities inside biofilm triggers most mechanisms involved in biofilm-specific phenotypes. Using genetically engineered hydrophilic and hydrophobic cells of
Lactococcus lactis
yielding similar biofilm architectures, we demonstrated by fluorescence correlation spectroscopy that bacterial surface properties affect diffusion of nanoparticles through the biofilm matrix.
Expanding the Genetic Toolbox for
Leptospira
Species by Generation of Fluorescent Bacteria
Authors: Aviat Florence , Slamti Leyla , Cerqueira Gustavo M. , Lourdault Kristel , Picardeau Mathieu
Published: October 2010

Our knowledge of the genetics and molecular basis of the pathogenesis associated with
Leptospira
, in comparison to those of other bacterial species, is very limited. An improved understanding of pathogenic mechanisms requires reliable genetic tools for functional genetic analysis. Here, we report the expression of
gfp
and
mRFP1
genes under the control of constitutive spirochetal promoters in both saprophytic and pathogenic
Leptospira
strains. We were able to reliably measure the fluorescence of
Leptospira
by fluorescence microscopy and a fluorometric microplate reader-based assay. We showed that the expression of the
gfp
gene had no significant effects on growth
in vivo
and pathogenicity in
L. interrogans
. We constructed an expression vector for
L. biflexa
that contains the
lacI
repressor, an inducible
lac
promoter, and
gfp
as the reporter, demonstrating that the
lac
system is functional in
Leptospira
. Green fluorescent protein (GFP) expression was induced by the addition of isopropyl-β-
d
-thiogalactopyranoside (IPTG) in
L. biflexa
transformants harboring the expression vector. Finally, we showed that GFP can be used as a reporter to assess promoter activity in different environmental conditions. These results may facilitate further advances for studying the genetics of
Leptospira
spp.
Influence of the opposition in throwing accuracy in elite and amateur handball players
Authors: Rivilla-García J , Sampedro-Molinuevo J
Published: November 2010

The success of goal shooting in handball depends mostly on accuracy and throwing velocity. Several researchers have investigated the relationship between ball velocity and accuracy, but few investigations have included opposition, and there is no evidence on how opposition affects throwing accuracy. The present study analysed differences in throwing accuracy according to the opposition in handball players. Forty-three elite (E) and amateur (A) handball players (24±3 years; 187±3 cm; 91.8±9.1 kg) were assessed in two throwing tests: without (T1) and with opposition (T2). The instructions were: throw the ball at the highest possible speed, using the technique appropriate in handball, with three steps before throwing, from behind the free-throw line, at 9 m from the goal. The players were instructed to make precise shots following the goalkeeper intervention difficulty criterion1 2: throws had to target the corner of the goal. The goalkeeper (T2) was situated on the goal line. An observer assessed the impact location of the ball in the goal or goalkeeper using a slow motion camera. Each release was scored according to its precision: 0 (minimum) to 5 (maximum accuracy). E players (T1=4.46±0.66, T2=4.31±0.75) achieved better precision values than As (T1=3.63±1.09, T2=3.37±1.18) in T1 (p=0.016, t=2.519, df=41) and T2 (p<0.01, t=2.809, df=41). The analysis of mean differences showed that accuracy was lower with than without opposition (T1-T2=0.651±0.376; p<0.01; t=3.267; gl=42). The greatest difference between T1 and T2 was found in the A group (T1-T2=0.867±1.5, p<0.01, t=3.159, df=29) while in the E group there was no significant effect (T1-T2=0.154, p=0.165; t=1.477, df=12). The competitive level determines throwing accuracy, with and without opposition. The opposition has a negative effect on throwing accuracy, especially in A players.
Gastric emptying rate and perceived hunger after rest and exercise in man
Authors: Evans G H , Shirreffs S M , Watson P , Maughan R J
Published: November 2010

The rate at which ingested fluid is emptied from the stomach is influenced by a number of factors. Exercise at intensities greater than 70% VO2maxhas been shown to reduce gastric emptying rates in healthy individuals,1 but to date, no studies have reported the effects of differing exercise intensities on gastric emptying characteristics after the cessation of exercise. Five males and three females participated in this investigation following prior ethical approval. Each subject undertook a measurement of VO2maxand a familiarisation trial before participating in three randomly assigned experimental trials. These included 30 min of rest, continuous cycling at 33% of peak power obtained during the VO2maxtest (LI) and ten 1-min sprints at peak power separated by rest periods of 2 min (HI). 30 min after completion of rest or exercise, a gastric tube was inserted and the stomach emptied before ingestion of 595 ml of a 5% glucose solution. Stomach volumes were determined at 10-min intervals for 1 h using the double sampling technique.2 3 Subjective feelings of hunger were determined before and after rest or exercise, before drinking and at 10-min intervals after drink ingestion. No differences (p>0.05) in subjective feelings of hunger were observed from pre-exercise or pre-ingestion values at any time during the rest or LI trial. Subjective feelings of hunger were significantly reduced (p=0.005) from pre-exercise values during the HI trial but returned to pre-exercise values before fluid ingestion. Mean±SD half emptying times for the test drink were similar (p=0.999) during the three trials: rest 22±10 min; LI 22±8 min HI 22±7 min. Subjective feelings of hunger in the hour after fluid ingestion were negatively correlated with total stomach volume (R2(rest) −0.655, p=0.110, LI:−0.897, p=0.006, HI−0.833, p=0.02). Previous investigations have observed that gastrointestinal function appears to be affected during high intensity exercise, but the results of the present study show that gastric emptying was not impaired 30 min after high intensity exercise. Perceived feelings of hunger and gastrointestinal function appear to be closely linked.
Child injury surveillance that guides interventions: the Beijing primary healthcare experience
Authors: Linnan Huan , Duan Jianhua , Chen Xinxin , Yan Shujuan
Published: October 2010

Objectives

To provide feedback to guide injury prevention interventions and to test the feasibility of integrating injury surveillance into the existing primary healthcare service for children under 6 years of age.

Design

This surveillance system was integrated into existing primary healthcare services at the community primary healthcare centre (PHC) and community kindergartens. Parents reported injury incidents during their child's routine health services at scheduled intervals. Kindergarten nurses registered injury incidents at the absentee recording system. A total of 8358 children annually were included into the surveillance in 2006–07.

Setting

Two urban communities and three rural communities in Beijing, China.

Results

The coverage rates were 93.7% in PHCs and 98% in kindergartens. The injury incidence rates in year 1 and year 2 were 2.7% and 1.9% respectively. The leading causes were falls, being hit by blunt object, and animal injury. Major causes of injury were different between urban and rural children. Over the two-year surveillance period, injury incidence rates declined significantly from 2.7% to 1.7% in urban communities. No significant decrease was seen in rural communities.

Conclusion

Surveillance through the primary healthcare system in Beijing was useful in child injury prevention as data collected allowed managers to design targeted interventions that resulted in decreased injury. In comparison with hospital based surveillance, PHC based surveillance demonstrated an advantage in wide access to children and allowed calculation of injury incidence rates to monitor trends over time. PHC based surveillance can serve as a useful venue to collect child injury data.
Diagnostic reasoning in Nizāmī ‘Arūzī’sFour Discourses
Authors: Aggarwal Neil Krishan
Published: October 2010

Background

Most studies on medical reasoning focus on contemporary allopathic practitioners. Here, the significance of diagnostic sense in Nizāmī ‘Arūzī’sFour Discourses(Chahār Maqāle), an influential text that circulated widely throughout the Islamic world, is explored.

Methods

After a brief introduction, key passages are translated on how doctors should cultivate analytical skills.

Results

Nizāmī ‘Arūzī cites three sources of diagnostic authority: (1) education in the texts of medical experts, (2) formal logic and (3) belief in the power of God.

Conclusions

‘Arūzī’s methods, though rooted in a religious faith that may seem foreign to contemporary doctors and educators, has much to recommend regarding its clarity of approach, its high ethical standards and expectations of doctors, and its commitment to best practices for the patient. Crosscultural studies of medical education and professionalism can offer valuable insights by demonstrating how doctors across history and geography have grappled with the common concerns of diagnosis and treatment.
When smokers move out and non-smokers move in: residential thirdhand smoke pollution and exposure
Authors: Matt Georg E , Quintana Penelope J E , Zakarian Joy M , Fortmann Addie L , Chatfield Dale A , Hoh Eunha , Uribe Anna M , Hovell Melbourne F
Published: October 2010

Background

This study examined whether thirdhand smoke (THS) persists in smokers' homes after they move out and non-smokers move in, and whether new non-smoking residents are exposed to THS in these homes.

Methods

The homes of 100 smokers and 50 non-smokers were visited before the residents moved out. Dust, surfaces, air and participants' fingers were measured for nicotine and children's urine samples were analysed for cotinine. The new residents who moved into these homes were recruited if they were non-smokers. Dust, surfaces, air and new residents' fingers were examined for nicotine in 25 former smoker and 16 former non-smoker homes. A urine sample was collected from the youngest resident.

Results

Smoker homes' dust, surface and air nicotine levels decreased after the change of occupancy (p<0.001); however dust and surfaces showed higher contamination levels in former smoker homes than former non-smoker homes (p<0.05). Non-smoking participants' finger nicotine was higher in former smoker homes compared to former non-smoker homes (p<0.05). Finger nicotine levels among non-smokers living in former smoker homes were significantly correlated with dust and surface nicotine and urine cotinine.

Conclusions

These findings indicate that THS accumulates in smokers' homes and persists when smokers move out even after homes remain vacant for 2 months and are cleaned and prepared for new residents. When non-smokers move into homes formerly occupied by smokers, they encounter indoor environments with THS polluted surfaces and dust. Results suggest that non-smokers living in former smoker homes are exposed to THS in dust and on surfaces.