bluuebunny/crossref_metadata_2025 huggingface dataset:
Organic sulfur and organic matter redox processes contribute to electron flow in anoxic incubations of peat
Authors: Yu Zhi-Guo , Göttlicher Jörg , Steininger Ralph , Knorr Klaus-Holger
Published: April 2016

Environmental contextThe extent to which organic matter decomposition generates carbon dioxide or methane in anaerobic ecosystems is determined by the presence or absence of particular electron acceptors. Evaluating carbon dioxide and methane production in anaerobic incubation of peat, we found that organic matter predominated as an electron acceptor over considered inorganic electron acceptors. We also observed changes in organic sulfur speciation suggesting a contribution of organic sulfur species to the electron-accepting capacity of organic matter. AbstractAn often observed excess of CO2 production over CH4 production in freshwater ecosystems presumably results from a direct or indirect role of organic matter (OM) as electron acceptor, possibly supported by a cycling of oxidised and reduced sulfur species. To confirm the role of OM electron-accepting capacities (EACOM) in anaerobic microbial respiration and to elucidate internal sulfur cycling, peat soil virtually devoid of inorganic electron acceptors was incubated under anaerobic conditions. Thereby, production of CO2 and CH4 at a cumulative ratio of 3.2:1 was observed. From excess CO2 production and assuming a nominal oxidation state of carbon in OM of zero, we calculated a net consumption rate of EACOM of 2.36µmol electron (e–)cm–3day–1. Addition of sulfate (SO42–) increased CO2 and suppressed CH4 production. Moreover, subtracting the EAC provided though SO42–, net consumption rates of EACOM had increased to 3.88–4.85µmol e–cm–3day–1, presumably owing to a re-oxidation of sulfide by OM at sites otherwise not accessible for microbial reduction. As evaluated by sulfur K-edge X-ray absorption near-edge structure spectroscopy, bacterial sulfate reduction presumably involved not only a recycling of inorganic sulfur species, but also a sulfurisation of OM, yielding reduced organic sulfur, and changes in oxidised organic sulfur species. Organic matter thus contributes to anaerobic respiration: (i) directly by EAC of redox-active functional groups; (ii) directly by oxidised organic sulfur; and (iii) indirectly by re-oxidation of sulfide to maintain bacterial sulfate reduction.
Spatiotemporal redox dynamics in a freshwater lake sediment under alternating oxygen availabilities: combined analyses of dissolved and particulate electron acceptors
Authors: Lau Maximilian P. , Sander Michael , Gelbrecht Jörg , Hupfer Michael
Published: April 2016

Environmental contextAt sediment surfaces, the availability of oxygen is controlled by its downward transport from the water surface and its consumption in microbial metabolism. Microorganisms can also consume substances other than oxygen to dispose of the surplus charge that is generated during microbial metabolism. We investigate the complex dynamics of these other substances when the oxygen availability fluctuates, and thereby contribute to the mechanistic understanding of oxygen-consuming processes in aquatic environments. AbstractBenthic mineralisation in lakes largely controls the availability of oxygen in the water column above the sediment. In stratified lakes with anoxic hypolimnetic waters, mineralisation proceeds by anaerobic respiration using terminal electron acceptors (TEAs) other than O2. In past work, hypolimnetic oxygen consumption has been estimated from vertical concentration profiles of redox-active dissolved species in the water column and the underlying sediment. Electron transfer to and from particulate mineral and organic phases in the sediments was, however, not accounted for, mainly because of methodological constraints. In this work we use an electrochemical approach, mediated electrochemical analysis, to directly quantify changes in the redox states of particulate geochemical phases in a lake sediment. In mesocosm incubations, sediments were subjected to shifting oxygen availability similar to conditions during and after lake overturn events. The temporal redox dynamics of both dissolved and particulate phases in sediments were monitored at a high spatial resolution. We used a combination of experimental and modelling approaches to couple the observed changes in the redox state of dissolved and particulate species in the sediment to the oxygen turnover in the overlying water column. For the studied freshwater sediment, the amount of O2 consumed during the re-oxidation of these phases in the top 21mm of the sediment after switching from hypoxic to oxic conditions corresponded to ~50% of the total sediment oxygen consumption that was estimated from in-lake measurements after the onset of summer stratification. We found that solid phases in the sediments play a more profound role in electron accepting processes than previously considered. Based on these results, we propose that the herein presented analytical method offers the possibility to constrain parameters in theoretical models that simulate benthic redox dynamics including the electron transfer to and from geochemical phases in the sediments.
Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding
Authors: Fabbretti Attilio , Schedlbauer Andreas , Brandi Letizia , Kaminishi Tatsuya , Giuliodori Anna Maria , Garofalo Raffaella , Ochoa-Lizarralde Borja , Takemoto Chie , Yokoyama Shigeyuki , Connell Sean R. , Gualerzi Claudio O. , Fucini Paola
Published: April 2016

Significance

Eubacterial protein synthesis entails formation of an unlocked preinitiation complex consisting of the 30S ribosomal subunit, initiation factors, mRNA, and initiator tRNA. A conformational change in the subunit accompanies mRNA–tRNA codon–anticodon base-pairing generating a locked 30S complex. If correctly formed, this complex associates with the 50S ribosomal subunit forming a 70S complex, and the initiation factors are ejected. We show that the translational inhibitor GE81112 targets this essential step, hampering formation of a canonical codon–anticodon interaction and stalling the 30S in an unlocked state. Moreover, in the presence of GE81112 three rRNA helices, h44/h45/h24a, are stabilized in a disengaged conformation, suggesting that their conformation is associated with tRNA/mRNA decoding and transition of the 30S from unlocked to locked state.
Screening for ADHD Among Offenders of Intimate Partner Violence
Authors: Buitelaar Nannet J.L. , Ferdinand Robert F. , Posthumus Jocelyne A. , Buitelaar Jan K.
Published: April 2016

Since Attention-Deficit/Hyperactivity Disorder (ADHD) is presumed to be a risk factor for intimate partner violence (IPV) it is important to screen for the presence of ADHD in this population. Screening instruments for ADHD however have not been tested for use in forensic psychiatry. The aim of the present study was to assess the screening capacity of the Adult ADHD Self-Report Scale-Version 1.1 (ASRS-V 1.1), the ultra short questionnaire for ADHD (UKV) and the ADHD DSM-IV Rating Scale for adults (ADHD RS) among offenders of IPV in forensic psychiatry. One hundred and fifty participants, all of them outpatients of a forensic mental health service and referred for IPV, filled in the screeners upon intake and were subsequently assessed with the structured diagnostic interview for ADHD in adults 2.0 (DIVA 2.0). Diagnostic accuracy was moderate for ASRS-V 1.1 (AUC = .85; 95% CI = .79–.91) and UKV (AUC = .81; 95% CI = .74–.88) and high for ADHD RS (AUC = .94; 95% CI = .90–.97). Screening capacities were moderate for ASRS-V 1.1 (PPV = .81; 95% CI = .71−.88) and UKV (PPV = .78; 95% CI = .67–.85) and very good for ADHD RS (PPV = .90; 95% CI = .81–.95).
Tree community reassembly after selective and clear-cut logging in an Afro-tropical rainforest
Authors: Owiny Arthur A.
Published: April 2016

Understanding the process of community reassembly is crucial for the conservation of biodiversity and rehabilitation of ecosystems. This study tested whether tree communities in logged forests follow an equilibrium (deterministic) or non-equilibrium (stochastic) model of succession. We assessed reassembly of tree communities in different size classes along a successional gradient consisting of nine differently aged successional forests, namely, four regenerating former clear-cuts (9–19 years), three selectively logged (42–43 years) and two primary forests (PFs) in Kibale National Park, Uganda. The results show that the forests are converging and undergoing reassembly towards PFs. The species composition of seedlings, saplings and poles declined in similarity to the PF with age but that of mature trees in the different successional stages increased towards the PFs. These differences in tree species composition among the different size classes might be due to dominance of some particular species. Recovery of tree species density, diversity and dominance in all the size classes showed directional patterns as predicted by the deterministic model of succession. Compared to other variables, tree species density and diversity in selectively logged forests recovered relatively faster and was equivalent to or higher than that of PFs at 43 years. The results of the present study indicate that community reassembly in smaller sized trees followed a stochastic model of succession. However, as trees matured, they conform to the deterministic model of succession.
More than just a problem with faces: altered body perception in a group of congenital prosopagnosics
Authors: Rivolta Davide , Lawson Rebecca P. , Palermo Romina
Published: April 2016

It has been estimated that one out of 40 people in the general population suffer from congenital prosopagnosia (CP), a neurodevelopmental disorder characterized by difficulty identifying people by their faces. CP involves impairment in recognizing faces, although the perception of non-face stimuli may also be impaired. Given that social interaction depends not only on face processing, but also on the processing of bodies, it is of theoretical importance to ascertain whether CP is also characterized by body perception impairments. Here, we tested 11 CPs and 11 matched control participants on the Body Identity Recognition Task (BIRT), a forced-choice match-to-sample task, using stimuli that require processing of body-specific, not clothing-specific, features. Results indicated that the group of CPs were as accurate as controls on the BIRT, which is in line with the lack of body perception complaints by CPs. However, the CPs were slower than controls, and when accuracy and response times were combined into inverse efficiency scores (IESs), the group of CPs were impaired, suggesting that the CPs could be using more effortful cognitive mechanisms to be as accurate as controls. In conclusion, our findings demonstrate that CP may not generally be limited to face processing difficulties, but may also extend to body perception.
Rab43 regulates the sorting of a subset of membrane protein cargo through the medial Golgi
Authors: Cox John V. , Kansal Rita , Whitt Michael A.
Published: April 2016

To evaluate the role of cytoplasmic domains of membrane-spanning proteins in directing trafficking through the secretory pathway, we generated fluorescently tagged VSV G tsO45 with either the native G tail (G) or a cytoplasmic tail derived from the chicken AE1-4 anion exchanger (GAE). We previously showed that these two proteins progressed through the Golgi with distinct kinetics. To investigate the basis for the differential sorting of G and GAE, we analyzed the role of several Golgi-associated small GTP-binding proteins and found that Rab43 differentially regulated their transport through the Golgi. We show that the expression of GFP-Rab43 arrested the anterograde transport of GAEin a Rab43-positive medial Golgi compartment. GFP-Rab43 expression also inhibited the acquisition of endoH-resistant sugars and the surface delivery of GAE, as well as the surface delivery of the AE1-4 anion exchanger. In contrast, GFP-Rab43 expression did not affect the glycosylation or surface delivery of G. Unexpectedly, down-regulation of endogenous Rab43 using small interfering RNA resulted in an increase in the accumulation of GAEon the cell surface while having minimal effect on the surface levels of G. Our data demonstrate that Rab43 regulates the sorting of a subset of membrane-spanning cargo as they progress through the medial Golgi.
The negatively charged carboxy-terminal tail of β-tubulin promotes proper chromosome segregation
Authors: Fees Colby P. , Aiken Jayne , O’Toole Eileen T. , Giddings Thomas H. , Moore Jeffrey K.
Published: April 2016

Despite the broadly conserved role of microtubules in chromosome segregation, we have a limited understanding of how molecular features of tubulin proteins contribute to the underlying mechanisms. Here we investigate the negatively charged carboxy-terminal tail domains (CTTs) of α- and β-tubulins, using a series of mutants that alter or ablate CTTs in budding yeast. We find that ablating β-CTT causes elevated rates of chromosome loss and cell cycle delay. Complementary live-cell imaging and electron tomography show that β-CTT is necessary to properly position kinetochores and organize microtubules within the assembling spindle. We identify a minimal region of negatively charged amino acids that is necessary and sufficient for proper chromosome segregation and provide evidence that this function may be conserved across species. Our results provide the first in vivo evidence of a specific role for tubulin CTTs in chromosome segregation. We propose that β-CTT promotes the ordered segregation of chromosomes by stabilizing the spindle and contributing to forces that move chromosomes toward the spindle poles.
Synergistic role of fission yeast Alp16GCP6and Mzt1MOZART1in γ-tubulin complex recruitment to mitotic spindle pole bodies and spindle assembly
Authors: Masuda Hirohisa , Toda Takashi
Published: April 2016

In fission yeast, γ-tubulin ring complex (γTuRC)–specific components Gfh1GCP4, Mod21GCP5, and Alp16GCP6are nonessential for cell growth. Of these deletion mutants, only alp16Δ shows synthetic lethality with temperature-sensitive mutants of Mzt1MOZART1, a component of the γTuRC required for recruitment of the complex to microtubule-organizing centers. γ-Tubulin small complex levels at mitotic spindle pole bodies (SPBs, the centrosome equivalent in fungi) and microtubule levels for preanaphase spindles are significantly reduced in alp16Δ cells but not in gfh1Δ or mod21Δ cells. Furthermore, alp16Δ cells often form monopolar spindles and frequently lose a minichromosome when the spindle assembly checkpoint is inactivated. Alp16GCP6promotes Mzt1-dependent γTuRC recruitment to mitotic SPBs and enhances spindle microtubule assembly in a manner dependent on its expression levels. Gfh1GCP4and Mod21GCP5are not required for Alp16GCP6-dependent γTuRC recruitment. Mzt1 has an additional role in the activation of the γTuRC for spindle microtubule assembly. The ratio of Mzt1 to γTuRC levels for preanaphase spindles is higher than at other stages of the cell cycle. Mzt1 overproduction enhances spindle microtubule assembly without affecting γTuRC levels at mitotic SPBs. We propose that Alp16GCP6and Mzt1 act synergistically for efficient bipolar spindle assembly to ensure faithful chromosome segregation.
Single microfilaments mediate the early steps of microtubule bundling during preprophase band formation in onion cotyledon epidermal cells
Authors: Takeuchi Miyuki , Karahara Ichirou , Kajimura Naoko , Takaoka Akio , Murata Kazuyoshi , Misaki Kazuyo , Yonemura Shigenobu , Staehelin L. Andrew , Mineyuki Yoshinobu
Published: April 2016

The preprophase band (PPB) is a cytokinetic apparatus that determines the site of cell division in plants. It originates as a broad band of microtubules (MTs) in G2 and narrows to demarcate the future division site during late prophase. Studies with fluorescent probes have shown that PPBs contain F-actin during early stages of their development but become actin depleted in late prophase. Although this suggests that actins contribute to the early stages of PPB formation, how actins contribute to PPB-MT organization remains unsolved. To address this question, we used electron tomography to investigate the spatial relationship between microfilaments (MFs) and MTs at different stages of PPB assembly in onion cotyledon epidermal cells. We demonstrate that the PPB actins observed by fluorescence microscopy correspond to short, single MFs. A majority of the MFs are bound to MTs, with a subset forming MT-MF-MT bridging structures. During the later stages of PPB assembly, the MF-mediated links between MTs are displaced by MT-MT linkers as the PPB MT arrays mature into tightly packed MT bundles. On the basis of these observations, we propose that the primary function of actins during PPB formation is to mediate the initial bundling of the PPB MTs.
Pax7 is required for establishment of the xanthophore lineage in zebrafish embryos
Authors: Nord Hanna , Dennhag Nils , Muck Joscha , von Hofsten Jonas
Published: April 2016

The pigment pattern of many animal species is a result of the arrangement of different types of pigment-producing chromatophores. The zebrafish has three different types of chromatophores: black melanophores, yellow xanthophores, and shimmering iridophores arranged in a characteristic pattern of golden and blue horizontal stripes. In the zebrafish embryo, chromatophores derive from the neural crest cells. Using pax7a and pax7b zebrafish mutants, we identified a previously unknown requirement for Pax7 in xanthophore lineage formation. The absence of Pax7 results in a severe reduction of xanthophore precursor cells and a complete depletion of differentiated xanthophores in embryos as well as in adult zebrafish. In contrast, the melanophore lineage is increased in pax7a/pax7b double-mutant embryos and larvae, whereas juvenile and adult pax7a/pax7b double-mutant zebrafish display a severe decrease in melanophores and a pigment pattern disorganization indicative of a xanthophore- deficient phenotype. In summary, we propose a novel role for Pax7 in the early specification of chromatophore precursor cells.
Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species
Authors: Kim Sang-Chul , Kim Jung Sung , Kim Joo-Hwan
Published: April 2016

Genomic events including gene loss, duplication, pseudogenization and rearrangement in plant genomes are valuable sources for exploring and understanding the process of evolution in angiosperms. The family Melanthiaceae is distributed in temperate regions of the Northern Hemisphere and divided into five tribes (Heloniadeae, Chionographideae, Xerophylleae, Melanthieae and Parideae) based on the molecular phylogenetic analyses. At present, complete chloroplast genomes of the Melanthiaceae have been reported from three species. In the previous genomic study of Liliales, a trnI -CAU gene duplication event was reported from Paris verticillata , a member of Parideae. To clarify the significant genomic events of the tribe Parideae, we analysed the complete chloroplast genome sequences of two Trillium species representing two subgenera: Trillium and Phyllantherum . In Trillium tschonoskii (subgenus Trillium ), the circular double-stranded cpDNA sequence of 156 852 bp consists of two inverted repeat (IR) regions of 26 501 bp each, a large single-copy (LSC) region of 83 981 bp and a small single-copy (SSC) region of 19 869 bp. The chloroplast genome sequence of T. maculatum (subgenus Phyllantherum ) is 157 359 bp in length, consisting of two IRs (25 535 bp), one SSC (19 949 bp) and one LSC (86 340 bp), and is longer than that of T. tschonoskii . The results showed that the cpDNAs of Parideae are highly conserved across genome structure, gene order and contents. However, the chloroplast genome of T. maculatum contained a 3.4-kb inverted sequence between ndhC and rbcL in the LSC region, and it was a unique feature for subgenera Phyllantherum . In addition, we found three different types of gene duplication in the intergenic spacer between rpl23 and ycf2 containing trnI -CAU, which were in agreement with the circumscription of subgenera and sections in Parideae excluding T. govanianum . These genomic features provide informative molecular markers for identifying the infrageneric taxa of Trillium and improve our understanding of the evolution patterns of Parideae in Melanthiaceae.
Discovery of two new pulsars in 47 Tucanae (NGC 104)
Authors: Pan Z. , Hobbs G. , Li D. , Ridolfi A. , Wang P. , Freire P.
Published: April 2016

We report the discovery of two new millisecond pulsars (PSRs J0024−7204aa and J0024−7204ab) in the globular cluster 47 Tucanae (NGC 104). Our results bring the total number of pulsars in 47 Tucanae to 25. These pulsars were discovered by reprocessing archival observations from the Parkes radio telescope. We reprocessed the data using a standard search procedure based on the presto software package as well as using a new method in which we incoherently added the power spectra corresponding to ∼1100 h of observations. The newly discovered PSR J0024−7204aa, has a pulse frequency of ∼541 Hz (corresponding to a ∼1.84 ms period), which is higher than any other pulsars currently known in the cluster and ranks 12th amongst all the currently known pulsars. The dispersion measure of this pulsar, 24.941(7) cm−3 pc, is the highest in the cluster. The second discovered pulsar, PSR J0024−7204ab, is an isolated pulsar with a pulse frequency of ∼270 Hz (corresponding to a period of ∼3.70 ms).
A note on periodicity of long-term variations of optical continuum in active galactic nuclei
Authors: Lu Kai-Xing , Li Yan-Rong , Bi Shao-Lan , Wang Jian-Min
Published: April 2016

Graham et al. found a sample of active galactic nuclei (AGNs) and quasars from the Catalina Real-time Transient Survey (CRTS) that have long-term periodic variations in optical continuum. The nature of the periodicity remains uncertain. We investigate the periodic variability characteristics of the sample by testing the relations of the observed variability periods with AGN optical luminosity, black hole mass and accretion rates, and find no significant correlations. We also test the observed periods in several different aspects related to accretion discs surrounding single black holes, such as the Keplerian rotational periods of 5100 Å photon-emission regions and self-gravity dominated regions and the precessing period of warped discs. These tests shed new lights on understanding AGN variability in general. Under the assumption that the periodic behaviour is associated with supermassive black hole binary systems in particular, we compare the separations (${\scr {D}}_{\bullet }$) against characteristic radii of broad-line regions ($R_{\scriptscriptstyle {\rm BLR}}$) of the binaries and find ${\scr {D}}_{\bullet }\approx 0.05R_{\scriptscriptstyle {\rm BLR}}$. This interestingly implies that these binaries have only circumbinary BLRs.
Peripheral Intravenous Catheter Placement Is an Underrecognized Source of Staphylococcus aureus Bloodstream Infection
Authors: Austin Eloise D. , Sullivan Sean B. , Whittier Susan , Lowy Franklin D. , Uhlemann Anne-Catrin
Published: April 2016

Few studies have focused on the risks of peripheral intravenous catheters (PIVs) as sources for Staphylococcus aureus bacteremia (SAB), a life-threatening complication. We identified 34 PIV-related infections (7.6%) in a cohort of 445 patients with SAB. Peripheral intravenous catheter-related SAB was associated with significantly longer bacteremia duration and thrombophlebitis at old PIV sites rather than current PIVs.
Immunological Signaling During Herpes Simplex Virus-2 and Cytomegalovirus Vaginal Shedding After Initiation of Antiretroviral Treatment
Authors: Nason Martha C. , Patel Eshan U. , Kirkpatrick Allison R. , Prodger Jessica L. , Shahabi Kamnoosh , Tobian Aaron A. R. , Gianella Sara , Kalibbala Sarah , Ssebbowa Paschal , Kaul Rupert , Gray Ronald H. , Quinn Thomas C. , Serwadda David , Reynolds Steven J. , Redd Andrew D.
Published: April 2016

Vaginal proinflammatory cytokine expression during herpes virus reactivation was examined in human immunodeficiency virus-infected women before and after initiation of antiretroviral therapy (ART). Vaginal swabs were screened for levels of cytokines interleukin (IL)-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, tumor necrosis factor (TNF)-α, and interferon-γ. The relative risk (RR) of herpes simplex virus-2 or cytomegalovirus (CMV) shedding being associated with cytokine levels above the median were estimated. Herpes simplex virus-2 shedding was significantly associated with higher levels of IL-6 (RR = 1.4, P = .003) and TNF-α (RR = 1.3, P = .010), whereas CMV shedding was associated with higher IL-6 (RR = 1.3, P = .006) and IL-2 (RR = 1.4, P = .01). The association of viral shedding with higher IL-6 levels suggests that herpes virus reactivation may be playing a role in immune activation after ART initiation.
Characterization of a Segregation Distortion Locus with Powdery Mildew Resistance in a Wheat-Thinopyrum intermedium Introgression Line WE99
Authors: Ma Pengtao , Xu Hongxing , Han Guohao , Luo Qiaoling , Xu Yunfeng , Zhang Xiaotian , An Diaoguo , Li Lihui , Sun Yu
Published: April 2016

Exploitation of host resistance is important for controlling powdery mildew of wheat (Triticum aestivum L.). In this study, a wheat-Thinopyrum intermedium introgression line, designated WE99, conferred seedling resistance to 47 of 49 Blumeria graminis f. sp. tritici isolates. Genetic analysis demonstrated that the resistance segregation deviated significantly from a single gene Mendelian ratio. However, marker analysis indicated that only a single recessive resistance gene, temporarily designated PmWE99, conferred powdery mildew resistance (Pm). PmWE99 was mapped to chromosome arm 2BS and linked to the three simple-sequence repeat markers Gwm148, Gwm271, and Barc55. Using race spectrum analysis, PmWE99 was shown to be significantly different from the documented genes Pm42 and MlIW170 located on chromosome arm 2BS and, thus, appeared to be a new Pm gene. Examination of the genotype frequencies in the F2:3 families showed that a genetic variation in the PmWE99 interval that favored the transmission of the WE99 allele could be the cause of the deviated segregation. Further investigation revealed that the abnormal segregation only occurred at the PmWE99 interval and was not common at other loci in this population. Identification of PmWE99 will increase the diversity of the Pm genes for wheat improvement.
Spatial Genetic Structure and Population Dynamics of Gummy Stem Blight Fungi Within and Among Watermelon Fields in the Southeastern United States
Authors: Li Hao-Xi , Brewer Marin Talbot
Published: April 2016

The epidemiology of gummy stem blight (GSB) of cucurbits, particularly the sources of inoculum for epidemics, and the regional population genetic structure of the causal fungi Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), S. citrulli, and S. caricae are not well understood. Our goal was to better understand the population structure and fine-scale spatial genetic structure of Stagonosporopsis spp. in the southeastern United States. Overall, 528 isolates collected from nine fields in 2012, 2013, and 2014 were genotyped with 16 microsatellite markers. In 2013, S. caricae was first detected in the southeastern United States; however, S. citrulli remained the dominant species, representing 96.4% of the isolates. Principal coordinates analysis, discriminant analysis of principle components, and analysis of molecular variance indicated that most populations of S. citrulli were genotypically diverse, yet dominated by widely distributed clones that contributed to regional population structure. Spatial genetic structure resulting from aggregation of clonal genotypes at distances of less than 10 meters was detected within two of three fields in which isolate location was recorded. Studies on the epidemiological and fitness differences between S. citrulli and S. caricae and of prevalent and widespread clones will provide insight into the population structure and species dynamics observed in GSB epidemics.
An Improved Method for Measuring Quantitative Resistance to the Wheat PathogenZymoseptoria triticiUsing High-Throughput Automated Image Analysis
Authors: Stewart Ethan L. , Hagerty Christina H. , Mikaberidze Alexey , Mundt Christopher C. , Zhong Ziming , McDonald Bruce A.
Published: April 2016

Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. An improved method of quantifying STB symptoms was developed based on automated analysis of diseased leaf images made using a flatbed scanner. Naturally infected leaves (n = 949) sampled from fungicide-treated field plots comprising 39 wheat cultivars grown in Switzerland and 9 recombinant inbred lines (RIL) grown in Oregon were included in these analyses. Measures of quantitative resistance were percent leaf area covered by lesions, pycnidia size and gray value, and pycnidia density per leaf and lesion. These measures were obtained automatically with a batch-processing macro utilizing the image-processing software ImageJ. All phenotypes in both locations showed a continuous distribution, as expected for a quantitative trait. The trait distributions at both sites were largely overlapping even though the field and host environments were quite different. Cultivars and RILs could be assigned to two or more statistically different groups for each measured phenotype. Traditional visual assessments of field resistance were highly correlated with quantitative resistance measures based on image analysis for the Oregon RILs. These results show that automated image analysis provides a promising tool for assessing quantitative resistance to Z. tritici under field conditions.
Molecular Mapping of Stripe Rust Resistance Gene Yr76 in Winter Club Wheat Cultivar Tyee
Authors: Xiang C. , Feng J. Y. , Wang M. N. , Chen X. M. , See D. R. , Wan A. M. , Wang T.
Published: April 2016

Tyee, one of the wheat cultivars used to differentiate races of Puccinia striiformis f. sp. tritici in the United States, was identified to have a single gene for all-stage resistance, tentatively named YrTye. To map the gene, Tyee was crossed with ‘Avocet Susceptible’ (AvS). Genetic analysis of the F1, F2, F2:3, and BC1 progenies confirmed a single dominant gene for resistance to race PSTv-37 that is avirulent to YrTye. A mapping population of 135 F2 plants was phenotyped with PSTv-37 and the derived F2:3 lines were tested with races PSTv-37, PSTv-40, and PSTv-79. The F2 mapping population was genotyped with simple sequence repeat (SSR) markers. A genetic map comprising 13 SSR markers located YrTye in chromosome 3AS flanked distally by SSR marker wmc11 and proximally by wmc532 at 2.6 and 3.4 cM, respectively. Amplification of Chinese Spring 3A deletion lines placed the gene in the distal bin 3AS4-0.45 to 1.00. Because YrTye is different from all formally named Yr genes in chromosomal location, we permanently name the gene Yr76. A near-isogenic line of spring common wheat was developed and selected by testing F3 lines derived from a AvS*4/Tyee cross with Tyee-avirulent and virulent races and the flanking markers. The specific SSR alleles flanking Yr76 were validated using cultivars and breeding lines with and without the gene, and showed high polymorphisms. The specificity of Yr76 is useful in differentiating P. striiformis f. sp. tritici races, and its tightly linked markers will be useful in developing resistant cultivars when combining the gene with other genes for resistance to stripe rust.
Arkas: Rapid, Reproducible RNAseq Analysis as a Service
Authors: Colombo Anthony , Triche Timothy J. , Ramsingh Giridharan
Published: April 2016

The recently introduced Kallisto[1] pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments. However, as with all computational advances, reproducibility across experiments requires attention to detail. The elegant approach of Kallisto reduces dependencies, but we noted differences in quantification between versions of Kallisto, and both upstream preparation and downstream interpretation benefit from an environment that enforces a requirement for equivalent processing when comparing groups of samples. Therefore, we created the Arkas[3] and TxDbLite[4] R packages to meet these needs and to ease cloud-scale deployment of the above. TxDbLite extracts structured information directly from source FASTA files with per-contig metadata, while Arkas enforces versioning of the derived indices and annotations, to ensure tight coupling of inputs and outputs while minimizing external dependencies. The two packages are combined in Illumina's BaseSpace cloud computing environment to offer a massively parallel and distributed quantification step for power users, loosely coupled to biologically informative downstream analyses via gene set analysis (with special focus on Reactome annotations for ENSEMBL transcriptomes). Previous work (e.g. Soneson et al., 2016[34]) has revealed that filtering transcriptomes to exclude lowly-expressed isoforms can improve statistical power, while more-complete transcriptome assemblies improve sensitivity in detecting differential transcript usage. Based on earlier work by Bourgon et al., 2010[11], we included this type of filtering for both gene- and transcript-level analyses within Arkas. For reproducible and versioned downstream analysis of results, we focused our efforts on ENSEMBL and Reac-tome[2] integration within the qusage[19] framework, adapted to take advantage of the parallel and distributed environment in Illumina’s BaseSpace cloud platform. We show that quantification and interpretation of repetitive sequence element transcription is eased in both basic and clinical studies by just-in-time annotation and visualization. The option to retain pseudoBAM output for structural variant detection and annotation, while not insignificant in its demand for computation and storage, nonetheless provides a middle ground between de novo transcriptome assembly and routine quantification, while consuming a fraction of the resources used by popular fusion detection pipelines and providing options to quantify gene fusions with known breakpoints without reassembly. Finally, we describe common use cases where investigators are better served by cloud-based computing platforms such as BaseSpace due to inherent efficiencies of scale and enlightened common self-interest. Our experiences suggest a common reference point for methods development, evaluation, and experimental interpretation.
GenoGAM: Genome-wide generalized additive models for ChIP-seq analysis
Authors: Stricker Georg , Engelhardt Alexander , Schulz Daniel , Schmid Matthias , Tresch Achim , Gagneur Julien
Published: April 2016

Motivation

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective.

Results

Here, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad-hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays.

Availability

Software is available from Bioconductor:https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.html

Contact

gagneur@in.tum.de

Supplementary information

Supplementary information is available atBioinformaticsonline.
Isolation and Genomic Characterization ofDesulfuromonas soudanensisWTL, a Metal- and Electrode-Reducing Bacterium from Anoxic Deep Subsurface Brine
Authors: Badalamenti Jonathan P. , Summers Zarath M. , Chan Chi Ho , Gralnick Jeffrey A. , Bond Daniel R.
Published: April 2016

Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, Minnesota, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes depositedin situas bait, we enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium,Desul-furomonas soudanensisstrain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed thatD. soudanensisreleases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolateGeobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors.D. soudanensiscontains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multihemec-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentifiedN-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal transfer of respiratory proteins plays a role in respiratory flexibility among metal reducers. Isolation ofD. soudanensisunderscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.
High school principals as leaders: styles and sources of power
Authors: Brinia Vasiliki , PAPANTONIOU EVA
Published: April 2016

Purpose

This research presents the characteristics of leadership (style adopted, sources of power exercised and factors affecting leadership) of high school principals in Greece.

Design/methodology/approach

235 school principals were surveyed using questionnaires. These questionnaires assessed how often they adopted specific practices while managing their school, in relevance to their educational, managerial and administrative duties. Thus, the researchers were able to assess the leadership style of the principals (transactional or transformational) and the sources of power exercised (reward, punishment, expertise, example and information).

Findings

The majority of school principals in Greece prefer the transformational leadership style instead of the transactional one and they frequently exercise the power of information. There is a strong positive link between the transformational leadership style and the tendency to exercise the power of information. Furthermore, it is shown that the leadership skills grow with the educational/managerial work experience of a school principal.

Research limitations/implications

The researchers explored the notion of leadership within the context of a centralized educational system, where most critical decisions are taken by central educational administration (e.g. the Greek Ministry of Education). The findings reveal that being a transformational leader in this educational context is not due to the personal characteristics of the school manager (e.g. age, sex, studies). This fact provides insight on issues related to the recruitment/selection and training/development of school managers.

Originality/value

Taking into consideration the fact that there is currently a strong debate in Greece on whether school staff should be evaluated or not (and under what kind of criteria), these findings could be very useful to central education authorities as well as the whole educational community. Furthermore, they contribute towards a better understanding on school principals; what their personal characteristics are (education, work experience), what their leadership style is, how they manage their schools and what obstacles they face. Therefore, it is hoped that in the future, better processes could be followed on recruiting, evaluating and promoting managerial staff within school units.
IJHG review
Authors: MacVane Phipps Fiona
Published: April 2016

Purpose

– The purpose of this paper is to enable readers of International Journal of Health Governance (IJHG) to gain a quick overview of the key concepts explored in this issue of the journal.

Design/methodology/approach

– The review is prepared by the review editor to highlight key points within each paper.

Findings

– The paper enables readers to scan content and select articles of most interest or relevance to their needs.

Originality/value

–IJHG is the only Emerald health journal which provides a review section of this kind.
Certified in public health program: credentialing public health leaders
Authors: Foster Allison
Published: April 2016

Purpose

– Unlike other health professions, there has historically been no licensing, registration, or certification of public health practitioners to demonstrate their qualification to the public and employers. The purpose of this paper is to outline the rationale for developing public health workforce certification, describes the certification process developed by the National Board of Public Health Examiners (NBPHE), and explains how it is affecting public health education and practice.

Design/methodology/approach

– This paper is a narrative review from records of NBPHE.

Findings

– The Association of Schools and Programs of Public Health commissioned a formal study of health worker credentialing in 1989 and created a task force in 1999 to determine the need for public health credentialing. Based on input from public health leaders and stakeholders, the NBPHE was formed in 2005 to offer the Certified in Public Health (CPH) examination. The first CPH examination was administered in 2008. Uptake of the CPH was strong the first year (693 examinees), dropped by nearly half (369 examinees) in the second year, and then increased each year through 2015. Part of the increase may be due to eligibility revisions for taking the CPH examination. Eligibility for taking the CPH examination was revised in 2010 to include graduate students in public health and in 2015 to include candidates with a bachelor degree from any field and at least five years of work experience in public health. The NBPHE is piloting open professional eligibility for candidates with no formal education in public health and at least five year’s public health work experience. Schools and programs of public health accredited by the Council on Education for Public Health (CEPH) view the CPH examination as a useful tool in curriculum assessment and improvement and for maintaining CEPH accreditation. Several schools and programs of public health have begun requiring all graduate students to take the CPH examination. The CPH credential is also increasingly being used as a hiring factor among employers.

Originality/value

– NBPHE’s CPH credential is unique in the world. Foreign students graduating with American public health degrees have been taking the exam before returning to leadership roles in their own country. The CPH program described can serve as a model for other nations.
A contemporary TOC innovative thinking process in the backdrop of leagile supply chain
Authors: Banerjee Arnab , Mukhopadhyay Saroj Kumar
Published: April 2016

Purpose

– The purpose of this paper is to propose a fresh perspective to effectively adopt leagility in supply chain. The research adopts Theory of Constraints (TOC) methodology and amalgamates it with design thinking process, people’s opinion and mathematical approach to help achieve supply chain leagility.

Design/methodology/approach

– The proposed framework is a seven stepped approach to achieve supply chain leagility combination analytical and mathematical procedures. Data enveloping analysis (DEA) is used to identify high level constraint. The new designed thinking process is used to further evaluate the constraints. Nominal group technique (NGT) is used to help build the current reality tree and identify detail level constraints.

Findings

– The framework application on a case supply chain improves various parameters of leanness and agility over a period of one year. Improvements include reduced rework, improved cash flow, reduced operating cost, reduced order backlog and better customer interaction.

Research limitations/implications

– This research opens up TOC application in a totally new area of leagility adoption in supply chain. The framework needs to be explored with more implementation in various business scenarios.

Practical implications

– The proposed framework is extremely intuitive and pragmatic in approach. The case application demonstrates the framework can be easily adopted by supply chain managers to improve leagility.

Social implications

– The current study attempts to diversify the TOC application. Using thinking process, DEA and NGT in TOC parlance brings in objectivity and employees together for improvement.

Originality/value

– Amalgamating the mathematical approach of DEA, design thinking process and NGT within the TOC framework for supply chain leagility is new and novel.
Supplier selection in closed loop supply chain by an integrated simulation-Taguchi-DEA approach
Authors: Azadeh Ali , Zarrin Mansour , Salehi Nima
Published: April 2016

Purpose

– Reverse logistics refer to processes related to the reuse of products. The role of suppliers’ performance is crucial in achieving quality, cost, service and delivery aims of a supply chain. The selection of suppliers is regarded as one of the critical issues encountered by purchasing and operations managers in a supply chain to enhance organization’s global marketplace competitiveness. Most of the supply chain models are rather complex problems. Consequently, it is impossible to propose systematic models to handle them. Therefore, in this paper a new integrated approach based on experimental design and computer simulation is proposed for supplier selection. The paper aims to discuss these issues.

Design/methodology/approach

– In this study, a simulation approach is implemented to determine certain equivalent of parameters values in a CLSC network design which cannot be computed through mathematical model. Suppliers’ order quantities are investigated by Taguchi method for planning time horizon. Moreover, data envelopment analysis (DEA) is applied to assess suppliers based on quality, cost, delivery time, production capabilities, services and technology.

Findings

– In the numerical example, there are three suppliers for different regions. Purchase value of each supplier is measured in three years successively. According to the proposed method, the authors find the minimum level of costs together with the maximum number of high-quality products.

Practical implications

– The objective functions of model are minimizing the costs and maximizing number of high-quality products. The integrated approach introduced in this paper enables managers to select their suppliers effectively in their real system.

Originality/value

– Most supply chain models are complex and the identification of proper and optimal solutions in complex real-world systems often requires the solution of multi-objective problems involving multiple stochastic variables. Therefore, the paper introduces a new integrated approach for supplier selection in closed loop supply chain. To the best of the authors knowledge, this is the first study that integrates DEA, computer simulation and Taguchi method for supplier selection in closed loop supply chains.