bluuebunny/crossref_metadata_2025 huggingface dataset:
Language Acquisition and the Form of the Grammar
Authors: Lebeaux David
Published: January 2014

Language Acquisition and the Form of the Grammar attempts to re-think the ideal organization of the grammar, given its need to be learned. The book proposes a fundamental connection between the form of the adult grammar and the sequence of grammars which the child adopts in first language acquisition. Challenging the conventional division between language acquisition and syntax, this influential work constructs a new understanding of phrase structure, bringing syntactic data to bear on phrase structure composition. Two new phrase structure composition operations are proposed, Adjoin-α, which adjoins adjuncts into the structure, and Project-α, which fuses open class and closed class structures. The author also introduces the novel concept of subgrammars, successively larger grammars that take the child from the initial state to the adult grammar. This work will be of interest to those in the areas of syntax, language acquisition, learnability, and cognitive science in general.
Nonverbal Communication across Disciplines
Authors: Poyatos Fernando
Published: January 2014

This volume, based on the first two, identifies the verbal and nonverbal personal and environmental components of narrative and dramaturgic texts and the cinema — recreated in the first through the ‘reading act’ according to gaze mechanism and punctuation — and traces the coding-decoding processes of the characters’ semiotic-communicative itinerary between writer-creator and reader-recreator. In our total experience of a play or film we depend on the sensory and intellectual relationships between performers, audience and the environment of both, in a temporal dimension starting on the way to the theater and ending as one comes out. Two chapters discuss the speaking face and body of the characters and the explicit and implicit (at times ‘unstageable’) paralanguage, kinesics and quasiparalinguistic and extrasomatic and environmental sounds in the novel, the theater and the cinema, and the functions of personal and environmental silences. Another shows the functions, limitations and problems of punctuation systems in the creative-recreative processes and how a few new symbols and modifications would avoid some ambiguities. The stylistic, communicative and technical functions of nonverbal repertoires in the literary text are then identified as enriching critical analysis and offering new perspectives in translation. Finally, ‘literary anthropology’ (developed by the author in the 1970s) is is presented as an interdisciplinary area based on synchronic and diachronic analyses of the literatures of the different cultures as a source of anthropological and ethnological data.

Nearly 1200 quotes from 170 authors and 291 works are added to those in the first two volumes.
CAL1 is the Drosophila CENP-A assembly factor
Authors: Chen Chin-Chi , Dechassa Mekonnen Lemma , Bettini Emily , Ledoux Mary B. , Belisario Christian , Heun Patrick , Luger Karolin , Mellone Barbara G.
Published: January 2014

Centromeres are specified epigenetically by the incorporation of the histone H3 variant CENP-A. In humans, amphibians, and fungi, CENP-A is deposited at centromeres by the HJURP/Scm3 family of assembly factors, but homologues of these chaperones are absent from a number of major eukaryotic lineages such as insects, fish, nematodes, and plants. In Drosophila, centromeric deposition of CENP-A requires the fly-specific protein CAL1. Here, we show that targeting CAL1 to noncentromeric DNA in Drosophila cells is sufficient to heritably recruit CENP-A, kinetochore proteins, and microtubule attachments. CAL1 selectively interacts with CENP-A and is sufficient to assemble CENP-A nucleosomes that display properties consistent with left-handed octamers. The CENP-A assembly activity of CAL1 resides within an N-terminal domain, whereas the C terminus mediates centromere recognition through an interaction with CENP-C. Collectively, this work identifies the “missing” CENP-A chaperone in flies, revealing fundamental conservation between insect and vertebrate centromere-specification mechanisms.
Neuronal cell type–specific alternative splicing is regulated by the KH domain protein SLM1
Authors: Iijima Takatoshi , Iijima Yoko , Witte Harald , Scheiffele Peter
Published: January 2014

The unique functional properties and molecular identity of neuronal cell populations rely on cell type–specific gene expression programs. Alternative splicing represents a powerful mechanism for expanding the capacity of genomes to generate molecular diversity. Neuronal cells exhibit particularly extensive alternative splicing regulation. We report a highly selective expression of the KH domain–containing splicing regulators SLM1 and SLM2 in the mouse brain. Conditional ablation of SLM1 resulted in a severe defect in the neuronal isoform content of the polymorphic synaptic receptors neurexin-1, -2, and -3. Thus, cell type–specific expression of SLM1 provides a mechanism for shaping the molecular repertoires of synaptic adhesion molecules in neuronal populations in vivo.
The Kanenobu knots and Khovanov-Rozansky homology
Authors: Lobb Andrew
Published: January 2014

Kanenobu has given infinite families of knots with the same HOMFLYPT polynomials. We show that these knots also have the same

s
l
(
n
)

sl(n)

and HOMFLYPT homologies, thus giving the first example of an infinite family of knots indistinguishable by these invariants. This is a consequence of a structure theorem about the homologies of knots obtained by twisting up the ribbon of a ribbon knot with one ribbon.
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
Authors: Mirauta Bogdan , Nicolas Pierre , Richard Hugues
Published: January 2014

Motivation: The most common RNA-Seq strategy consists of random shearing, amplification and high-throughput sequencing of the RNA fraction. Methods to analyze transcription level variations along the genome from the read count profiles generated by the RNA-Seq protocol are needed.

Results: We developed a statistical approach to estimate the local transcription levels and to identify transcript borders. This transcriptional landscape reconstruction relies on a state-space model to describe transcription level variations in terms of abrupt shifts and more progressive drifts. A new emission model is introduced to capture not only the read count variance inside a transcript but also its short-range autocorrelation and the fraction of positions with zero counts. The estimation relies on a particle Gibbs algorithm whose running time makes it more suited to microbial genomes. The approach outperformed read-overlapping strategies on synthetic and real microbial datasets.

Availability: A program named Parseq is available at: http://www.lgm.upmc.fr/parseq/.

Contact:  bodgan.mirauta@upmc.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening
Authors: Musladin Sanja , Krietenstein Nils , Korber Philipp , Barbaric Slobodan
Published: January 2014

Although yeast PHO5 promoter chromatin opening is a founding model for chromatin remodeling, the complete set of involved remodelers remained unknown for a long time. The SWI/SNF and INO80 remodelers cooperate here, but nonessentially, and none of the many tested single or combined remodeler gene mutations could prevent PHO5 promoter opening. RSC, the most abundant and only remodeler essential for viability, was a controversial candidate for the unrecognized remodeling activity but unassessed in vivo. Now we show that remodels the structure of chromatin (RSC) is crucially involved in PHO5 promoter opening. Further, the isw1 chd1 double deletion also delayed chromatin remodeling. Strikingly, combined absence of RSC and Isw1/Chd1 or Snf2 abolished for the first time promoter opening on otherwise sufficient induction in vivo. Together with previous findings, we recognize now a surprisingly complex network of five remodelers (RSC, SWI/SNF, INO80, Isw1 and Chd1) from four subfamilies (SWI/SNF, INO80, ISWI and CHD) as involved in PHO5 promoter chromatin remodeling. This is likely the first described complete remodeler set for a physiological chromatin transition. RSC was hardly involved at the coregulated PHO8 or PHO84 promoters despite cofactor recruitment by the same transactivator and RSC’s presence at all three promoters. Therefore, promoter-specific chromatin rather than transactivators determine remodeler requirements.
Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data
Authors: Trieu Tuan , Cheng Jianlin
Published: January 2014

Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene–gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes interact and are regulated. Here, we describe a method to reconstruct preferred 3D structures of individual chromosomes of the human genome from chromosomal contact data generated by the Hi-C chromosome conformation capturing technique. A novel parameterized objective function was designed for modeling chromosome structures, which was optimized by a gradient descent method to generate chromosomal structural models that could satisfy as many intra-chromosomal contacts as possible. We applied the objective function and the corresponding optimization method to two Hi-C chromosomal data sets of both a healthy and a cancerous human B-cell to construct 3D models of individual chromosomes at resolutions of 1 MB and 200 KB, respectively. The parameters used with the method were calibrated according to an independent fluorescence in situ hybridization experimental data. The structural models generated by our method could satisfy a high percentage of contacts (pairs of loci in interaction) and non-contacts (pairs of loci not in interaction) and were compatible with the known two-compartment organization of human chromatin structures. Furthermore, structural models generated at different resolutions and from randomly permuted data sets were consistent.
A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism
Authors: Dy Ron L. , Przybilski Rita , Semeijn Koen , Salmond George P.C. , Fineran Peter C.
Published: January 2014

Bacterial abortive infection (Abi) systems are ‘altruistic’ cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin–antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase β family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins.
The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription
Authors: Yun Won Ju , Kim Yea Woon , Kang Yujin , Lee Jungbae , Dean Ann , Kim AeRi
Published: January 2014

TAL1 is a key hematopoietic transcription factor that binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. The complex mediates long-range interaction between the β-globin locus control region (LCR) and active globin genes, and although TAL1 is one of the two DNA-binding complex members, its role is unclear. To explore the role of TAL1 in transcription activation of the human γ-globin genes, we reduced the expression of TAL1 in erythroid K562 cells using lentiviral short hairpin RNA, compromising its association in the β-globin locus. In the TAL1 knockdown cells, the γ-globin transcription was reduced to 35% and chromatin looping of the Gγ-globin gene with the LCR was disrupted with decreased occupancy of the complex member Ldb1 and LMO2 in the locus. However, GATA-1 binding, DNase I hypersensitive site formation and several histone modifications were largely maintained across the β-globin locus. In addition, overexpression of TAL1 increased the γ-globin transcription and increased interaction frequency between the Gγ-globin gene and LCR. These results indicate that TAL1 plays a critical role in chromatin loop formation between the γ-globin genes and LCR, which is a critical step for the transcription of the γ-globin genes.
Functional signature for the recognition of specific target mRNAs by human Staufen1 protein
Authors: de Lucas Susana , Oliveros Juan Carlos , Chagoyen Mónica , Ortín Juan
Published: January 2014

Cellular messenger RNAs (mRNAs) are associated to proteins in the form of ribonucleoprotein particles. The double-stranded RNA-binding (DRB) proteins play important roles in mRNA synthesis, modification, activity and decay. Staufen is a DRB protein involved in the localized translation of specific mRNAs during Drosophila early development. The human Staufen1 (hStau1) forms RNA granules that contain translation regulation proteins as well as cytoskeleton and motor proteins to allow the movement of the granule on microtubules, but the mechanisms of hStau1-RNA recognition are still unclear. Here we used a combination of affinity chromatography, RNAse-protection, deep-sequencing and bioinformatic analyses to identify mRNAs differentially associated to hStau1 or a mutant protein unable to bind RNA and, in this way, defined a collection of mRNAs specifically associated to wt hStau1. A common sequence signature consisting of two opposite-polarity Alu motifs was present in the hStau1-associated mRNAs and was shown to be sufficient for binding to hStau1 and hStau1-dependent stimulation of protein expression. Our results unravel how hStau1 identifies a wide spectrum of cellular target mRNAs to control their localization, expression and fate.
X-ray phase imaging: from synchrotron to hospital
Authors: Momose Atsushi , Yashiro Wataru , Kido Kazuhiro , Kiyohara Junko , Makifuchi Chiho , Ito Tsukasa , Nagatsuka Sumiya , Honda Chika , Noda Daiji , Hattori Tadashi , Endo Tokiko , Nagashima Masabumi , Tanaka Junji
Published: January 2014

With the aim of clinical applications of X-ray phase imaging based on Talbot–Lau-type grating interferometry to joint diseases and breast cancer, machines employing a conventional X-ray generator have been developed and installed in hospitals. The machine operation especially for diagnosing rheumatoid arthritis is described, which relies on the fact that cartilage in finger joints can be depicted with a dose of several milligray. The palm of a volunteer observed with 19 s exposure (total scan time: 32 s) is reported with a depicted cartilage feature in joints. This machine is now dedicated for clinical research with patients.
Medicine, material science and security: the versatility of the coded-aperture approach
Authors: Munro P. R. T. , Endrizzi M. , Diemoz P. C. , Hagen C. K. , Szafraniec M. B. , Millard T. P. , Zapata C. E. , Speller R. D. , Olivo A.
Published: January 2014

The principal limitation to the widespread deployment of X-ray phase imaging in a variety of applications is probably versatility. A versatile X-ray phase imaging system must be able to work with polychromatic and non-microfocus sources (for example, those currently used in medical and industrial applications), have physical dimensions sufficiently large to accommodate samples of interest, be insensitive to environmental disturbances (such as vibrations and temperature variations), require only simple system set-up and maintenance, and be able to perform quantitative imaging. The coded-aperture technique, based upon the edge illumination principle, satisfies each of these criteria. To date, we have applied the technique to mammography, materials science, small-animal imaging, non-destructive testing and security. In this paper, we outline the theory of coded-aperture phase imaging and show an example of how the technique may be applied to imaging samples with a practically important scale.
Compact laser accelerators for X-ray phase-contrast imaging
Authors: Najmudin Z. , Kneip S. , Bloom M. S. , Mangles S. P. D. , Chekhlov O. , Dangor A. E. , Döpp A. , Ertel K. , Hawkes S. J. , Holloway J. , Hooker C. J. , Jiang J. , Lopes N. C. , Nakamura H. , Norreys P. A. , Rajeev P. P. , Russo C. , Streeter M. J. V. , Symes D. R. , Wing M.
Published: January 2014

Advances in X-ray imaging techniques have been driven by advances in novel X-ray sources. The latest fourth-generation X-ray sources can boast large photon fluxes at unprecedented brightness. However, the large size of these facilities means that these sources are not available for everyday applications. With advances in laser plasma acceleration, electron beams can now be generated at energies comparable to those used in light sources, but in university-sized laboratories. By making use of the strong transverse focusing of plasma accelerators, bright sources of betatron radiation have been produced. Here, we demonstrate phase-contrast imaging of a biological sample for the first time by radiation generated by GeV electron beams produced by a laser accelerator. The work was performed using a greater than 300 TW laser, which allowed the energy of the synchrotron source to be extended to the 10–100 keV range.
Investigation of the application of phase contrast imaging using a point X-ray source to industrial non-destructive testing
Authors: Suzuki Kazuaki , Haig Ian
Published: January 2014

X-Tek Systems, a division of Nikon Metrology UK, designs, develops and manufactures microfocus X-ray radiography and computed tomography systems for industrial non-destructive testing. The range of X-ray acceleration voltages of its current standard products is 130–450 kV. It is widely known that X-ray images can be created using phase contrast formed by the natural propagation of X-rays. Simulation of the natural propagation of X-rays through a cylindrical test sample predicted a small contrast peak at the boundary between the cylinder material and air. Comparison data were obtained using an X-ray source with acceleration voltage above 100 kV. The simulation results correlated well with the experimental data. A further practical example (a ‘magic mirror’ amulet from an old Japanese shrine) is introduced and discussed. In this specimen, we detected intensity variation including the effect of phase contrast in the operating region above 100 kV. In summary, natural propagation phase contrast was observed in radiographic images from a standard point X-ray source with acceleration voltages exceeding 100 kV.
Coherent Bragg nanodiffraction at the hard X-ray Nanoprobe beamline
Authors: Hruszkewycz S. O. , Holt M. V. , Maser J. , Murray C. E. , Highland M. J. , Folkman C. M. , Fuoss P. H.
Published: January 2014

Bragg coherent diffraction with nanofocused hard X-ray beams provides unique opportunities for quantitative
in situ
studies of crystalline structure in nanoscale regions of complex materials and devices by a variety of diffraction-based techniques. In the case of coherent diffraction imaging, a major experimental challenge in using nanoscale coherent beams is maintaining a constant scattering volume such that coherent fringe visibility is maximized and maintained over the course of an exposure lasting several seconds. Here, we present coherent Bragg diffraction patterns measured from different nanostructured thin films at the Sector 26 Nanoprobe beamline at the Advanced Photon Source and demonstrate that with nanoscale positional control, coherent diffraction patterns can be measured with source-limited fringe visibilities more than 50% suitable for imaging by coherent Bragg ptychography techniques.
Sensitivity of edge illumination X-ray phase-contrast imaging
Authors: Diemoz P. C. , Endrizzi M. , Bravin A. , Robinson I. K. , Olivo A.
Published: January 2014

Recently, we developed a theoretical model that can predict the signal-to-noise ratio for edge-like features in phase-contrast images. This model was then applied for the estimation of the sensitivity of three different X-ray phase-contrast techniques: propagation-based imaging, analyser-based imaging and grating interferometry. We show here how the same formalism can be used also in the case of the edge illumination (EI) technique, providing results that are consistent with those of a recently developed method for the estimation of noise in the retrieved refraction image. The new model is then applied to calculate, in the case of a given synchrotron radiation set-up, the optimum positions of the pre-sample aperture and detector edge to maximize the sensitivity. Finally, an example of the extremely high angular resolution achievable with the EI technique is presented.
Priors for X-ray in-line phase tomography of heterogeneous objects
Authors: Langer Max , Cloetens Peter , Hesse Bernhard , Suhonen Heikki , Pacureanu Alexandra , Raum Kay , Peyrin Françoise
Published: January 2014

We present a new prior for phase retrieval from X-ray Fresnel diffraction patterns. Fresnel diffraction patterns are achieved by letting a highly coherent X-ray beam propagate in free space after interaction with an object. Previously, either homogeneous or multi-material object assumptions have been used. The advantage of the homogeneous object assumption is that the prior can be introduced in the Radon domain. Heterogeneous object priors, on the other hand, have to be applied in the object domain. Here, we let the relationship between attenuation and refractive index vary as a function of the measured attenuation index. The method is evaluated using images acquired at beamline ID19 (ESRF, Grenoble, France) of a phantom where the prior is calculated by linear interpolation and of a healing bone obtained from a rat osteotomy model. It is shown that the ratio between attenuation and refractive index in bone for different levels of mineralization follows a power law. Reconstruction was performed using the mixed approach but is compatible with other, more advanced models. We achieve more precise reconstructions than previously reported in literature. We believe that the proposed method will find application in biomedical imaging problems where the object is strongly heterogeneous, such as bone healing and biomaterials engineering.
Molecular epidemiology of colonizing and disease-causing Klebsiella pneumoniae in paediatric patients
Authors: Little Malaika L. , Qin Xuan , Zerr Danielle M. , Weissman Scott J.
Published: January 2014

Klebsiella pneumoniae causes a range of clinical disease in paediatric patients and is of increasing concern due to growing antibiotic resistance, yet little is known about the relative distribution of commensal and pathogens throughout the population structure of K. pneumoniae. We conducted a prospective, observational study of 92 isolates from Seattle Children’s Hospital, including 49 disease isolates from blood and urine (13 and 36 isolates, respectively) and 43 colonization isolates from stool. Susceptibility to 20 antimicrobials was evaluated using disc diffusion, VITEK 2 and Etest. Strain relatedness was investigated using multilocus sequence typing (MLST). Demographic and clinical characteristics were largely similar between disease and colonization cohorts, with 85.7 and 74.4 % of disease and colonization cohort patients, respectively, having an underlying medical condition; the sole exception was a relative abundance of patients with urologic or renal abnormalities in the disease cohort, consistent with the predominance of urine specimens among the disease isolates. With regard to antibiotic susceptibility properties, no significant differences were noted between the disease and colonization cohorts. Using molecular analysis, 71 unique sequence types (STs) were distinguished, with novel MLST findings evident in both cohorts; 43 (46.7 %) isolates represented novel STs, including 22 with a novel allele sequence. Thirteen STs contained multiple isolates and all seven isolates with resistance to three or more antibiotic classes were within one of four multirepresentative STs. This study demonstrates that nearly half of paediatric Klebsiella isolates represent novel STs, with clustering of multidrug resistance within specific STs. These findings expand our understanding of the intersection of bacterial population structure, human colonization ecology and multidrug resistance in K. pneumoniae.
Is there any value in measuring faecal calprotectin in Clostridium difficile positive faecal samples?
Authors: Whitehead Simon J. , Shipman Kate E. , Cooper Mike , Ford Clare , Gama Rousseau
Published: January 2014

Markers of intestinal inflammation have been proposed for inclusion in Clostridium difficile diagnostic algorithms. Faecal calprotectin (f-Cp), a sensitive marker of intestinal inflammation, was evaluated for utility in C. difficile diagnosis in the hospital setting. One hundred and twenty C. difficile positive and 99 C. difficile negative faecal samples of hospital-acquired diarrhoea were analysed for f-Cp using a quantitative ELISA. C. difficile positivity was confirmed using ELISAs for either toxins (n = 45) or glutamate dehydrogenase (GDH) with toxin gene confirmation (n = 75). Non-parametric ANOVA (Kruskal–Wallis) was used for data analysis. C. difficile positive samples had higher (P<0.05) median (interquartile range) f-Cp levels; 336 µg g−1 (208–536) for toxin and 249 µg g−1 (155–498) for GDH and toxin gene positive compared with 106 µg g−1 (46–176) for C. difficile and culture-negative faecal samples. Five C. difficile positive samples were f-Cp negative (<50 µg g−1). A f-Cp concentration >50 µg g−1 was 96 % sensitive and 26 % specific for C. difficile, with area under the ROC curve of 0.82. There is no role for f-CP alone in predicting C. difficile infection in hospital-acquired diarrhoea due to its low specificity.
Molecular evolution of the haemagglutinin–neuraminidase gene in human parainfluenza virus type 3 isolates from children with acute respiratory illness in Yamagata prefecture, Japan
Authors: Mizuta Katsumi , Tsukagoshi Hiroyuki , Ikeda Tatsuya , Aoki Yoko , Abiko Chieko , Itagaki Tsutomu , Nagano Manami , Noda Masahiro , Kimura Hirokazu
Published: January 2014

We conducted detailed genetic analyses of the haemagglutinin–neuraminidase (HN) gene in 272 human parainfluenza virus type 3 (HPIV3) isolates from children with acute respiratory illness during the period 2002–2009 in Yamagata prefecture, Japan. A phylogenetic tree reconstructed by the Bayesian Markov chain Monte Carlo method showed that the strains diversified at around 1946 and that the rate of molecular evolution was 1.10×10−3substitutions per site per year. Identity was high among the present strains (<90 %) and thepairwise-distances were short. Furthermore, we found four positive selection sites and some key amino acid substitutions in active/catalytic sites of the HN protein. The results suggest that theHNgene of HPIV3 in the present strains evolved rapidly, similarly to other virus genes such as theGgene of respiratory syncytial virus. However, the biological functions and detailed structures of the HN glycoprotein in some of these strains may have been altered.
Faecal Escherichia coli from patients with E. coli urinary tract infection and healthy controls who have never had a urinary tract infection
Authors: Nielsen Karen L. , Dynesen Pia , Larsen Preben , Frimodt-Møller Niels
Published: January 2014

Urinary tract infections (UTIs) are primarily caused by Escherichia coli with the patient’s own faecal flora acting as a reservoir for the infecting E. coli. Here we sought to characterize the E. coli faecal flora of UTI patients and healthy controls who had never had a UTI. Up to 20 E. coli colonies from each rectal swab were random amplified polymorphic DNA (RAPD) typed for clonality, dominance in the sample and correlation to the infecting UTI isolate in patients. Each distinct clone was phylotyped and tested for antimicrobial susceptibility. Eighty-seven per cent of the UTI patients carried the infecting strain in their faecal flora, and faecal clones causing UTI were more often dominant in the faecal flora. Patients had a larger diversity of E. coli in their gut flora by carrying more unique E. coli clones compared to controls, and patient faecal clones were more often associated with multidrug resistance compared to controls. We found a similar phylotype distribution of faecal clones from UTI patients and healthy controls, including a large proportion of B2 isolates in the control group. Faecal-UTI isolates from patients were more often associated with multidrug resistance compared to faecal-only clones, indicating a link between UTI virulence and antimicrobial resistance. Intake of any antibiotic less than 6 months prior to inclusion in the experiment occurred significantly more in patients with UTI than in controls. In contrast, presence of an intrauterine device was significantly more common in controls indicating a protective effect against UTI. In conclusion, healthy controls have a large proportion of potentially pathogenic E. coli phylotypes in their faecal flora without this causing infection.
Role of Pseudomonas aeruginosa AmpR on β-lactam and non-β-lactam transient cross-resistance upon pre-exposure to subinhibitory concentrations of antibiotics
Authors: Kumari Hansi , Balasubramanian Deepak , Zincke Diansy , Mathee Kalai
Published: January 2014

Pseudomonas aeruginosais one of the most dreaded opportunistic pathogens accounting for 10 % of hospital-acquired infections, with a 50 % mortality rate in chronically ill patients. The increased prevalence of drug-resistant isolates is a major cause of concern. Resistance inP. aeruginosais mediated by various mechanisms, some of which are shared among different classes of antibiotics and which raise the possibility of cross-resistance. The goal of this study was to explore the effect of subinhibitory concentrations (SICs) of clinically relevant antibiotics and the role of a global antibiotic resistance and virulence regulator, AmpR, in developing cross-resistance. We investigated the induction of transient cross-resistance inP. aeruginosaPAO1 upon exposure to SICs of antibiotics. Pre-exposure to carbapenems, specifically imipenem, even at 3 ng ml−1, adversely affected the efficacy of clinically used penicillins and cephalosporins. The high β-lactam resistance was due to elevated expression of bothampCandampR, encoding a chromosomal β-lactamase and its regulator, respectively. Differences in the susceptibility ofampRandampCmutants suggested non-AmpC-mediated regulation of β-lactam resistance by AmpR. The increased susceptibility ofP. aeruginosain the absence ofampRto various antibiotics upon SIC exposure suggests that AmpR plays a major role in the cross-resistance. AmpR was shown previously to be involved in resistance to quinolones by regulating MexEF–OprN efflux pump. The data here further indicate the role of AmpR in cross-resistance between quinolones and aminoglycosides. This was confirmed using quantitative PCR, where expression of themexEFefflux pump was further induced by ciprofloxacin and tobramycin, its substrate and a non-substrate, respectively, in the absence ofampR. The data presented here highlight the intricate cross-regulation of antibiotic resistance pathways at SICs of antibiotics and the need for careful assessment of the order of antibiotic regimens as this may have dire consequences. Targeting a global regulator such as AmpR that connects diverse pathways is a feasible therapeutic approach to combatP. aeruginosapathogenesis.
Simultaneous isolation of emm89-type Streptococcus pyogenes strains with a wild-type or mutated covS gene from a single streptococcal toxic shock syndrome patient
Authors: Masuno Katsuaki , Okada Ryo , Zhang Yan , Isaka Masanori , Tatsuno Ichiro , Shibata Shinichiro , Hasegawa Tadao
Published: January 2014

Streptococcal toxic shock syndrome (STSS) is a re-emerging infectious disease in many developed countries. Recent studies have suggested that mutations in CovRS, a two-component regulatory system in Streptococcus pyogenes, play important roles in the pathogenesis of STSS. However, in vivo evidence of the significance of CovRS in human infections has not been fully demonstrated. We investigated five S. pyogenes strains isolated simultaneously from the pharynx, sputum, knee joint, cerebrospinal fluid and blood of a single STSS patient. All were emm89-type strains, and multilocus sequence typing (MLST) analysis revealed that the strains of pharynx and blood were isogenic. The growth rates of the strains from pharynx and sputum were faster than those of the other strains. Protein profiles of the culture supernatants of strains from the pharynx and sputum were also different from those of the other strains. Sequence analyses revealed that strains from the knee joint, cerebrospinal fluid and blood contained a single nucleotide difference in the covS coding region, resulting in one amino acid change, compared with the other strains. Introduction of a plasmid containing the covS gene from the pharynx strain to the blood strain increased the production of SpeB protein. This suggests that the one amino acid alteration in CovS was relevant to pathogenesis. This report supports the idea that mutated CovS plays important roles in vivo in the dissemination of S. pyogenes from the upper respiratory tract of human to aseptic tissues such as blood and cerebrospinal fluid.
A novel high-throughput method for molecular serotyping and serotype-specific quantification of Streptococcus pneumoniae using a nanofluidic real-time PCR system
Authors: Dhoubhadel Bhim Gopal , Yasunami Michio , Yoshida Lay-Myint , Thi Hien Anh Nguyen , Thi Thu Huong Vu , Thi Thuy Ai Nguyen , Watanabe Kiwao , Suzuki Motoi , Morimoto Konosuke , Dang Duc Anh , Ariyoshi Koya
Published: January 2014

Serotype-specific quantification data are essential for elucidating the complex epidemiology of Streptococcus pneumoniae and evaluating pneumococcal vaccine efficacy. Various PCR-based assays have been developed to circumvent the drawback of labour-intensive and time-consuming culture-based procedures for serotype determination and quantification of pneumococcus. Here, we applied a nanofluidic real-time PCR system to establish a novel assay. Twenty-nine primer pairs, 13 of which were newly designed, were selected for the assay to cover 50 serotypes including all currently available conjugate and polysaccharide vaccine serotypes. All primer pairs were evaluated for their sensitivity, specificity, efficiency, repeatability, accuracy and reproducibility on the Fluidigm Biomark HD System, a nanofluidic real-time PCR system, by drawing standard curves with a serial dilution of purified DNA. We applied the assay to 52 nasopharyngeal swab samples from patients with pneumonia confirmed by chest X-ray to validate its accuracy. Minimum detection levels of this novel assay using the nanofluidic real-time PCR system were comparable to the conventional PCR-based assays (between 30 and 300 copies per reaction). They were specific to their targets with good repeatability (sd of copy number of 0.1), accuracy (within ±0.1 fold difference in log10 copy number) and reproducibility (sd of copy number of 0.1). When artificially mixed DNA samples consisting of multiple serotypes in various ratios were tested, all the serotypes were detected proportionally, including a minor serotype of one in 1000 copies. In the nasopharyngeal samples, the PCR system detected all the culture-positive samples and 22 out of 23 serotypes identified by the conventional method were matched with PCR results. We conclude that this novel assay, which is able to differentially quantify 29 pneumococcus groups for 45 test samples in a single run, is applicable to the large-scale epidemiological study of pneumococcus. We believe that this assay will facilitate our understanding of the roles of serotype-specific bacterial loads and implications of multiple serotype detections in pneumococcal diseases.
Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles
Authors: Beauchamp Kyle A. , Pande Vijay S. , Das Rhiju
Published: January 2014

Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computa- tional model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian Energy Landscape Tilting (BELT) scheme for computing Bayesian “hyperensembles” over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and3Jmeasurements gives convergent values of the peptide’sα,β, andPPIIconformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accu- rate errors, even when starting from highly inaccurate simulations. BELT’s principled fxramework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data.
Holsteins Favor Heifers, Not Bulls: Biased Milk Production Programmed during Pregnancy as a Function of Fetal Sex
Authors: Katie Hinde , Abigail J. Carpenter , John S. Clay , Barry J. Bradford
Published: January 2014

Mammalian females pay high energetic costs for reproduction, the greatest of which is imposed by lactation. The synthesis of milk requires, in part, the mobilization of bodily reserves to nourish developing young. Numerous hypotheses have been advanced to predict how mothers will differentially invest in sons and daughters, however few studies have addressed sex-biased milk synthesis. Here we leverage the dairy cow model to investigate such phenomena. Using 2.39 million lactation records from 1.49 million dairy cows, we demonstrate that the sex of the fetus influences the capacity of the mammary gland to synthesize milk during lactation. Cows favor daughters, producing significantly more milk for daughters than for sons across lactation. Using a sub-sample of this dataset (N = 113,750 subjects) we further demonstrate that the effects of fetal sex interact dynamically across parities, whereby the sex of the fetus being gestated can enhance or diminish the production of milk during an established lactation. Moreover the sex of the fetus gestated on the first parity has persistent consequences for milk synthesis on the subsequent parity. Specifically, gestation of a daughter on the first parity increases milk production by ∼445 kg over the first two lactations. Our results identify a dramatic and sustained programming of mammary function by offspringin utero. Nutritional and endocrine conditionsin uteroare known to have pronounced and long-term effects on progeny, but the ways in which the progeny has sustained physiological effects on the dam have received little attention to date.
Crystallographic study of FABP5 as an intracellular endocannabinoid transporter
Authors: Sanson Benoît , Wang Tao , Sun Jing , Wang Liqun , Kaczocha Martin , Ojima Iwao , Deutsch Dale , Li Huilin
Published: January 2014

In addition to binding intracellular fatty acids, fatty-acid-binding proteins (FABPs) have recently been reported to also transport the endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), arachidonic acid derivatives that function as neurotransmitters and mediate a diverse set of physiological and psychological processes. To understand how the endocannabinoids bind to FABPs, the crystal structures of FABP5 in complex with AEA, 2-AG and the inhibitor BMS-309403 were determined. These ligands are shown to interact primarily with the substrate-binding pocketviahydrophobic interactions as well as a common hydrogen bond to the Tyr131 residue. This work advances our understanding of FABP5–endocannabinoid interactions and may be useful for future efforts in the development of small-molecule inhibitors to raise endocannabinoid levels.
Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry
Authors: Sliwiak Joanna , Jaskolski Mariusz , Dauter Zbigniew , McCoy Airlie J. , Read Randy J.
Published: January 2014

Translational noncrystallographic symmetry (tNCS) is a pathology of protein crystals in which multiple copies of a molecule or assembly are found in similar orientations. Structure solution is problematic because this breaks the assumptions used in current likelihood-based methods. To cope with such cases, new likelihood approaches have been developed and implemented inPhaserto account for the statistical effects of tNCS in molecular replacement. Using these new approaches, it was possible to solve the crystal structure of a protein exhibiting an extreme form of this pathology with seven tetrameric assemblies arrayed along thecaxis. To resolve space-group ambiguities caused by tetartohedral twinning, the structure was initially solved by placing 56 copies of the monomer in space groupP1 and using the symmetry of the solution to define the true space group,C2. The resulting structure of Hyp-1, a pathogenesis-related class 10 (PR-10) protein from the medicinal herb St John's wort, reveals the binding modes of the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS), providing insight into the function of the protein in binding or storing hydrophobic ligands.
Unit-cell determination of epitaxial thin films based on reciprocal-space vectors by high-resolution X-ray diffractometry
Authors: Yang Ping , Liu Huajun , Chen Zuhuang , Chen Lang , Wang John
Published: January 2014

A new approach, based on reciprocal-space vectors (RSVs), is developed to determine Bravais lattice types and accurate lattice parameters of epitaxial thin films by high-resolution X-ray diffractometry. The lattice parameters of single-crystal substrates are employed as references to correct the systematic experimental errors of RSVs of thin films. The general procedure is summarized, involving correction of RSVs, derivation of the raw unit cell, and subsequent conversion to the Niggli unit cell and the Bravais unit cell by matrix calculation. Two methods of this procedure are described: in three-dimensional reciprocal space and in six-dimensionalG6space. The estimation of standard error in the lattice parameters derived by this new approach is discussed. The whole approach is illustrated by examples of experimental data. The error of the best result is 0.0006 Å for the lattice parameter of indium tin oxide film. This new RSV method provides a practical and concise route to the crystal structure study of epitaxial thin films and could also be applied to the investigation of surface and interface structures.
Serosurvey of Rickettsia typhi and Rickettsia felis in HIV‐infected patients
Authors: Nogueras María Mercedes , Pons Immaculada , Sanfeliu Isabel , Sala Montserrat , Segura Ferran
Published: January 2014

Consistent with the effects of HIV on cell‐mediated immunity, an increased susceptibility to intracellular microorganisms has been observed. Rickettsiae are obligate intracellular microorganisms. The aim of this study was to examine Rickettsia typhi and Rickettsia felis infections in HIV+ population. Sera of 341 HIV+ patients were evaluated by indirect immunofluorescent assay. Age, sex, residential locality, risk behavior, stage according to criteria of the Center for Disease Control and Prevention, CD4+/CD8+ T cells, Hepatitis B antigen, and Hepatitis C serology were surveyed. Seroprevalences of R. typhi and R. felis infection were 7.6% and 4.4%, respectively. No associations were found between seropositivities and the assessed variables. Findings were similar to those obtained in healthy subjects from the same region.
Rapid acclimation to cold allows the cane toad to invade montane areas within its Australian range
Authors: McCann Samantha , Greenlees Matthew J. , Newell David , Shine Richard
Published: January 2014

The cane toad (Rhinella marina) invasion of Australia has now reached areas much colder than most of its native range in tropical America. Understanding the toad's ability to function in such conditions can clarify its potential for further spread.

In northeastern New South Wales (NSW), cane toads have been recorded up to 1100 m above sea level (asl). Our monitoring over summer 2012–2013 confirmed that ground temperatures were lower at three high‐elevation (750–1010 m asl) sites than at two nearby lower (100–210 m asl) sites (by day, 18°C vs. 25°C; at night, 17–18°C vs. 20–25°C, respectively).

Critical thermal minima (CTmins) of field‐collected toads (loss of the righting reflex) were lower for high‐elevation than low‐elevation toads (5·5°C vs. 7·5°C), but laboratory acclimation abolished this difference. A toad's CTmin was not affected by site of collection, nor by 1 month's exposure to warm (24°C) or cool (12°C) conditions; instead, a toad's CTmin was determined by its thermal exposure over the previous 12 h. Locomotor ability was affected by test temperature, by elevation and by acclimation. Toads from high elevations exhibited equal endurance at cold and warm test temperatures after month‐long acclimation to cold conditions, whereas toads from low elevations performed better at high temperatures regardless of previous temperature treatments.

Cane toads at the southern edge of their expanding Australian range can function under cool conditions by adjusting their thermal tolerance within a few hours of encountering low temperatures.

The toads' ability for rapid thermal acclimation suggests that current models underestimate the potential range of abiotic conditions accessible to this invading species.