bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data
Authors: Yuan Yuan , Xu Yanxun , Xu Jianfeng , Ball Robyn L. , Liang Han
Published: March 2012

Motivation: The phenotypes of knockout mice provide crucial information for understanding the biological functions of mammalian genes. Among various knockout phenotypes, lethality is of great interest because those involved genes play essential roles. With the availability of large-scale genomic data, we aimed to assess how well the integration of various genomic features can predict the lethal phenotype of single-gene knockout mice.

Results: We first assembled a comprehensive list of 491 candidate genomic features derived from diverse data sources. Using mouse genes with a known phenotype as the training set, we integrated the informative genomic features to predict the knockout lethality through three machine learning methods. Based on cross-validation, our models could achieve a good performance (accuracy = 73% and recall = 63%). Our results serve as a valuable practical resource in the mouse genetics research community, and also accelerate the translation of the knowledge of mouse genes into better strategies for studying human disease.

Contact:  hliang1@mdanderson.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
SEQanswers: an open access community for collaboratively decoding genomes
Authors: Li Jing-Woei , Schmieder Robert , Ward R. Matthew , Delenick Joann , Olivares Eric C. , Mittelman David
Published: March 2012

Summary: The affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers.

Availability: The SEQanswers community is freely accessible at http://SEQanswers.com/

Contact:  david.mittelman@vt.edu; ecolivares@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
On the anomalous laminar heat transfer intensification in developing region of nanofluid flow in channels or tubes
Authors: Liu J. T. C.
Published: March 2012

The present work theoretically addresses the experimental observations of nanofluid flow exhibiting highly intensified laminar heat transfer rates at the leading edge of channels or tubes. The basis for this study is the continuum conservation equations for nanofluids. The Rayleigh–Stokes approximation is applied to the nonlinear advective effects and a perturbation scheme, in ascending powers of the nanoparticle volume fraction, is applied. The disparate thicknesses of momentum, heat and volume fraction is exploited to advantage in securing analytical, similar solutions. The volume fraction layer is ‘infinitely’ thin in that its effect on the momentum and thermal transport is essentially its bulk value far from the wall. The composite resulting zeroth- and first-order perturbations show that an increasing modification in the velocity and temperature profiles occur with increasing volume fraction and that this is caused, and quantitatively assessed, by inertial effects of advection and enhanced nanofluid transport properties. Some satisfactory explanations of experiments are made for aluminium oxide nanoparticles in water, in terms of the ratio of nanofluid to base fluid heat transfer coefficients, local heat transfer coefficient and the Nusselt number.
Role of porcine reproductive and respiratory syndrome virus nucleocapsid protein in induction of interleukin-10 and regulatory T-lymphocytes (Treg)
Authors: Wongyanin Piya , Buranapraditkul Supranee , Yoo Dongwan , Thanawongnuwech Roongroje , Roth James A. , Suradhat Sanipa
Published: March 2012

Porcine reproductive and respiratory syndrome virus (PRRSV) infection induces interleukin (IL)-10 production and increased numbers of PRRSV-specific regulatory T-lymphocytes in infected pigs. In the present study, the roles of the nucleocapsid (N) protein in induction of IL-10 and CD4+CD25+Foxp3+lymphocytes (Treg) were investigated. Transfection of porcine monocyte-derived dendritic cells (MoDCs) and pulmonary alveolar macrophages (PAMs) with a plasmid encoding N protein resulted in significant upregulation of IL-10 gene expression in the gene-transfected cells. Structural conformation, but not nuclear localization, of the expressed N protein was indicated to be essential for the ability to induce IL-10. Furthermore, the presence of recombinant N proteins in cultured PBMCs increased the number of IL-10-producing lymphocytes. Strong induction of IL-10-producing cells and Tregwas observed when using N protein-pulsed MoDCs, suggesting an important role of MoDCs in induction of IL-10 and Tregby the N protein. Neutralization of IL-10 by addition of an anti-IL-10 antibody in the culture system resulted in marked reduction of PRRSV-induced Tregin the cultured PBMCs. Together, the data demonstrate the immunomodulatory properties of the PRRSV N protein and the linkage between IL-10 production and development of PRRSV-induced Treg. Our results reveal an immunomodulatory function of the PRRSV N protein that may contribute to the unique immunological outcome observed following PRRSV infection.
Barley ROP Binding Kinase1 Is Involved in Microtubule Organization and in Basal Penetration Resistance to the Barley Powdery Mildew Fungus
Authors: Huesmann Christina , Reiner Tina , Hoefle Caroline , Preuss Jutta , Jurca Manuela E. , Domoki Mónika , Fehér Attila , Hückelhoven Ralph
Published: March 2012

Certain plant receptor-like cytoplasmic kinases were reported to interact with small monomeric G-proteins of the RHO of plant (ROP; also called RAC) family in planta and to be activated by this interaction in vitro. We identified a barley (Hordeum vulgare) partial cDNA of a ROP binding protein kinase (HvRBK1) in yeast (Saccharomyces  cerevisiae) two-hybrid screenings with barley HvROP bait proteins. Protein interaction of the constitutively activated (CA) barley HvROPs CA HvRACB and CA HvRAC1 with full-length HvRBK1 was verified in yeast and in planta. Green fluorescent protein-tagged HvRBK1 appears in the cytoplasm and nucleoplasm, but CA HvRACB or CA HvRAC1 can recruit green fluorescent protein-HvRBK1 to the cell periphery. Barley HvRBK1 is an active kinase in vitro, and activity is enhanced by CA HvRACB or GTP-loaded HvRAC1. Hence, HvRBK1 might act downstream of active HvROPs. Transient-induced gene silencing of barley HvRBK1 supported penetration by the parasitic fungus Blumeria graminis f. sp. hordei, suggesting a function of the protein in basal disease resistance. Transient knockdown of HvRBK1 also influenced the stability of cortical microtubules in barley epidermal cells. Hence, HvRBK1 might function in basal resistance to powdery mildew by influencing microtubule organization.
Light Intensity-Dependent Modulation of Chlorophyll b Biosynthesis and Photosynthesis by Overexpression of Chlorophyllide a Oxygenase in Tobacco
Authors: Biswal Ajaya K. , Pattanayak Gopal K. , Pandey Shiv S. , Leelavathi Sadhu , Reddy Vanga S. , Govindjee  , Tripathy Baishnab C.
Published: March 2012

Chlorophyll b is synthesized by the oxidation of a methyl group on the B ring of a tetrapyrrole molecule to a formyl group by chlorophyllide a oxygenase (CAO). The full-length CAO from Arabidopsis (Arabidopsis thaliana) was overexpressed in tobacco (Nicotiana tabacum) that grows well at light intensities much higher than those tolerated by Arabidopsis. This resulted in an increased synthesis of glutamate semialdehyde, 5-aminolevulinic acid, magnesium-porphyrins, and chlorophylls. Overexpression of CAO resulted in increased chlorophyll b synthesis and a decreased chlorophyll a/b ratio in low light-grown as well as high light-grown tobacco plants; this effect, however, was more pronounced in high light. The increased potential of the protochlorophyllide oxidoreductase activity and chlorophyll biosynthesis compensated for the usual loss of chlorophylls in high light. Increased chlorophyll b synthesis in CAO-overexpressed plants was accompanied not only by an increased abundance of light-harvesting chlorophyll proteins but also of other proteins of the electron transport chain, which led to an increase in the capture of light as well as enhanced (40%–80%) electron transport rates of photosystems I and II at both limiting and saturating light intensities. Although the quantum yield of carbon dioxide fixation remained unchanged, the light-saturated photosynthetic carbon assimilation, starch content, and dry matter accumulation increased in CAO-overexpressed plants grown in both low- and high-light regimes. These results demonstrate that controlled up-regulation of chlorophyll b biosynthesis comodulates the expression of several thylakoid membrane proteins that increase both the antenna size and the electron transport rates and enhance carbon dioxide assimilation, starch content, and dry matter accumulation.
Validating classical line profile analyses using microbeam diffraction from individual dislocation cell walls and cell interiors
Authors: Levine Lyle E. , Geantil Peter , Larson Bennett C. , Tischler Jonathan Z. , Kassner Michael E. , Liu Wenjun
Published: March 2012

Dislocation structures in deformed metals produce broad asymmetric diffraction line profiles. During analysis, these profiles are generally separated into two nearly symmetric subprofiles corresponding to diffraction by dislocation cell walls and cell interiors. These subprofiles are then interpreted using complex models of dislocation-based line broadening. Until now, it has not been possible to test the many assumptions that are made in such an analysis. Here, depth-resolved microbeam diffraction was used to measure diffraction line profiles from numerous individual dislocation cell walls and cell interiors in a heavily deformed Cu single crystal. Summing these profiles directly constructed the cell-interior and cell-wall subprofiles that have been approximated in the line profile analysis literature for the past 30 years. Direct comparison between the reconstructed subprofiles and the macroscopic asymmetric line profile from the same sample allows the first direct tests of many of the assumptions that have been used for interpreting these X-ray measurements.
Analysis of randomly oriented structures by grazing-incidence small-angle neutron scattering
Authors: Korolkov Denis , Busch Peter , Willner Lutz , Kentzinger Emmanuel , Rücker Ulrich , Paul Amitesh , Frielinghaus Henrich , Brückel Thomas
Published: March 2012

A formalism is presented which allows the quantitative evaluation of data from grazing-incidence small-angle neutron and X-ray scattering – GISANS and GISAXS – in the framework of the distorted wave Born approximation. While several aspects have been reported previously, this formalism combines solutions for scattering intensities in both reflection and transmission hemispheres, taking into account instrumental resolution effects. This formalism is applied to the case of GISANS from self-organized diblock copolymers, ordered in perpendicular lamellar structures on an Si wafer in randomly oriented short-range-ordered regions. The periodicity ofD= 85 (9) nm found for deuterated polystyrene–polybutadiene of molecular weight  Mw= 165 kg mol−1and a molecular weight fraction of the deuterated polystyrene block of 52% is consistent with atomic force microscopy and specular neutron reflectivity results.
Nika: software for two-dimensional data reduction
Authors: Ilavsky Jan
Published: March 2012

Nikais anIgor Pro-based package for correction, calibration and reduction of two-dimensional area-detector data into one-dimensional data (`lineouts'). It is free (although the user needs a paid license forIgor Pro), open source and highly flexible. While typically used for small-angle X-ray scattering (SAXS) data, it can also be used for grazing-incidence SAXS data, wide-angle diffraction data and even small-angle neutron scattering data. It has been widely available to the user community since about 2005, and it is currently used at the SAXS instruments of selected large-scale facilities as their main data reduction package. It is, however, also suitable for desktop instruments when the manufacturer's software is not available or appropriate. Since it is distributed as source code, it can be scrutinized, verified and modified by users to suit their needs.
A fibre-based crystal mounting technique for protein cryocrystallography
Authors: Sugahara Michihiro
Published: March 2012

The CryoFibre, a crystal mounting tool, has been developed for protein cryocrystallography. The technique attaches single crystals to the tips of polyester fibres, allowing removal of excess liquid around each crystal. Single-wavelength anomalous dispersion phasing using a Cu Kα X-ray source (Cu SAD) was applied to crystals from five proteins without any derivatization, demonstrating a clear improvement in the success rate of Cu SAD compared with the conventional loop technique. In addition, a xylanase crystal on the surface of a synthetic zeolite as a hetero-epitaxic nucleant was directly mounted on the CryoFibre without separation treatment of the crystal from the zeolite. The crystal had a lower mosaicity than that observed using the conventional technique, indicating that the fibre technique is suitable for high-quality data collection from zeolite-mediated crystals.
To B or not to B: a question of resolution?
Authors: Merritt Ethan A.
Published: March 2012

In choosing and refining any crystallographic structural model, there is tension between the desire to extract the most detailed information possible and the necessity to describe no more than what is justified by the observed data. A more complex model is not necessarily a better model. Thus, it is important to validate the choice of parameters as well as validating their refined values. One recurring task is to choose the best model for describing the displacement of each atom about its mean position. At atomic resolution one has the option of devoting six model parameters (a `thermal ellipsoid') to describe the displacement of each atom. At medium resolution one typically devotes at most one model parameter per atom to describe the same thing (a `B factor'). At very low resolution one cannot justify the use of even one parameter per atom. Furthermore, this aspect of the structure may be described better by an explicit model of bulk displacements, the most common of which is the translation/libration/screw (TLS) formalism, rather than by assigning some number of parameters to each atom individually. One can sidestep this choice between atomic displacement parameters and TLS descriptions by including both treatments in the same model, but this is not always statistically justifiable. The choice of which treatment is best for a particular structure refinement at a particular resolution can be guided by general considerations of the ratio of model parameters to the number of observations and by specific statistics such as the Hamilton R-factor ratio test.
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution
Authors: Headd Jeffrey J. , Echols Nathaniel , Afonine Pavel V. , Grosse-Kunstleve Ralf W. , Chen Vincent B. , Moriarty Nigel W. , Richardson David C. , Richardson Jane S. , Adams Paul D.
Published: March 2012

Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a `reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a φ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R
free and a decreased gap between R
work and R
free.
Conventions and workflows for using Situs
Authors: Wriggers Willy
Published: March 2012

Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs to be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.
Challenges and surprises that arise with nucleic acids during model building and refinement
Authors: Scott William G.
Published: March 2012

The process of building and refining crystal structures of nucleic acids, although similar to that for proteins, has some peculiarities that give rise to both various complications and various benefits. Although conventional isomorphous replacement phasing techniques are typically used to generate an experimental electron-density map for the purposes of determining novel nucleic acid structures, it is also possible to couple the phasing and model-building steps to permit the solution of complex and novel RNA three-dimensional structures without the need for conventional heavy-atom phasing approaches.
Towards automated crystallographic structure refinement with phenix.refine
Authors: Afonine Pavel V. , Grosse-Kunstleve Ralf W. , Echols Nathaniel , Headd Jeffrey J. , Moriarty Nigel W. , Mustyakimov Marat , Terwilliger Thomas C. , Urzhumtsev Alexandre , Zwart Peter H. , Adams Paul D.
Published: March 2012

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
JLigand: a graphical tool for the CCP4 template-restraint library
Authors: Lebedev Andrey A. , Young Paul , Isupov Michail N. , Moroz Olga V. , Vagin Alexey A. , Murshudov Garib N.
Published: March 2012

Biological macromolecules are polymers and therefore the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers. The CCP4 template-restraint library contains three types of data entries defining template restraints: descriptions of monomers and their modifications, both used for intramonomer restraints, and descriptions of links for intermonomer restraints. The library provides generic descriptions of modifications and links for protein, DNA and RNA chains, and for some post-translational modifications including glycosylation. Structure-specific template restraints can be defined in a user's additional restraint library. Here, JLigand, a new CCP4 graphical interface to LibCheck and REFMAC that has been developed to manage the user's library and generate new monomer entries is described, as well as new entries for links and associated modifications.
Biology of the silky shark Carcharhinus falciformis (Carcharhinidae) in the eastern Indian Ocean, including an approach to estimating age when timing of parturition is not well defined
Authors: Hall N. G. , Bartron C. , White W. T. , Dharmadi  , Potter I. C.
Published: March 2012

Biological data were recorded for 1265 silky sharks Carcharhinus falciformis collected from fish landing sites in eastern Indonesia. These represented catches taken in most calendar months by gillnetting and longlining in the eastern Indian Ocean and contained individuals ranging from embryos to fully mature adults. The growth zones in centra, which were shown to form annually, were counted in the vertebrae in a sub‐sample of 200 fish for ageing purposes. The embryo lengths in the 5 months for which there were such data, and the presence of neonates in virtually all months, however, indicated that birth occurs throughout the year and thus there was no well‐defined birth date for ageing individual fish. The approximate birth date of each individual was thus estimated from a combination of the total length (LT) at capture and backcalculated LT at the formation of the birth zone and at the first and last growth zones in the vertebral centra, together with the period that had elapsed between the formation of those last two growth zones. The number of eggs or embryos in uteri ranged from two to 14, with a mean of 7·2. The estimated mean LT at birth of females (811 mm, range: 799–823 mm) and males (812 mm, range: 794–830 mm), derived from the backcalculations corresponding to the birth zones in the centra, were not significantly different (P > 0·05). The LT ranges in the catches of post‐natal females (570–2592 mm) and males (553–2289 mm) taken by gillnetting were wider than those of the females (1177–2623 mm) and males (1184–2409 mm) taken by longlining. The oldest female and male were 19 and 20 years‐old, respectively. The von Bertalanffy growth curves for the two sexes did not differ significantly. The growth coefficient, k, and the asymptotic length, LT∞. were 0·066 year−1 and 2994 mm for the curve fitted to the combined data for females and males. The lengths LT50 and ages A50 at which C. falciformis attained maturity were 2156 mm and 15 years for females and 2076 mm and 13 years for males. The very high proportion of C. falciformis with lengths <LT50 in current catches places sustainability of the stock at risk.
Resveratrol enhances radiation sensitivity in prostate cancer by inhibiting cell proliferation and promoting cell senescence and apoptosis
Authors: Fang Yujiang , DeMarco Vincent G. , Nicholl Michael B.
Published: March 2012

Radiation therapy (XRT) for treatment of localized prostate cancer (PCA) has outcomes similar to surgery and medical therapy. Toxicities of XRT and the relative radioresistance of PCA limit the effectiveness of this treatment method. Safe and effective radiosensitizing agents are lacking to enhance the effectiveness for XRT for PCA. In this study, the effect of XRT in combination with the radiosensitizing agent resveratrol (RSV) was investigated in a radioresistant PCA cell line, PC‐3. Our results show the addition of RSV to XRT (XRT/RSV) synergistically enhanced XRT‐induced apoptosis and inhibition of PC‐3 proliferation. The antiproliferative effect of XRT/RSV treatment correlated with increased expression of p15, p21, and mutant p53 and decreased expression of cyclin B, cyclin D, and cdk2. Increased apoptosis correlated with increased expression of Fas and TRAILR1. Furthermore, XRT/RSV had little effect on the expression of p‐AKT, whereas it increased the expression level of p‐H2A.X, a marker for senescence. These data highlight the potential of RSV as a radiation sensitizer for PCA treatment and warrant further investigation. (Cancer Sci 2012; 103: 1090–1098)
The educational value of using cumulative sum charts
Authors: Smith S. E. , Tallentire V. R. , Spiller J. , Wood S. M. , Cameron H. S.
Published: March 2012

Various workplace‐based assessment tools are available, but none have been shown to improve performance in procedural skills. This study aimed to assess the impact of using one such tool, cumulative sum charts, on procedural skill ability. A single‐blind randomised controlled trial was conducted on 82 final year medical students. Control group students received the usual teaching; in addition to this, intervention group students were provided with cumulative sum charts to log their cannulation attempts over a 7‐month period. At the end of the year, students from both groups undertook a validated test of automaticity of cannulation skill. Students in the intervention group obtained median (IQR [range]) scores of 68.2 (60.5–74.3 [42.7–81.1]) vs 62.2 (52.2–68.8 [40.7–80.5]) for the control group (p = 0.013). The effect size was moderate (Cohen’s d = 0.608). This study therefore provides support for the hypothesis that use of cumulative sum charts improves performance when learning procedural skills.
A randomised controlled trial comparing rocuronium priming, magnesium pre‐treatment and a combination of the two methods*
Authors: Kim M. H. , Oh A. Y. , Jeon Y. T. , Hwang J. W. , Do S. H.
Published: March 2012

We investigated whether magnesium sulphate combined with rocuronium priming shortens the onset of neuromuscular blockade, compared with these methods used alone. Ninety‐two patients scheduled for general anaesthesia were randomly allocated to one of four groups: controls were given 0.6 mg.kg−1 rocuronium; patients in the prime group were given 0.06 mg.kg−1 rocuronium three minutes before a further dose of 0.54 mg.kg−1 rocuronium; patients in the magnesium group were given an infusion of 50 mg.kg−1 magnesium sulphate before rocuronium and patients in the magnesium and prime group were given both the magnesium sulphate and the priming dose of rocuronium. Tracheal intubation was attempted 40 s after the rocuronium injection. The time to onset of neuromuscular blockade was the primary outcome; duration of blockade and tracheal intubating conditions were also measured. The group allocation and study drugs were coded and concealed until statistical analyses were completed. The magnesium and prime group had the shortest mean (SD) onset time (55 (16) s; p < 0.001), and best tracheal intubating conditions (p < 0.05). No statistical difference was found for the duration of blockade. As for adverse events, a burning or heat sensation was reported in eight (35%) and six (26%) patients in the magnesium and magnesium and prime groups, respectively. The combination of magnesium sulphate and rocuronium priming accelerated the onset or neuromuscular blockade and improved rapid‐sequence intubating conditions, compared with either magnesium sulphate or priming used alone.
Karyotyping and cytogenetic mapping of Atlantic cod (Gadus morhua Linnaeus, 1758)
Authors: Ghigliotti L. , Fevolden S.‐E. , Cheng C.‐H. C. , Babiak I. , Dettai A. , Pisano E.
Published: March 2012

The Atlantic cod (Gadus morhua) is an important natural resource for northern societies and is now also considered to be a promising candidate for aquaculture. In recent years, much effort has been directed towards the development of genomic tools, and genome initiatives for Atlantic cod have been established. Despite the growing attention devoted to the Atlantic cod genomics, basic aspects of its genome structure and organization remain unknown. Thus, the present work aims to study cytogenetic features of the Atlantic cod as a contribution to the knowledge of this species' genome. The Atlantic cod displays a diploid number of 46 chromosomes, with a karyotypic formula 16 m/sm + 30 st/t. Conventional karyotyping was improved by chromosomal mapping of two classes of repetitive sequences. 18S rDNA clusters were assigned to pairs 2 and 4; small amounts of 18S rDNA clusters were occasionally detected on pair 5. These findings could not be related to the geographical origin of the specimens, but were consistent with the variability of these repeated genes in fish in general. 5S ribosomal gene clusters, apparently corresponding to a single 5S rDNA class, were detected on twelve chromosomes (pairs 11, 12, 14, 17, 20 and 21). The present update of the existing but meagre information on the karyotype of Atlantic cod, plus the first physical mapping of repetitive genes in this species herein, opens the way for an integrated approach that combines genetic and physical mapping with the assembly of the genome of this commercially important species.
Prediction of soil organic and inorganic carbon contents at a national scale (France) using mid‐infrared reflectance spectroscopy (MIRS)
Authors: Grinand C. , Barthès B. G. , Brunet D. , Kouakoua E. , Arrouays D. , Jolivet C. , Caria G. , Bernoux M.
Published: March 2012

This work aimed to evaluate the potential of mid‐infrared reflectance spectroscopy (MIRS) to predict soil organic and inorganic carbon contents with a 2086‐sample set representative of French topsoils (0–30 cm). Ground air‐dried samples collected regularly using a 16 × 16‐km grid were analysed for total (dry combustion) and inorganic (calcimeter) carbon; organic carbon was calculated by difference. Calibrations of MIR spectra with partial least square regressions were developed with 10–80% of the set and five random selections of samples. Comparisons between samples with contrasting organic or inorganic carbon content and regression coefficients of calibration equations both showed that organic carbon was firstly associated with a wide spectral region around 2500–3500 cm−1 (which was a reflection of its complex nature), and inorganic carbon with narrow spectral bands, especially around 2520 cm−1. Optimal calibrations for both organic and inorganic carbon were achieved by using 20% of the total set: predictions were not improved much by including more of the set and were less stable, probably because of atypical samples. At the 20% rate, organic carbon predictions over the validation set (80% of the total) yielded mean R2, standard error of prediction (SEP) and RPD (ratio of standard deviation to SEP) of 0.89, 6.7 g kg−1 and 3.0, respectively; inorganic carbon predictions yielded 0.97, 2.8 g kg−1 and 5.6, respectively. This seemed appropriate for large‐scale soil inventories and mapping studies but not for accurate carbon monitoring, possibly because carbonate soils were included. More work is needed on organic carbon calibrations for large‐scale soil libraries.
Comparative adaptations of Aphanizomenon and Anabaena for nitrogen fixation under weak irradiance
Authors: BRADBURN MARK J. , LEWIS WILLIAM M. , McCUTCHAN JAMES H.
Published: March 2012

1. In situ measurements of nitrogen fixation rates for Aphanizomenon in fertile Colorado lakes with low inorganic nitrogen concentrations demonstrated high efficiency of nitrogen fixation at low irradiance.

2. For study populations, rates of N2 fixation in darkness and with alternating exposure to light and darkness were a higher percentage of light‐saturated rates for Aphanizomenon than for Anabaena, suggesting storage of reduced metabolites at high irradiance that are used subsequently by Aphanizomenon when cells are forced by mixing into zones of low irradiance. Also, saturation of N2 fixation occurred over a lower range of irradiance for Aphanizomenon than for Anabaena.

3. High efficiency of N2 fixation in Aphanizomenon at low or fluctuating irradiance is complementary to its previously demonstrated high efficiency of photosynthesis at low irradiance. Nitrogen fixation rate was also strongly related to DIN concentration; fixation was highest at low DIN (maximum < 5 μg L−1) but was also most vulnerable to photoinhibition under such conditions.

4. The fixation capabilities of Aphanizomenon under weak or varying irradiance could explain its commonly observed domination over Anabaena when transparency is low and available nitrogen is scarce.
Early HER2 dysregulation in gastric and oesophageal carcinogenesis
Authors: Fassan Matteo , Mastracci Luca , Grillo Federica , Zagonel Vittorina , Bruno Sara , Battaglia Giorgio , Pitto Francesca , Nitti Donato , Celiento Tiziana , Zaninotto Giovanni , Fiocca Roberto , Rugge Massimo
Published: March 2012

Fassan M, Mastracci L, Grillo F, Zagonel V, Bruno S, Battaglia G, Pitto F, Nitti D, Celiento T, Zaninotto G, Fiocca R & Rugge M  (2012) Histopathology 61, 769–776

Early HER2 dysregulation in gastric and oesophageal carcinogenesis

Aims:  To explore human epidermal growth factor receptor 2 (HER2) status in the histological phenotypes [metaplasia, intraepithelial neoplasia (IEN, i.e. dysplasia), and adenocarcinoma] involved in the morphogenesis of both intestinal‐type gastric cancer (GC) and Barrett’s adenocarcinoma (BAc).

Methods and results:  A consecutive series of 275 samples of stomach and oesophagus tissue (representing the whole spectrum of the phenotypic changes involved in gastric and Barrett’s carcinogenesis) was studied. HER2 status was assessed by applying two immunohistochemistry (IHC) protocols, using the antibodies 4B5 and CB11. Dual‐colour silver chromogenic in‐situ hybridization (SISH) was also performed on the same tissue samples. In both oesophageal and gastric samples, the rate of HER2 overexpression rose significantly from low‐grade to high‐grade IEN to adenocarcinoma (P < 0.001), with the two IHC protocols showing consistent staining (consistency 95%; k = 0.78; P < 0.001). Intratumour heterogeneity was documented in both GC and BAc (using both IHC protocols). The rate of HER2 amplification (using SISH) increased significantly along with IEN dedifferentiation (P < 0.001). Neither native nor metaplastic mucosa samples (obtained from either stomach or oesophagus) ever showed HER2 amplification. There was excellent agreement between HER2 amplification and protein overexpression (both IHC protocols: SISH/4B5––consistency 97.8%, k = 0.89, P < 0.001; SISH/CB11—consistency 97.8%, k = 0.91, P < 0.001).

Conclusions:  There is early involvement of HER2 dysregulation (amplification and protein overexpression) in both gastric (intestinal‐type) and Barrett’s oncogenesis.
Differences in the clinical characteristics between young and elderly men with varicocoele
Authors: Chen S.‐S.
Published: March 2012

Information concerning the clinical characteristics in elderly men with varicocoele is relatively limited. This study was assessed to evaluate the differences in clinical characteristics between young and elderly patients with varicocoele by retrospective chart review. Between June 2003 and February 2011, 169 young (18–30 years) men and 156 elderly (45–55 years) men with varicocoele, and 30 age‐matched men without varicocoele were recruited for this study. All the patients were divided into six groups. Thirty‐one infertile patients were assigned to Group 1, 138 fertile patients to Group 2, 35 infertile patients to Group 3 and 121 fertile patients to Group 4. Group 5 (15 young) and 6 (15 elderly) were control groups. The parameters for comparison included body mass index (BMI), semen quality (sperm motility, morphology and density) and pH value, serum concentration of follicle‐stimulating hormone (FSH), luteinizing hormones (LH), testosterone, testicular volume, grade of varicocoele and peak retrograde flow (PRF) and maximal vein diameter (MVD) by colour Doppler ultrasound (CDS). Elderly men with varicocoele had a higher incidence of bilateral varicocoele (25.5% vs. 14.8%), but a lower incidence of unilateral right varicocoele (2.6% vs. 7.7%) than young patients with varicocoele. In addition, patients with varicocoele had lower BMI than those without, and infertile young patients with varicocoele had the lowest levels of BMI. Furthermore, infertile patients (Groups 1 and 3) with varicocoele had significantly lower testicular volume and semen pH, lower levels of testosterone, higher levels of FSH and LH and higher PRF than fertile men with varicocoele (Groups 2 and 4). In conclusion, infertile elderly patients with varicocoele had significantly lower levels of testosterone and higher levels of FSH and LH than infertile young men with varicocoele. In addition, infertile elderly patients with bilateral varicocoele (Group 3, n = 8) had the lowest levels of testosterone.
Species formation and geographical range evolution in a genus of Central American cloud forest salamanders (Dendrotriton)
Authors: Rovito Sean M. , Wake David B. , Papenfuss Theodore J. , Parra‐Olea Gabriela , Muñoz‐Alonso Antonio , Vásquez‐Almazán Carlos R.
Published: March 2012

Aim  Montane Central America offers an ideal system for testing geographical hypotheses of species diversification. We examined how the complex geological history of Nuclear Central America has shaped the diversification of a genus of cloud‐forest‐inhabiting salamanders (Dendrotriton). We applied parametric models of geographical range evolution to determine the predominant mode of species formation within the genus and to test existing hypotheses of geographical species formation in the region.

Location  Montane cloud forests of Nuclear Central America.

Methods  We estimated a species tree for Dendrotriton using a multi‐locus DNA sequence data set and several coalescent methods, and performed molecular dating for divergence events within the genus. We then applied the species‐tree estimate to a likelihood‐based time‐stratified model of geographical range evolution, based on current species distributions and available geological information for Central America.

Results  Species trees from all methods contain two groups, one corresponding to species from the Sierra de los Cuchumatanes and the other containing all remaining species. In most cases, species formation within the genus involved an even division of the geographical range of the ancestral species between descendant species. The ancestor of extant Dendrotriton species was estimated to have occurred in either the Sierra de los Cuchumatanes or the Sierra Madre de Chiapas, and both of these areas appear to have been important for diversification within the genus. The single species found in the Quaternary‐age Guatemalan volcanic cordillera dispersed to the volcanoes from an older highland area.

Main conclusions  Models of geographical range evolution, when combined with robust species‐tree estimates, provide insight into the historical biogeography of taxa not available from phylogenies or distributional data alone. Vicariant species formation, rather than peripatric or gradient speciation, appears to have been the dominant process of diversification, with most divergence events occurring within or between ancient highland areas. The apparent dispersal of Dendrotriton to the Quaternary‐age volcanoes raises the possibility that the rich salamander community there is composed of species that dispersed from geologically older areas. The Motagua Valley appears not to have been as important in vicariant species formation within Dendrotriton as it is within other groups.
Evaluation of programmatic changes to an antimicrobial stewardship program with house officer feedback
Authors: Hong Steven Y. , Epstein Lauren H. , Lawrence Kenneth , Davidson Lisa , Taur Ying , Nadkarni Lauren , Doron Shira
Published: March 2012

Rationale, aims and objectives  A collegial relationship between prescribers and antimicrobial stewards, along with an appreciation of the importance of antimicrobial stewardship, is essential for optimal functioning of an antimicrobial stewardship program (ASP). Programmatic adjustments based on feedback may be beneficial to the success of ASPs. The objective of this study is to assess the experience of house officers with the ASP and the effect of programmatic improvements.

Methods  A survey of house officers at an academic medical centre was conducted assessing their experience with the ASP before (2008) and after (2010) programmatic interventions were instituted.

Results  Of 225 house officer surveys sent, we received 97 responses (88% from medical doctors). The majority indicated that ASP was either very or somewhat important in fighting antibiotic resistance (100%), improving patient care (97%), preventing medication errors (91%) and containing health care costs (89%). Ninety‐one per cent indicated either a very good or good educational experience with the ASP. The ASP often reminded respondents of a patient's allergy (31%), to adjust for renal function (78%), and 38% were prevented from making a medication error. Comparing 2008 and 2010, a higher proportion of respondents in 2010 said they had a very good or good educational experience with ASP [84% versus 98%, odds ratio (OR) = 8.40, P = 0.022] and a lower proportion of respondents reported confusion about ASP procedures (59% versus 39%, OR = 0.43, P = 0.048).

Conclusions  House officer feedback resulted in ASP policy changes which improved the ASP experience.
Genetic trade‐offs and conditional neutrality contribute to local adaptation
Authors: ANDERSON JILL T. , LEE CHENG‐RUEI , RUSHWORTH CATHERINE A. , COLAUTTI ROBERT I. , MITCHELL‐OLDS THOMAS
Published: March 2012

Divergent natural selection promotes local adaptation and can lead to reproductive isolation of populations in contrasting environments; however, the genetic basis of local adaptation remains largely unresolved in natural populations. Local adaptation might result from antagonistic pleiotropy, where alternate alleles are favoured in distinct habitats, and polymorphism is maintained by selection. Alternatively, under conditional neutrality some alleles may be favoured in one environment but neutral at other locations. Antagonistic pleiotropy maintains genetic variation across the landscape; however, there is a systematic bias against discovery of antagonistic pleiotropy because the fitness benefits of local alleles need to be significant in at least two environments. Here, we develop a generally applicable method to investigate polygenic local adaptation and identify loci that are the targets of selection. This approach evaluates allele frequency changes after selection at loci across the genome to distinguish antagonistic pleiotropy from conditional neutrality and deleterious variation. We investigate local adaptation at the qualitative trait loci (QTL) level in field experiments, in which we expose 177 F6 recombinant inbred lines and parental lines of Boechera stricta (Brassicaceae) to their parental environments over two seasons. We demonstrate polygenic selection for native alleles in both environments, with 2.8% of the genome exhibiting antagonistic pleiotropy and 8% displaying conditional neutrality. Our study strongly supports antagonistic pleiotropy at one large‐effect flowering phenology QTL (nFT): native homozygotes had significantly greater probabilities of flowering than foreign homozygotes in both parental environments. Such large‐scale field studies are essential to elucidate the genetic basis of adaptation in natural populations.
Geographical structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremula L., Salicaceae)
Authors: BERNHARDSSON CAROLINA , INGVARSSON PÄR K.
Published: March 2012

When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation because alternative alleles are favoured in different geographical locations. Here, we study 71 single nucleotide polymorphisms (SNPs) from seven genes associated with inducible defence responses in a sample of Populus tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation, and a principal component analyses conducted on the defence SNPs divides the Swedish population into three distinct clusters. Several defence SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographical variation has been found in genes involved in plant defence against antagonists.
Clinical and molecular analysis of RASopathies in a group of Turkish patients
Authors: Şimşek‐Kiper PÖ , Alanay Y , Gülhan B , Lissewski C , Türkyılmaz D , Alehan D , Çetin M , Utine GE , Zenker M , Boduroğlu K
Published: March 2012

Şimşek‐Kiper PÖ, Alanay Y, Gülhan B, Lissewski C, Türkyılmaz D, Alehan D, Çetin M, Utine GE, Zenker M, Boduroğlu K. Clinical and molecular analysis of patients with RASopathies in Turkish patients.

The ‘RASopathies’ are a group of disorders sharing many clinical features and a common pathophysiology. In this study, we aimed to clinically evaluate a group of Turkish patients and elucidate the underlying genetic etiology. Thirty‐one patients with a clinical diagnosis of one of the RASopathy syndromes were included in the study. Of these, 26 (83.8%) had a clinical diagnosis of Noonan syndrome, whereas 5 had a clinical diagnosis of either Costello, LEOPARD or cardio‐facio‐cutaneous syndromes. Twenty of 31 (64.5%) patients were found to be mutation positive. Mutations in PTPN11, SOS1 and SHOC2 genes were detected in patients with Noonan syndrome (57.6%). Mutations in MEK1, PTPN11, BRAF and HRAS genes were detected in the remaining. Pulmonary stenosis was the most common (61.5%) cardiac anomaly. Among Noonan syndrome patients with a confirmed mutation, mild intellectual disability tended to be more common in patients with PTPN11 mutation than in those with SOS1 mutation. Hematologic evaluation revealed coagulation defects in three Noonan syndrome patients with a mutation. This is currently the largest clinical and molecular study in Turkish RASopathy patients. Our findings indicate that molecular epidemiology and genotype–phenotype correlations in RASopathies are relatively independent from the ethnic population background.