bluuebunny/crossref_metadata_2025 huggingface dataset:
Observation of multiple current free helicon double layers
Authors: Sahu B. B. , Ganguli A. , Tarey R. D.
Published: November 2013

A combination of three strong current free double layers (CFDLs) characterized by strength (eΔΦ/Te) ∼ 10 and widths (Δz/λD) ∼ 7.6, 8, and 8.3 has been observed in argon helicon plasma. In contrast to other works report on the same subject, in the present investigations the DLs form in a mirror-like magnetic field topology and present in the plateau regions of magnetic field. Using the measurement of radio frequency compensated Langmuir Probe consistent with the B-dot probe diagnostic, a qualitative mechanism of DL formation has also been discussed.
Latitudinal variation of genecological traits in native grasses of Patagonian rangelands
Authors: Leva Paula E. , Aguiar Martín R. , Premoli Andrea C.
Published: November 2013

Geographical variation in genetically based traits helps to elucidate the effect of distinct ecological and evolutionary processes on widespread plants. Whereas abundant information exists on genetic patterns of woody species in western humid Andes, such information is scarce for the neighbouring dry Patagonian steppe. We examined genecological traits of two native forage species vulnerable to overgrazing (Bromus pictus and Poa ligularis) in dry Occidental Phytogeographical District. We compared within-population genetic diversity and among-population (n = 6) divergence by using isozyme electrophoresis. We also cultivated plants under common garden to compare genetically based morphology (plant height, number of tillers by plant and weight per tiller). Analysis showed that 8 and 13 loci were polymorphic of 9 and 19 resolved loci in at least one population for Bromus and Poa, respectively. In general, plant traits decreased from north to south in both species. Genetic and quantitative results (FST/QST index) showed evidence of local adaptation in populations of both species. Genetic divergence among populations was significant. We detected two different geographical groups divided at the same latitude (42–43°S) in both species, supporting the hypothesis of a past vicariance event. Sustainable management of these forage species to cope with land-use and climate change will be enriched by the inclusion of genecological knowledge.
Natural and cultural histories of fire differ between Tasmanian and mainland Australian alpine vegetation
Authors: Kirkpatrick Jamie B. , Bridle Kerry L.
Published: November 2013

We ask how and why mainland Australia and Tasmania differ in the natural and cultural history of alpine fire. Indigenous people seem unlikely to have extensively burned the alpine landscape in either of mainland Australia or Tasmania, whereas anthropogenic fire increased markedly after the European invasion. In Tasmania, where lightning ignition is uncommon, alpine fires have been rare post-1980, whereas mainland alpine vegetation has been extensively burned. The current distributions of the eight Australian alpine plant species that have no mechanisms for recovery from fire suggest that climate and natural fire barriers have been important in their survival. Mainland Australian pre-fire vegetation cover is typically attained in less than a decade, whereas in Tasmania, half a century or more after fire, bare ground persists at high levels, and continues to decrease only where mammalian herbivores are excluded. These differences appear to be ultimately related to the climatic contrast between the maritime mountains of Tasmania and the continental mainland mountains, through the effects of continentality on snow cover, which, in turn affect marsupial herbivore grazing, exposure of soil and vegetation to extreme microclimatic conditions and the degree of shrub dominance.
Defining the paramedic process
Authors: Carter Holly , Thompson James
Published: November 2013

The use of a ‘process of care’ is well established in several health professions, most evidently within the field of nursing. Now ingrained within methods of care delivery, it offers a logical approach to problem solving and ensures an appropriate delivery of interventions that are specifically suited to the individual patient. Paramedicine is a rapidly advancing profession despite a wide acknowledgement of limited research provisions. This frequently results in the borrowing of evidence from other disciplines. While this has often been useful, there are many concerns relating to the acceptable limit of evidence transcription between professions. To date, there is no formally recognised ‘process of care’-defining activity within the pre-hospital arena. With much current focus on the professional classification of paramedic work, it is considered timely to formally define a formula that underpins other professional roles such as nursing. It is hypothesised that defined processes of care, particularly the nursing process, may have features that would readily translate to pre-hospital practice. The literature analysed was obtained through systematic searches of a range of databases, including Ovid MEDLINE, Cumulative Index to Nursing and Allied Health. The results demonstrated that the defined process of care provides nursing with more than just a structure for practice, but also has implications for education, clinical governance and professional standing. The current nursing process does not directly articulate to the complex and often unstructured role of the paramedic; however, it has many principles that offer value to the paramedic in their practice. Expanding the nursing process model to include the stages of Dispatch Considerations, Scene Assessment, First Impressions, Patient History, Physical Examination, Clinical Decision-Making, Interventions, Re-evaluation, Transport Decisions, Handover and Reflection would provide an appropriate model for pre-hospital practices.
MSPrep—Summarization, normalization and diagnostics for processing of mass spectrometry–based metabolomic data
Authors: Hughes Grant , Cruickshank-Quinn Charmion , Reisdorph Richard , Lutz Sharon , Petrache Irina , Reisdorph Nichole , Bowler Russell , Kechris Katerina
Published: October 2013

Motivation: Although R packages exist for the pre-processing of metabolomic data, they currently do not incorporate additional analysis steps of summarization, filtering and normalization of aligned data. We developed the MSPrep R package to complement other packages by providing these additional steps, implementing a selection of popular normalization algorithms and generating diagnostics to help guide investigators in their analyses.

Availability:  http://www.sourceforge.net/projects/msprep

Contact:  grant.hughes@ucdenver.edu

Supplementary Information:  Supplementary materials are available at Bioinformatics online.
EXPANDS: expanding ploidy and allele frequency on nested subpopulations
Authors: Andor Noemi , Harness Julie V. , Müller Sabine , Mewes Hans W. , Petritsch Claudia
Published: November 2013

Motivation: Several cancer types consist of multiple genetically and phenotypically distinct subpopulations. The underlying mechanism for this intra-tumoral heterogeneity can be explained by the clonal evolution model, whereby growth advantageous mutations cause the expansion of cancer cell subclones. The recurrent phenotype of many cancers may be a consequence of these coexisting subpopulations responding unequally to therapies. Methods to computationally infer tumor evolution and subpopulation diversity are emerging and they hold the promise to improve the understanding of genetic and molecular determinants of recurrence.

Results: To address cellular subpopulation dynamics within human tumors, we developed a bioinformatic method, EXPANDS. It estimates the proportion of cells harboring specific mutations in a tumor. By modeling cellular frequencies as probability distributions, EXPANDS predicts mutations that accumulate in a cell before its clonal expansion. We assessed the performance of EXPANDS on one whole genome sequenced breast cancer and performed SP analyses on 118 glioblastoma multiforme samples obtained from TCGA. Our results inform about the extent of subclonal diversity in primary glioblastoma, subpopulation dynamics during recurrence and provide a set of candidate genes mutated in the most well-adapted subpopulations. In summary, EXPANDS predicts tumor purity and subclonal composition from sequencing data.

Availability and implementation: EXPANDS is available for download at http://code.google.com/p/expands (matlab version - used in this manuscript) and http://cran.r-project.org/web/packages/expands (R version).

Contact: claudia.petritsch@ucsf.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data
Authors: Li Jun , Wei Hairong , Liu Tingsong , Zhao Patrick Xuechun
Published: November 2013

The accurate construction and interpretation of gene association networks (GANs) is challenging, but crucial, to the understanding of gene function, interaction and cellular behavior at the genome level. Most current state-of-the-art computational methods for genome-wide GAN reconstruction require high-performance computational resources. However, even high-performance computing cannot fully address the complexity involved with constructing GANs from very large-scale expression profile datasets, especially for the organisms with medium to large size of genomes, such as those of most plant species. Here, we present a new approach, GPLEXUS (http://plantgrn.noble.org/GPLEXUS/), which integrates a series of novel algorithms in a parallel-computing environment to construct and analyze genome-wide GANs. GPLEXUS adopts an ultra-fast estimation for pairwise mutual information computing that is similar in accuracy and sensitivity to the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) method and runs ∼1000 times faster. GPLEXUS integrates Markov Clustering Algorithm to effectively identify functional subnetworks. Furthermore, GPLEXUS includes a novel ‘condition-removing’ method to identify the major experimental conditions in which each subnetwork operates from very large-scale gene expression datasets across several experimental conditions, which allows users to annotate the various subnetworks with experiment-specific conditions. We demonstrate GPLEXUS’s capabilities by construing global GANs and analyzing subnetworks related to defense against biotic and abiotic stress, cell cycle growth and division in Arabidopsis thaliana.
Defining and Modeling State-Dependent Dynamic Systems
Authors: Esarey Justin , DeMeritt Jacqueline H. R.
Published: November 2013

A state-dependent dynamic system is one in which (1) the marginal effect ofxonyat timet() depends on the prior value of the dependent variable, and (2) the persistence of the dependent variable () depends onxt. We present a methodological strategy for dealing with state-dependent dynamic systems and demonstrate the consequences of ignoring state-dependence. As an applied example, we find evidence of state-dependence in the relationship between presidential approval and economic performance: high unemployment rates are most damaging to presidential approval among presidents with the highest initial approval ratings.
Quantifying the Effect of Pyraclostrobin on Grainfill Period and Kernel Dry Matter Accumulation in Maize
Authors: Byamukama E. , Abendroth L. J. , Elmore R. W. , Robertson A. E.
Published: November 2013

Strobilurin fungicides are effective against a wide range of foliar fungal diseases on several crops and may offer additional physiological benefits, including plants staying green longer than normal (the “stay-green effect”). It has been hypothesized that the stay-green effect may extend the grain fill period leading to increased grain yield due to a longer period of dry matter accumulation. We investigated the effect of pyraclostrobin fungicide applied at tasseling on foliar disease suppression, stalk rot severity, the stay-green effect of leaves in the upper canopy, dry matter accumulation, time at physiological maturity, grain yield, and moisture at harvest in maize from 2008 through 2010 in Iowa at six location years. Foliar disease severity was <5% in all location years. Pyraclostrobin-treated plots had a significantly higher area under green leaves incidence curve compared to non-treated maize. Although grain yield and grain moisture at harvest were not different (P > 0.1) between pyraclostrobin-treated and non-treated maize in all location years, treated plots tended to have higher yield and grain moisture. Time at physiological maturity did not differ between pyraclostrobin-treated and non-treated plots (P > 0.1). Although we demonstrated an application of pyraclostrobin to maize delayed senescence of the leaves thus contributing to the stay-green effect, our data did not show grain-fill period extension.

Accepted for publication 21 August 2013. Published 24 October 2013.
Kidney Protection by Hypothermic Total Liquid Ventilation after Cardiac Arrest in Rabbits
Authors: Tissier Renaud , Giraud Sebastien , Quellard Nathalie , Fernandez Béatrice , Lidouren Fanny , Darbera Lys , Kohlhauer Matthias , Pons Sandrine , Chenoune Mourad , Bruneval Patrick , Goujon Jean-Michel , Ghaleh Bijan , Berdeaux Alain , Hauet Thierry
Published: November 2013

Background:

Total liquid ventilation (TLV) with perfluorocarbons has been shown to induce rapid protective cooling in animal models of myocardial ischemia and cardiac arrest, with improved neurological and cardiovascular outcomes after resuscitation. In this study, the authors hypothesized that hypothermic TLV can also limit kidney injury after cardiac arrest.

Methods:

Anesthetized rabbits were submitted to 15 min of untreated ventricular fibrillation. After resuscitation, three groups of eight rabbits each were studied such as (1) life support plus hypothermia (32°–33°C) induced by cold TLV (TLV group), (2) life support without hypothermia (control group), and (3) Sham group (no cardiac arrest). Life support was continued for 6 h before euthanasia and kidney removal.

Results:

Time to target esophageal temperature was less than 5 min in the TLV group. Hypothermia was accompanied by preserved renal function in the TLV group as compared with control group regarding numerous markers including creatinine blood levels (12 ± 1 vs. 16 ± 2 mg/l, respectively; mean ± SEM), urinary N-acetyl-β-(d)-glucosaminidase (1.70 ± 0.11 vs. 3.07 ± 0.10 U/mol of creatinine), γ-glutamyltransferase (8.36 ± 0.29 vs. 12.96 ± 0.44 U/mol of creatinine), or β2-microglobulin (0.44 ± 0.01 vs. 1.12 ± 0.04 U/mol of creatinine). Kidney lesions evaluated by electron microscopy and conventional histology were also attenuated in TLV versus control groups. The renal-protective effect of TLV was not related to differences in delayed inflammatory or immune renal responses because transcriptions of, for example, interferon-γ, tumor necrosis factor-α, interleukin-1β, monocyte chemoattractant protein-1, toll-like receptor-2, toll-like receptor-4, and vascular endothelial growth factor were similarly altered in TLV and control versus Sham.

Conclusion:

Ultrafast cooling with TLV is renal protective after cardiac arrest and resuscitation, which could increase kidney availability for organ donation.
Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395
Authors: Buddruhs Nora , Pradella Silke , Göker Markus , Päuker Orsola , Pukall Rüdiger , Spröer Cathrin , Schumann Peter , Petersen Jörn , Brinkhoff Thorsten
Published: November 2013

The marine genus

Phaeobacter

currently comprises six species, some of which were intensively studied mainly due to their ability to produce secondary metabolites. The type strain of the type species,

Phaeobacter gallaeciensis

BS107T, has been deposited at several public culture collections worldwide. Based on differences in plasmid profiles, we detected that the alleged

P. gallaeciensis

type strains deposited at the Collection Institute Pasteur (CIP; Paris, France) as CIP 105210 and at the German Collection of Microorganisms and Cell Cultures (DSMZ; Braunschweig, Germany) as DSM 17395 are not identical. To determine the identity of these strains, we conducted DNA–DNA hybridization, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), 16S rRNA gene and internal transcribed spacer (ITS) sequence analyses, as well as physiological experiments. Based on the detailed 16S rRNA gene reanalysis we showed that strain CIP 105210 most likely corresponds to the original

P. gallaeciensis

type strain BS107T. In contrast, the

Phaeobacter

strain DSM 17395 exhibits a much closer affiliation to

Phaeobacter inhibens

DSM 16374T ( = T5T) and should thus be allocated to this species. The detection of the dissimilarity of strains CIP 105210T and DSM 17395 will influence future comparative studies within the genus

Phaeobacter

.
Designation of type strains for seven species of the order Myxococcales and proposal for neotype strains of Cystobacter ferrugineus, Cystobacter minus and Polyangium fumosum
Authors: Lang Elke , Reichenbach Hans
Published: November 2013

Ten species of the order

Myxococcales

with validly published names are devoid of living type strains. Four species of the genus

Chondromyces

are represented by dead herbarium samples as the type material. For a species of the genus

Melittangium

and two species of the genus

Polyangium

, no physical type material was assigned at the time of validation of the names or later on. In accordance with rule 18f of the International Code of Nomenclature of Bacteria the following type strains are designated for these species: strain Cm a14T ( = DSM 14605T = JCM 12615T) as the type strain of

Chondromyces apiculatus

, strain Cm c5T ( = DSM 14714T = JCM 12616T) as the type strain of

Chondromyces crocatus

, strain Sy t2T ( = DSM 14631T = JCM 12617T) as the type strain of

Chondromyces lanuginosus

, strain Cm p51T ( = DSM 14607T = JCM 12618T) as the type strain of

Chondromyces pediculatus

, strain Me b8T ( = DSM 14713T = JCM 12633T) as the type strain of

Melittangium boletus

, strain Pl s12T ( = DSM 14670T = JCM 12637T) as the type strain of

Polyangium sorediatum

and strain Pl sm5T ( = DSM 14734T = JCM 12638T) as the type strain of

Polyangium spumosum

. Furthermore, the type strains given for three species of the genera

Cystobacter

and

Polyangium

had been kept at one university institute and have been lost according to our investigations. In accordance with Rule 18c of the Bacteriological Code, we propose the following neotype strains: strain Cb fe18 ( = DSM 14716  = JCM 12624) as the neotype strain of

Cystobacter ferrugineus

, strain Cb m2 ( = DSM 14751 = JCM 12627) as the neotype strain of

Cystobacter minus

and strain Pl fu5 ( = DSM 14668 = JCM 12636) as the neotype strain of

Polyangium fumosum

. The proposals of the strains are based on the descriptions and strain proposals given in the respective chapters of Bergey’s Manual of Systematic Bacteriology (2005).
Ovine herpesvirus-2-encoded microRNAs target virus genes involved in virus latency
Authors: Riaz Aayesha , Dry Inga , Levy Claire S. , Hopkins John , Grey Finn , Shaw Darren J. , Dalziel Robert G.
Published: October 2013

Herpesviruses encode microRNAs (miRNAs) that target both virus and host genes; however, their role in herpesvirus biology is understood poorly. We identified previously eight miRNAs encoded by ovine herpesvirus-2 (OvHV-2), the causative agent of malignant catarrhal fever (MCF), and have now investigated the role of these miRNAs in regulating expression of OvHV-2 genes that play important roles in virus biology. ORF20 (cell cycle inhibition), ORF50 (reactivation) and ORF73 (latency maintenance) each contain predicted targets for several OvHV-2 miRNAs. Co-transfection of miRNA mimics with luciferase reporter constructs containing the predicted targets showed the 5′ UTRs of ORF20 and ORF73 contain functional targets for ovhv-miR-2 and ovhv2-miR-8, respectively, and the 3′ UTR of ORF50 contains a functional target for ovhv2-miR-5. Transfection of BJ1035 cells (an OvHV-2-infected bovine T-cell line) with the relevant miRNA mimic resulted in a significant decrease in ORF50 and a smaller but non-significant decrease in ORF20. However, we were unable to demonstrate a decrease in ORF73. MCF is a disease of dysregulated lymphocyte proliferation; miRNA inhibition of ORF20 expression may play a role in this aberrant lymphocyte proliferation. The proteins encoded by ORF50 and ORF73 play opposing roles in latency. It has been hypothesized that miRNA-induced inhibition of virus genes acts to ensure that fluctuations in virus mRNA levels do not result in reactivation under conditions that are unfavourable for viral replication and our data supported this hypothesis.
Dual regulation of Dmc1-driven DNA strand exchange by Swi5–Sfr1 activation and Rad22 inhibition
Authors: Murayama Yasuto , Kurokawa Yumiko , Tsutsui Yasuhiro , Iwasaki Hiroshi
Published: November 2013

Both ubiquitously expressed Rad51 and meiosis-specific Dmc1 are required for crossover production during meiotic recombination. The budding yeast Rad52 and its fission yeast ortholog, Rad22, are “mediators;” i.e., they help load Rad51 onto ssDNA coated with replication protein A (RPA). Here we show that the Swi5–Sfr1 complex from fission yeast is both a mediator that loads Dmc1 onto ssDNA and a direct “activator” of DNA strand exchange by Dmc1. In stark contrast, Rad22 inhibits Dmc1 action by competing for its binding to RPA-coated ssDNA. Thus, Rad22 plays dual roles in regulating meiotic recombination: activating Rad51 and inhibiting Dmc1.
3D chromatin interactions organize Yan chromatin occupancy and repression at the even-skipped locus
Authors: Webber Jemma L. , Zhang Jie , Mitchell-Dick Aaron , Rebay Ilaria
Published: November 2013

Long-range integration of transcriptional inputs is critical for gene expression, yet the mechanisms remain poorly understood. We investigated the molecular determinants that confer fidelity to expression of the heart identity gene even-skipped (eve). Targeted deletion of regions bound by the repressor Yan defined two novel enhancers that contribute repressive inputs to stabilize tissue-specific output from a third enhancer. Deletion of any individual enhancer reduced Yan occupancy at the other elements, impacting eve expression, cell fate specification, and cardiac function. These long-range interactions may be stabilized by three-dimensional chromatin contacts that we detected between the elements. Our work provides a new paradigm for chromatin-level integration of general repressive inputs with specific patterning information to achieve robust gene expression.
Structure and function of Norrin in assembly and activation of a Frizzled 4–Lrp5/6 complex
Authors: Ke Jiyuan , Harikumar Kaleeckal G. , Erice Clara , Chen Chen , Gu Xin , Wang Liren , Parker Naomi , Cheng Zhihong , Xu Wenqing , Williams Bart O. , Melcher Karsten , Miller Laurence J. , Xu H. Eric
Published: November 2013

Norrin is a cysteine-rich growth factor that is required for angiogenesis in the eye, ear, brain, and female reproductive organs. It functions as an atypical Wnt ligand by specifically binding to the Frizzled 4 (Fz4) receptor. Here we report the crystal structure of Norrin, which reveals a unique dimeric structure with each monomer adopting a conserved cystine knot fold. Functional studies demonstrate that the novel Norrin dimer interface is required for Fz4 activation. Furthermore, we demonstrate that Norrin contains separate binding sites for Fz4 and for the Wnt ligand coreceptor Lrp5 (low-density lipoprotein-related protein 5) or Lrp6. Instead of inducing Fz4 dimerization, Norrin induces the formation of a ternary complex with Fz4 and Lrp5/6 by binding to their respective extracellular domains. These results provide crucial insights into the assembly and activation of the Norrin–Fz4–Lrp5/6 signaling complex.
Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
Authors: Auer Thomas O. , Duroure Karine , De Cian Anne , Concordet Jean-Paul , Del Bene Filippo
Published: November 2013

Sequence-specific nucleases like TALENs and the CRISPR/Cas9 system have greatly expanded the genome editing possibilities in model organisms such as zebrafish. Both systems have recently been used to create knock-out alleles with great efficiency, and TALENs have also been successfully employed in knock-in of DNA cassettes at defined loci via homologous recombination (HR). Here we report CRISPR/Cas9-mediated knock-in of DNA cassettes into the zebrafish genome at a very high rate by homology-independent double-strand break (DSB) repair pathways. After co-injection of a donor plasmid with a short guide RNA (sgRNA) and Cas9 nuclease mRNA, concurrent cleavage of donor plasmid DNA and the selected chromosomal integration site resulted in efficient targeted integration of donor DNA. We successfully employed this approach to convert eGFP into Gal4 transgenic lines, and the same plasmids and sgRNAs can be applied in any species where eGFP lines were generated as part of enhancer and gene trap screens. In addition, we show the possibility of easily targeting DNA integration at endogenous loci, thus greatly facilitating the creation of reporter and loss-of-function alleles. Due to its simplicity, flexibility, and very high efficiency, our method greatly expands the repertoire for genome editing in zebrafish and can be readily adapted to many other organisms.
High-Yield Synthesis of RNA Using T7 RNA Polymerase and Plasmid DNA or Oligonucleotide Templates
Authors: Nilsen Timothy W. , Rio Donald C. , Ares Manuel
Published: November 2013

When a large amount (milligram quantities) of RNA is desired (e.g., for making RNAs for RNA interference studies or for structural analyses), it is advantageous to use optimized transcription conditions. The method described here uses high millimolar concentrations of rNTPs, pyrophosphatase, and a specially formulated high-yield transcription buffer. These conditions prevent product (pyrophosphate) inhibition of RNA polymerase, which permits the accumulation of large quantities of RNA.
Effective Utilization and Appropriate Selection of Genetically Engineered Mouse Models for Translational Integration of Mouse and Human Trials
Authors: Abate-Shen Cory , Pandolfi Pier Paolo
Published: November 2013

The landscape of cancer research and therapy has radically changed over the past decades in at least two major respects: Our ability to model cancer in the mouse has risen to an unprecedented level of accuracy at the same time that novel cancer drugs have been developed in record numbers. This has led to an explosion in genetically engineered mouse model (GEMM) research, as GEMMs can potentially be used to test and optimize drugs in a variety of ways: preclinically (before testing in human patients), coclinically (in parallel with human testing), and postclinically (to optimize standard of care therapy). Thus the potential applications of faithful GEMMs of cancer have expanded from analysis of causal relationships between genetic aberrancies and tumorigenesis in preclinical efforts to a more comprehensive and systematic utilization of GEMMs for drug testing and clinical trial optimization. As GEMM research has grown, however, few standard protocols have been put in place regarding GEMM trials done in parallel with human trials (the “coclinical” approach), or in situations in which the available cohort of human patients is too small for valid statistical analysis. The success of such efforts will require an increased attention to the rigor with which mouse and human clinical efforts are designed, executed, and integrated.
HFR1 Sequesters PIF1 to Govern the Transcriptional Network Underlying Light-Initiated Seed Germination in Arabidopsis
Authors: Shi Hui , Zhong Shangwei , Mo Xiaorong , Liu Na , Nezames Cynthia D. , Deng Xing Wang
Published: November 2013

Seed germination is the first step for seed plants to initiate a new life cycle. Light plays a predominant role in promoting seed germination, where the initial phase is mediated by photoreceptor phytochrome B (phyB). Previous studies showed that PHYTOCHROME-INTERACTING FACTOR1 (PIF1) represses seed germination downstream of phyB. Here, we identify a positive regulator of phyB-dependent seed germination, LONG HYPOCOTYL IN FAR-RED1 (HFR1). HFR1 blocks PIF1 transcriptional activity by forming a heterodimer with PIF1 that prevents PIF1 from binding to DNA. Our whole-genomic analysis shows that HFR1 and PIF1 oppositely mediate the light-regulated transcriptome in imbibed seeds. Through the HFR1–PIF1 module, light regulates expression of numerous genes involved in cell wall loosening, cell division, and hormone pathways to initiate seed germination. The functionally antagonistic HFR1–PIF1 pair constructs a fail-safe mechanism for fine-tuning seed germination during low-level illumination, ensuring a rapid response to favorable environmental changes. This study identifies the HFR1–PIF1 pair as a central module directing the whole genomic transcriptional network to rapidly initiate light-induced seed germination.
Complexity of the Alternative Splicing Landscape in Plants
Authors: Reddy Anireddy S.N. , Marquez Yamile , Kalyna Maria , Barta Andrea
Published: November 2013

Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
Absolute configuration determination of theanti-head-to-head photocyclodimer of anthracene-2-carboxylic acid through cocrystallization withL-prolinol
Authors: Kawanami Yuko , Tanaka Hidekazu , Mizoguchi Jun-ichi , Kanehisa Nobuko , Fukuhara Gaku , Nishijima Masaki , Mori Tadashi , Inoue Yoshihisa
Published: October 2013

The absolute configuration has been established of the enantiopureanti-head-to-head cyclodimer of anthracene-2-carboxylic acid (AC) cocrystallized with L-propinol and dichloromethane [systematic name: (S)-2-(hydroxymethyl)pyrrolidin-1-ium (5R,6S,11R,12S)-8-carboxy-5,6,11,12-tetrahydro-5,12:6,11-bis([1,2]benzeno)dibenzo[a,e][8]annulene-2-carboxylate dichloromethane monosolvate], C5H12NO+·C30H19O4−·CH2Cl2. In the crystal structure, the AC dimer interacts with L-prolinol through a nine-membered hydrogen-bonded ring [R22(9)], while the dichloromethane molecule is incorporated to fill the void space. The absolute configuration determined in this study verifies a recent assignment made by comparing theoreticalversusexperimental circular dichroism spectra.
The glycogen phosphorylase inhibitor 2-(3-benzylamino-2-oxo-1,2-dihydropyridin-1-yl)-N-(3,4-dichlorobenzyl)acetamide
Authors: Popova Inessa , Healy Peter C. , Loughlin Wendy A. , Karis N. David , Jenkins Ian D.
Published: October 2013

The molecular structure of the title compound, C21H19Cl2N3O2, a potent glycogen phosphorylase a (GPa) inhibitor (IC50of 6.3 µM), consists of four distinct conjugated π systems separated by rotatable C—C bonds at the methylene groups. Molecules are linked into dimers disposed about a crystallographic centre of symmetry through a cyclic N—H...O hydrogen-bonding motif [graph setR22(10)]. These dimers are further connected along the crystallographiccaxis by N—H...O hydrogen bonding between the amide groups [graph setC(4)]. A comparison of this structure with that of the monohydrate of the significantly less active analogue (S)-2-(3-benzylamino-2-oxo-1,2-dihydropyridin-1-yl)-N-(2-hydroxy-1-phenylethyl)acetamide (IC50of 120 µM) is presented.
The principles underlying the use of powder diffraction data in solving pharmaceutical crystal structures
Authors: Shankland Kenneth , Spillman Mark J. , Kabova Elena A. , Edgeley David S. , Shankland Norman
Published: October 2013

Solving pharmaceutical crystal structures from powder diffraction data is discussed in terms of the methodologies that have been applied and the complexity of the structures that have been solved. The principles underlying these methodologies are summarized and representative examples of polymorph, solvate, salt and cocrystal structure solutions are provided, together with examples of some particularly challenging structure determinations.
Utilizing proton transfer to produce molecular salts in bromanilic acid substituted-pyridine molecular complexes – predictable synthons?
Authors: Thomas Lynne H. , Adam Martin S. , O'Neill Andrew , Wilson Chick C.
Published: October 2013

Controlled introduction of proton transfer into the design of a series of molecular complexes is described, delivering the systematic production of ionic molecular complexes (molecular salts). The controlled production of molecular salts has relevance as a potential strategy in the design of pharmaceutical materials. In nine molecular complexes consisting of bromanilic acid with the N-heterocyclic compounds 2-, 3- and 4-picoline [bis(2/3/4-methylpyridinium) 2,5-dibromo-3,6-dioxocyclohexa-1,4-diene-1,4-diolate, 2C6H8N+·C6Br2O42−], 2,3-, 2,4-, 2,5- and 3,5-lutidine [2,3/2,4/2,5/3,5-dimethylpyridinium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate, C7H10N+·C6HBr2O4−], and 3-bromo-4-methylpyridine [3-bromo-4-methylpyridinium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate, C6H7BrN+·C6HBr2O4−] and 2-bromo-3-methylpyridine [2-bromo-3-methylpyridine–2,5-dibromo-3,6-dihydroxycyclohexa-2,5-diene-1,4-dione (1/1), C6H6BrN·C6H2Br2O4], proton transfer occurs readily between the bromanilic acid molecule and the N heteroatom of the pyridine ring, in all cases producing a charge-assisted bifurcated N—H...O hydrogen bond. This reinforces the value of this motif as a design tool in the crystal engineering of such complexes. The protonation state (and stoichiometry) significantly affect the supramolecular synthons obtained, but 1:2 stoichiometries reliably give rise to PBP synthons and 1:1 stoichiometries to PBBP synthons (where P indicates a methylpyridine co-molecule and B a bromanilic acid molecule). The influence of halogen interactions on the wider crystal packing is also discussed, with C—H...Br and Br...O interactions the most prevalent; only one Br...Br interaction is found.
Synchrotron X-ray footprinting on tour
Authors: Bohon Jen , D'Mello Rhijuta , Ralston Corie , Gupta Sayan , Chance Mark R.
Published: November 2013

Synchrotron footprinting is a valuable technique in structural biology for understanding macromolecular solution-state structure and dynamics of proteins and nucleic acids. Although an extremely powerful tool, there is currently only a single facility in the USA, the X28C beamline at the National Synchrotron Light Source (NSLS), dedicated to providing infrastructure, technology development and support for these studies. The high flux density of the focused white beam and variety of specialized exposure environments available at X28C enables footprinting of highly complex biological systems; however, it is likely that a significant fraction of interesting experiments could be performed at unspecialized facilities. In an effort to investigate the viability of a beamline-flexible footprinting program, a standard sample was taken on tour around the nation to be exposed at several US synchrotrons. This work describes how a relatively simple and transportable apparatus can allow beamlines at the NSLS, CHESS, APS and ALS to be used for synchrotron footprinting in a general user mode that can provide useful results.
Polymer electrolyte fuel cell performance degradation at different synchrotron beam intensities
Authors: Eller Jens , Büchi Felix N.
Published: November 2013

The degradation of cell performance of polymer electrolyte fuel cells under monochromatic X-ray irradiation at 13.5 keV was studied in galvanostatic and potentiostatic operation modes in a through-plane imaging direction over a range of two orders of magnitude beam intensity at the TOMCAT beamline of the Swiss Light Source. The performance degradation was found to be a function of X-ray dose and independent of beam intensity, whereas the degradation rate correlates with beam intensity. The cell performance was more sensitive to X-ray irradiation at higher temperature and gas feed humidity. High-frequency resistance measurements and the analysis of product water allow conclusions to be drawn on the dominating degradation processes, namely change of hydrophobicity of the electrode and sulfate contamination of the electrocatalyst.
Study of fossil bones by synchrotron radiation micro-spectroscopic techniques and scanning electron microscopy
Authors: Zougrou I. M. , Katsikini M. , Pinakidou F. , Paloura E. C. , Papadopoulou L. , Tsoukala E.
Published: November 2013

Earlymost Villafranchian fossil bones of an artiodactyl and a perissodactyl from the Milia excavation site in Grevena, Greece, were studied in order to evaluate diagenetic effects. Optical microscopy revealed the different bone types (fibro-lamellar and Haversian, respectively) of the two fragments and their good preservation state. The spatial distribution of bone apatite and soil-originating elements was studied using micro-X-ray fluorescence (µ-XRF) mapping and scanning electron microscopy. The approximate value of the Ca/P ratio was 2.2, as determined from scanning electron microscopy measurements. Bacterial boring was detected close to the periosteal region and Fe bearing oxides were found to fill bone cavities,e.g.Haversian canals and osteocyte lacunae. In the perissodactyl bone considerable amounts of Mn were detected close to cracks (the Mn/Fe weight ratio takes values up to 3.5). Goethite and pyrite were detected in both samples by means of metallographic microscopy. The local Ca/P ratio determined with µ-XRF varied significantly in metal-poor spots indicating spatial inhomogeneities in the ionic substitutions. XRF line scans that span the bone cross sections revealed that Fe and Mn contaminate the bones from both the periosteum and medullar cavity and aggregate around local maxima. The formation of goethite, irrespective of the local Fe concentration, was verified by the FeK-edge X-ray absorption fine structure (XAFS) spectra. Finally, SrK-edge extended XAFS (EXAFS) revealed that Sr substitutes for Ca in bone apatite without obvious preference to the Ca1or Ca2unit-cell site occupation.
Scanning X-ray strain microscopy of inhomogeneously strained Ge micro-bridges
Authors: Etzelstorfer Tanja , Süess Martin J. , Schiefler Gustav L. , Jacques Vincent L. R. , Carbone Dina , Chrastina Daniel , Isella Giovanni , Spolenak Ralph , Stangl Julian , Sigg Hans , Diaz Ana
Published: November 2013

Strained semiconductors are ubiquitous in microelectronics and microelectromechanical systems, where high local stress levels can either be detrimental for their integrity or enhance their performance. Consequently, local probes for elastic strain are essential in analyzing such devices. Here, a scanning X-ray sub-microprobe experiment for the direct measurement of deformation over large areas in single-crystal thin films with a spatial resolution close to the focused X-ray beam size is presented. By scanning regions of interest of several tens of micrometers at different rocking angles of the sample in the vicinity of two Bragg reflections, reciprocal space is effectively mapped in three dimensions at each scanning position, obtaining the bending, as well as the in-plane and out-of-plane strain components. Highly strained large-area Ge structures with applications in optoelectronics are used to demonstrate the potential of this technique and the results are compared with finite-element-method models for validation.
Effect of biochar application in combination with domestic wastewater on biomass yield of bioenergy plantations
Authors: Ramola Sudipta , Kumar Srivastava Rajeev , Vasudevan Padma
Published: October 2013

Purpose

– The energy demand of growing population is on rise despite the fact that conventional energy reserves are limited and exhaustive in nature. To quench the ever-needing demand of energy, there is an urgent need to find out new energy options. In this regard, role of bioenergy plantation has gained enormous attention of scientist community all over the world. Biochar, a black pyrolysed carbonaceous product, is used as soil amendment and is reported to provide several benefits such as retention of nutrients in soil, better cation exchange capacity, soil carbon sequestration with better biomass yield. The paper aims to discuss these issues.

Design/methodology/approach

– The present study investigated the effect of domestic waste water (grey water) as well as biochar in combination for above-ground biomass of Eucalyptus hybrid (clone 413) and Anthocephalus cadamba plantations under flooded irrigation.

Findings

– Height, girth and above-ground biomass of both plantations increased significantly from control. Above-ground biomass of A. cadamba was observed to be better than Eucalyptus hybrid during initial period of establishment. After application of biochar, treatment WW+BBm was found to produce maximum above-ground biomass followed by treatment WW and WW+ BBg in both plantations system.

Originality/value

– The present study encompassed a real sustainable approach for environmental management by integrating the use of waste water (source of nutrients) as well as biochar (a solid waste pyrolysed material that act as soil fertilizer, an efficient adsorbent as well as a sink for carbon sequestration) for the better biomass yield of bioenergy plantations.
When P-J fit and P-O fit meet guanxi in a Chinese selection context
Authors: Chen Wan-Yu , Wang Mei-Ling , Hsu Bi-Fen
Published: November 2013

Purpose

– Human resource management may have great distinctions in different cultural contexts; past researches have increasingly discovered the differences between Eastern and Western perspectives. For employee selection, Chinese bosses usually employ acquaintances and relative bases on accumulated favors and relationship intensity in Chinese society. This study aims to investigate the relative importance of P-J fit, P-O fit and guanxi when Chinese recruiters judge the qualifications of job applicants.

Design/methodology/approach

– To test the hypotheses in this paper, the authors use a policy capturing methodology that is widely used for analyses of human judgment and decision making. This design enables the authors to infer the way managers integrate different indices of selection in making decisions. During the period of time, the study was running, 95 participants with hiring experience in Chinese regions completed the task, and they were from several industries for the generalization of this study.

Findings

– The results indicate that P-J fit, P-O fit and guanxi all have a unique impact on manager's hiring decisions in Chinese society, and P-J fit is weighted more heavily than P-O fit and guanxi.

Originality/value

– This is the first study that integrates the Eastern and the Western perspectives, supplements the gap between selection and fit theory in the West and proves that P-J fit, P-O fit and Chinese guanxi all have individual influence on hiring decisions. “Guanxi” is the key factor that has great impact on the process of hiring decisions in Chinese societies compared with Western organizations.
“Ask me what I read”: readers' advisory and immigrant adaptation
Authors: Dali Keren
Published: November 2013

Purpose

– The purpose of this paper is to investigate the potential of readers' advisory (RA) in libraries to help immigrants with psychological and socio-cultural adaptation in a new country.

Design/methodology/approach

– The data were empirically collected from a sample of Russian-speaking immigrant readers residing in the Greater Toronto Area, Ontario, Canada, by means of background surveys and in-depth interviews.

Findings

– The RA interaction is not merely a conversation about leisure books; it is a powerful intercultural encounter that has the potential to raise the levels of intimacy and attraction between host and immigrant populations, break negative stereotypes, help to build shared networks and create favorable contacts, change intergroup attitudes, and improve readers' mastery of the second language and knowledge of a new country.

Originality/value

– This article makes a contribution to three areas related to RA. It provides insight into the views and perceptions of RA by a selected group of readers; it gives voice to immigrant readers whose experiences with RA are particularly under-represented in the Library and Information Science literature; and it conceptualizes the RA interaction as an intercultural encounter, using the uncertainty reduction based theory of intercultural adaptation to frame the discussion.
Library partnerships: a key to growth
Authors: Massis Bruce
Published: November 2013

Purpose

– The purpose of this column is to review several recent library partnerships and highlight the benefit of such endeavors for the libraries and their partner institutions.

Design/methodology/approach

– This is a literature review and commentary on this topic that has been addressed by professionals, researchers and practitioners.

Findings

– Visibility and access to the library in some unexpected locations, thanks to a number of creative partnerships, can serve as greater a function to the library as to its partner and the community. The vitality of the library can be at least partially sustained by its partnerships and can serve as a model for other public/private and public/public associations where both sides of the partnership benefit in the estimation of the public.

Originality/value

– The value in addressing this issue is to examine the creative public/private and public/public partnerships of which libraries can avail themselves in an effort to best serve their patrons.