bluuebunny/crossref_metadata_2025 huggingface dataset:
Disorders, diseases and pests.
Authors: Bosland P. W. , Votava E. J.
Published: April 2012

This chapter focuses on the types and symptoms of abiotic disorders, bacterial diseases, fungal diseases, viral diseases and pests affecting peppers. The type and amount of losses in pepper caused by these plant diseases and pests and various methods used in their control are discussed and the importance of the use of resistant cultivars in pepper production are highlighted.
Intensification of animal production from grassland and ecosystem services: a trade-off.
Authors: Lemaire G.
Published: April 2012

Grasslands have to be considered not only as a means for human food production but also as a means for providing ecosystem services. Coupling of C and N cycles through soil-vegetation interactions gives grassland ecosystems a high capacity for reduction of environmental impacts. Moreover, the high biodiversity within grasslands gives them a high-adaptive capacity to changes and perturbations. Nevertheless, the C-N decoupling by grazing animals annihilates partly these ecosystem services as the intensification and hence the production increase. Research is necessary for optimizing this trade-off through spatial and temporal interactions with other land use systems at farm and landscape level.
Collective identity and wellbeing of Roma minority adolescents in Bulgaria
Authors: Dimitrova Radosveta , Chasiotis Athanasios , Bender Michael , van de Vijver Fons
Published: April 2012

In Europe and particularly in Bulgaria, Roma represent the largest low‐status minority group that is subjected to marked public intolerance and discrimination. This study examined links among Roma (N = 207) and Bulgarian (N = 399) adolescents’ ethnic, familial, and religious identities as salient identity aspects for their psychological wellbeing. Results indicated that, as expected, Roma youth reported lower levels of wellbeing than Bulgarian youth. The latter revealed a weaker religious identity than Roma youth, whereas no ethnic group differences emerged regarding Bulgarian or familial identity. Furthermore, we observed that collective identity was higher in older participants of both groups. Finally, a multigroup analysis using structural equation modeling showed that collective identity was a positive predictor of wellbeing for both Roma and Bulgarian adolescents. Findings demonstrated differences in salience as well as structural communalities regarding ways in which collective identity affects wellbeing of youth from two ethnically diverse communities.
Contrast Effects in Typicality Judgements: A Hierarchical Bayesian Approach
Authors: Voorspoels Wouter , Storms Gert , Vanpaemel Wolf
Published: April 2012

We examine the influence of contrast categories on the internal graded membership structure of everyday concepts using computational models proposed in the artificial category learning tradition. In particular, the generalized context model (Nosofsky, 1986), which assumes that only members of a given category contribute to the typicality of a category member, is contrasted to the similarity–dissimilarity generalized context model (SD-GCM; Stewart & Brown, 2005), which assumes that members of other categories are also influential in determining typicality. The models are compared in a hierarchical Bayesian framework in their account of the typicality gradient of five animal categories and six artefact categories. For each target category, we consider all possible relevant contrast categories. Three separate issue are examined: (a) whether contrast effects can be found, (b) which categories are responsible for these effects, and (c) whether more than one category influences the typicality. Results indicate that the internal category structure is codetermined by dissimilarity towards potential contrast categories. In most cases, only a single contrast category contributed to the typicality. The present findings suggest that contrast effects might be more widespread than has previously been assumed. Further, they stress the importance of characteristics particular of everyday concepts, which require careful consideration when applying computational models of representation of the artificial category learning tradition to everyday concepts.
Studies of reflectivity degradation of retroreflectors in LHD and mitigation of impurity deposition using shaped diagnostic ducts and protective windows
Authors: Akiyama T. , Yoshida N. , Kawahata K. , Tokitani M. , Iwakiri H. , Okajima S. , Nakayama K.
Published: April 2012

Maintaining the reflectivity of first mirrors is indispensable in future fusion devices. While a retroreflector (corner cube mirror) is useful for laser diagnostics, impurities tend to accumulate and form a thick deposition layer in the central region, which causes degradation of reflectivity, due to the hollow shape of the retroreflector. Two mirror structures are tested to retain the reflectivity in the Large Helical Device (LHD). One is a bending mirror structure with a protective cylinder with fins and it could maintain the reflectivity over a three-month experimental campaign. The other is a cover window just in front of the reflector. Candidates of the window materials were exposed to the LHD plasmas and the degradation of the transmissivity of ZnSe and silicon, which are used for infrared and far infrared laser light, respectively, were small.
Scaling radiative divertor solutions to high power in DIII-D
Authors: Leonard A.W. , Mahdavi M.A. , Lasnier C.J. , Petrie T.W. , Stangeby P.C.
Published: April 2012

Detached radiative divertor plasmas are examined in DIII-D as a function of power. The 2D profile of plasma electron density and temperature is reconstructed from divertor Thomson data while energy transport is deduced from power balance measurements. The combination of plasma and energy diagnostics reveals that parallel energy transport transitions to convective flow at a constant 5–10 eV as a function of power. Simple considerations would imply divertor density proportional to power density for Mach 1 flow. However, the divertor, upstream separatrix and core plasma densities increase significantly less than linear with power density. During detached divertor operation H-mode core confinement is maintained though the edge pedestal can experience moderate degradation.
Costs of elaborate weapons in a rhinoceros beetle: how difficult is it to fly with a big horn?
Authors: McCullough Erin L. , Weingarden Paul R. , Emlen Douglas J.
Published: April 2012

The giant horns of rhinoceros beetles exemplify the extreme morphologies that can result from sexual selection. Ornaments and weapons help males obtain mates but may also impose fitness costs. Intuitively, exaggerated sexually selected traits should impair locomotion, yet compensatory morphologies often make it difficult to detect locomotor costs. Here, we tested whether horns of the rhinoceros beetle Trypoxylus dichotomus impair flight and whether males compensate by developing larger wings or flight muscles. Contrary to our expectation that horns are costly for flight, males flew as fast as females, and among males, horn length was not correlated with flight speed or distance flown. We found some evidence for compensations in the male flight apparatus; males had relatively larger wings and flight muscles than females, and males with long horns for their body size had larger wings than males with relatively short horns. Flight muscle mass, however, was unaffected by horn length. We conclude that T. dichotomus horns may have been costly in the past and led to morphological compensations in wing and flight muscle size, but they do not currently impose significant flight costs. Fitness costs are a central tenet of sexual selection theory, and the large horns of rhinoceros beetles are expected to impose particularly strong costs on locomotion. Given our finding that T. dichotomus horns are surprisingly easy to carry, future work will be needed to identify the potential costs that have been important in shaping the evolution of elaborate horn morphologies.
e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design
Authors: Pihan Emilie , Colliandre Lionel , Guichou Jean-François , Douguet Dominique
Published: April 2012

Motivation: In the drug discovery field, new uses for old drugs, selective optimization of side activities and fragment-based drug design (FBDD) have proved to be successful alternatives to high-throughput screening. e-Drug3D is a database of 3D chemical structures of drugs that provides several collections of ready-to-screen SD files of drugs and commercial drug fragments. They are natural inputs in studies dedicated to drug repurposing and FBDD.

Availability: e-Drug3D collections are freely available at http://chemoinfo.ipmc.cnrs.fr/e-drug3d.html either for download or for direct in silico web-based screenings.

Contact:  douguet@ipmc.cnrs.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
RNA-SeQC: RNA-seq metrics for quality control and process optimization
Authors: DeLuca David S. , Levin Joshua Z. , Sivachenko Andrey , Fennell Timothy , Nazaire Marc-Danie , Williams Chris , Reich Michael , Winckler Wendy , Getz Gad
Published: April 2012

Summary: RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3′/5′ bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis.

Availability and implementation: See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

Contact:  ddeluca@broadinstitute.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Statistical interpretation of machine learning-based feature importance scores for biomarker discovery
Authors: Huynh-Thu Vân Anh , Saeys Yvan , Wehenkel Louis , Geurts Pierre
Published: April 2012

Motivation: Univariate statistical tests are widely used for biomarker discovery in bioinformatics. These procedures are simple, fast and their output is easily interpretable by biologists but they can only identify variables that provide a significant amount of information in isolation from the other variables. As biological processes are expected to involve complex interactions between variables, univariate methods thus potentially miss some informative biomarkers. Variable relevance scores provided by machine learning techniques, however, are potentially able to highlight multivariate interacting effects, but unlike the p-values returned by univariate tests, these relevance scores are usually not statistically interpretable. This lack of interpretability hampers the determination of a relevance threshold for extracting a feature subset from the rankings and also prevents the wide adoption of these methods by practicians.

Results: We evaluated several, existing and novel, procedures that extract relevant features from rankings derived from machine learning approaches. These procedures replace the relevance scores with measures that can be interpreted in a statistical way, such as p-values, false discovery rates, or family wise error rates, for which it is easier to determine a significance level. Experiments were performed on several artificial problems as well as on real microarray datasets. Although the methods differ in terms of computing times and the tradeoff, they achieve in terms of false positives and false negatives, some of them greatly help in the extraction of truly relevant biomarkers and should thus be of great practical interest for biologists and physicians. As a side conclusion, our experiments also clearly highlight that using model performance as a criterion for feature selection is often counter-productive.

Availability and implementation: Python source codes of all tested methods, as well as the MATLAB scripts used for data simulation, can be found in the Supplementary Material.

Contact:  vahuynh@ulg.ac.be, or p.geurts@ulg.ac.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
CNVRuler: a copy number variation-based case–control association analysis tool
Authors: Kim Ji-Hong , Hu Hae-Jin , Yim Seon-Hee , Bae Joon Seol , Kim Seon-Young , Chung Yeun-Jun
Published: April 2012

Summary: The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)–GWAS. Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies. Here we present a user-friendly program called CNVRuler for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification. CNVRuler is based on the open-source programs R and Java from Sun Microsystems.

Availability: CNVRuler software is available with an online manual at the website, www.ircgp.com/CNVRuler/index.html

Contact:  yejun@catholic.ac.kr.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Improving the TFold test for differential shotgun proteomics
Authors: Carvalho Paulo C. , Yates John R. , Barbosa Valmir C.
Published: April 2012

Summary: We present an updated version of the TFold software for pinpointing differentially expressed proteins in shotgun proteomics experiments. Given an FDR bound, the updated approach uses a theoretical FDR estimator to maximize the number of identifications that satisfy both a fold-change cutoff that varies with the t-test P-value as a power law and a stringency criterion that aims to detect lowly abundant proteins. The new version has yielded significant improvements in sensitivity over the previous one.

Availability: Freely available for academic use at http://pcarvalho.com/patternlab.

Contact:  paulo@pcarvalho.com
DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets
Authors: Cereto-Massagué Adrià , Guasch Laura , Valls Cristina , Mulero Miquel , Pujadas Gerard , Garcia-Vallvé Santiago
Published: April 2012

Summary: Decoys are molecules that are presumed to be inactive against a target (i.e. will not likely bind to the target) and are used to validate the performance of molecular docking or a virtual screening workflow. The Directory of Useful Decoys database (http://dud.docking.org/) provides a free directory of decoys for use in virtual screening, though it only contains a limited set of decoys for 40 targets.To overcome this limitation, we have developed an application called DecoyFinder that selects, for a given collection of active ligands of a target, a set of decoys from a database of compounds. Decoys are selected if they are similar to active ligands according to five physical descriptors (molecular weight, number of rotational bonds, total hydrogen bond donors, total hydrogen bond acceptors and the octanol–water partition coefficient) without being chemically similar to any of the active ligands used as an input (according to the Tanimoto coefficient between MACCS fingerprints). To the best of our knowledge, DecoyFinder is the first application designed to build target-specific decoy sets.

Availability: A complete description of the software is included on the application home page. A validation of DecoyFinder on 10 DUD targets is provided as Supplementary Table S1. DecoyFinder is freely available at http://URVnutrigenomica-CTNS.github.com/DecoyFinder

Contact:  santi.garcia-vallve@urv.cat

Supplementary information:  Supplementary data are available at Bioinformatics online.
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
Authors: Hoehndorf Robert , Harris Midori A. , Herre Heinrich , Rustici Gabriella , Gkoutos Georgios V.
Published: April 2012

Motivation: The systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed. Applying ontologies to unify phenotype descriptions in the domain of physiology has been a particular challenge due to the high complexity of the underlying domain.

Results: In this study, we present the outline of a theory and its implementation for an ontology of physiology-related phenotypes. We provide a formal description of process attributes and relate them to the attributes of their temporal parts and participants. We apply our theory to create the Cellular Phenotype Ontology (CPO). The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created.

Availability and implementation: The CPO and the source code we generated to create the CPO are freely available on http://cell-phenotype.googlecode.com.

Contact:  rh497@cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Membrane targeting of an alpha-like tetravirus replicase is directed by a region within the RNA-dependent RNA polymerase domain
Authors: Short James R. , Dorrington Rosemary A.
Published: April 2012

The members of the familyTetraviridaeare small positive-sense insect RNA viruses that exhibit stringent host specificity and a high degree of tissue tropism, suggesting that complex virus–host interactions are likely to occur during infection and viral replication. The alpha-like replicase ofHelicoverpa armigerastunt virus (HaSV) (genusOmegatetravirus) has been proposed to associate with membranes of the endocytic pathway, which is similar to Semliki Forest virus, Sindbis virus and rubella virus. Here, we have used replicase–EGFP fusion proteins and recombinant baculovirus expression to demonstrate that the HaSV replicase associates strongly with cellular membranes, including detergent-resistant membranes, and that this association is maintained through a novel membrane targeting domain within the C-terminal region of the RNA-dependent RNA polymerase domain. We show a similar subcellular localization and strong association with detergent-resistant membranes for the carmo-like replicase of another tetravirus, Providence virus, in replicating cells, suggesting a common site of replication for these two tetraviruses.
Conversion of viable but nonculturable enteric bacteria  to culturable by co‐culture with eukaryotic cells
Authors: Senoh Mitsutoshi , Ghosh‐Banerjee Jayeeta , Ramamurthy Thandavarayan , Colwell Rita R. , Miyoshi Shin‐ichi , Nair G. Balakrish , Takeda Yoshifumi
Published: April 2012

Viable but nonculturable (VBNC) Vibrio cholerae non‐O1/non‐O139, V. parahaemolyticus, enterohemorrhagic Escherichia coli, enterotoxigenic E. coli, enteropathogenic E. coli, Shigella flexneri, and Salmonella enterica were converted to the culturable state by co‐culture with selected eukaryotic cells, e.g., HT‐29, Caco‐2, T84, HeLa, Intestine 407, and CHO cells.
Phenotypic characterization of Aspergillus niger and Candida albicans grown under simulated microgravity using a three‐dimensional clinostat
Authors: Yamazaki Takashi , Yoshimoto Maki , Nishiyama Yayoi , Okubo Yoichiro , Makimura Koichi
Published: April 2012

The living and working environments of spacecraft become progressively contaminated by a number of microorganisms. A large number of microorganisms, including pathogenic microorganisms, some of which are fungi, have been found in the cabins of space stations. However, it is not known how the characteristics of microorganisms change in the space environment. To predict how a microgravity environment might affect fungi, and thus how their characteristics could change on board spacecraft, strains of the pathogenic fungi Aspergillus niger and Candida albicans were subjected to on‐ground tests in a simulated microgravity environment produced by a three‐dimensional (3D) clinostat. These fungi were incubated and cultured in a 3D clinostat in a simulated microgravity environment. No positive or negative differences in morphology, asexual reproductive capability, or susceptibility to antifungal agents were observed in cultures grown under simulated microgravity compared to those grown in normal earth gravity (1 G). These results strongly suggest that a microgravity environment, such as that on board spacecraft, allows growth of potentially pathogenic fungi that can contaminate the living environment for astronauts in spacecraft in the same way as they contaminate residential areas on earth. They also suggest that these organisms pose a similar risk of opportunistic infections or allergies in astronauts as they do in people with compromised immunity on the ground and that treatment of fungal infections in space could be the same as on earth.
Immunohistochemical Ki67 labeling index has similar proliferation predictive power to various gene signatures in breast cancer
Authors: Niikura Naoki , Iwamoto Takayuki , Masuda Shinobu , Kumaki Nobue , Xiaoyan Tang , Shirane Masatoshi , Mori Kazushige , Tsuda Banri , Okamura Takuho , Saito Yuki , Suzuki Yasuhiro , Tokuda Yutaka
Published: April 2012

The objective of this study was to examine the association between the immunohistochemical Ki67 labeling index (IHC Ki67), Ki67 mRNA expression level, and first‐generation gene signatures in a cohort of breast cancer patients. We assessed associations between IHC Ki67 and first‐generation gene signatures in a panel of 39 tumor samples, using an oligonucleotide microarray. Gene expression analyses included Ki67 alone (MKi67), 21‐gene signature, mitosis kinome score signature, and genomic grade index. Correlation coefficients were calculated by Spearman's rank correlation test. In all cases, IHC Ki67, MKi67, and three genetic markers were highly correlated (ρ, 0.71–0.97). Estrogen receptor (ER)‐positive cases showed strong correlations between IHC Ki67 and other signatures (ρ, 0.79–0.83). The ER‐negative cases showed slightly lower correlations (ρ, 0.58–0.73). In ER‐positive cases, the low IHC Ki67 group showed significantly longer relapse‐free survival than the high IHC Ki67 group (P = 0.007). This difference was confirmed by multivariate analysis. Our data indicate that IHC Ki67 shows similar predictive power for proliferation in ER‐positive cancers as genomic markers. Further study of IHC Ki67 is needed to define prognostic factors and predictive factors for chemotherapy using central laboratory assessment. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02319.x, 2012)
The impact of MMX mesalazine on disease‐specific health‐related quality of life in ulcerative colitis patients
Authors: Solomon D. , Yarlas A. , Hodgkins P. , Karlstadt R. , Yen L. , Kane S.
Published: April 2012

Background

Past studies with ulcerative colitis (UC) patients indicate that disease activity strongly predicts health‐related quality of life (HRQL).

Aim

To examine the degree to which daily treatment with MMX mesalazine predicts improved HRQL for patients with active UC and with stable HRQL for patients with quiescent UC.

Methods

Data from two phases of a multicentre open‐label trial were examined. In the acute phase, 132 patients with mild‐to‐moderate active UC received MMX mesalazine 2.4–4.8 g/day for 8 weeks, while 206 patients with quiescent UC received MMX mesalazine 2.4 g/day for a 12‐month maintenance phase. Disease‐specific HRQL was measured at baseline and endpoint of each phase using the Short Inflammatory Bowel Disease Questionnaire (SIBDQ). Repeated‐measures anova models examined baseline‐endpoint changes in SIBDQ, stool frequency (SF), and rectal bleeding severity (RBS). Correlations assessed the associations between SIBDQ and SF/RBS scores, while ancova techniques tested the sensitivity of SIBDQ to disease recurrence.

Results

SIBDQ scores significantly increased for active mild‐to‐moderate UC patients following 8 weeks of treatment, while SIBDQ scores remained stable for quiescent UC patients following 12 months of treatment. Changes in SIBDQ scores correlated significantly with changes in SF and RBS scores. Patients with recurrent UC at maintenance phase endpoint had significantly lower SIBDQ scores than nonrecurrent patients.

Conclusions

Daily MMX mesalazine therapy was associated with significant improvement in disease‐specific HRQL for patients with mild‐to‐moderate active UC and with the maintenance of HRQL for patients with quiescent UC. In both patient groups, HRQL was significantly associated with disease activity.
Identification and management of poor response to growth‐promoting therapy in children with short stature
Authors: Bang Peter , Ahmed S. Faisal , Argente Jesús , Backeljauw Philippe , Bettendorf Markus , Bona Gianni , Coutant Régis , Rosenfeld Ron G. , Walenkamp Marie‐José , Savage Martin O.
Published: April 2012

Growth hormone (GH) is widely prescribed for children with short stature across a range of growth disorders. Recombinant human (rh) insulin‐like growth factor‐1 (rhIGF‐1) therapy is approved for severe primary IGF‐I deficiency – a state of severe GH resistance. Evidence is increasing for an unacceptably high rate of poor or unsatisfactory response to growth‐promoting therapy (i.e. not leading to significant catch up growth) in terms of change in height standard deviation score (SDS) and height velocity (HV) in many approved indications. Consequently, there is a need to define poor response and to prevent or correct it by optimizing treatment regimens within accepted guidelines. Recognition of a poor response is an indication for action by the treating physician, either to modify the therapy or to review the primary diagnosis leading either to discontinuation or change of therapy. This review discusses the optimal investigation of the child who is a candidate for GH or IGF‐1 therapy so that a diagnosis‐based choice of therapy and dosage can be made. The relevant parameters in the evaluation of growth response are described together with the definitions of poor response. Prevention of poor response is addressed by discussion of strategy for first‐year management with GH and IGF‐1. Adherence to therapy is reviewed as is the recommended action following the identification of the poorly responding patient. The awareness, recognition and management of poor response to growth‐promoting therapy will lead to better patient care, greater cost‐effectiveness and increased opportunities for clinical benefit.
Warming effects on the early decomposition of three litter types, Eastern Tibetan Plateau, China
Authors: Xu Z. F. , Pu X. Z. , Yin H. J. , Zhao C. Z. , Liu Q. , Wu F. Z.
Published: April 2012

Temperature and litter quality are two of the key factors controlling litter decomposition. Predicted global warming and vegetation succession will therefore have profound impacts. This study was conducted to assess effects of experimental warming on litter decomposition and nutrient dynamics of two contrasting tree species (red birch,Betula albosinensisBurk., and dragon spruce,Picea asperataMast.) and a mixture of the two with the heating cable method in the eastern Tibetan Plateau of China. This treatment raised surface soil temperature by 3.2°C and resulted in a 5.2% decline in soil moisture 10 cm below the soil surface. The water content of dragon spruce, red birch and mixed litter was decreased by 18, 11 and 13%, respectively. Marked differences between the two species in the decomposition rates and nutrient remaining percentages were detected. Moreover, we found positive, non‐additive effects of litter mixture. Experimental warming did not affect mass loss and nutrient release of dragon spruce litter but significantly increased mass loss and affected nutrient release of red birch and mixed litter during the early decomposition period. Overall, inter‐specific (red birch and dragon spruce) differences in decomposability were substantially larger than warming‐induced responses. Thus, a warming‐induced community succession towards dragon spruce forests in the Tibetan Plateau region could have a greater impact on early litter decomposition than warming itself.
Yield, quality and ensilage characteristics of whole‐crop maize and of the cob and stover components: harvest date and hybrid effects
Authors: Lynch J. P. , O’Kiely P. , Doyle E. M.
Published: April 2012

The objective of the study was to determine the effects of maize hybrid and harvest date on the yield, quality and subsequent conservation characteristics of whole‐crop, cob and stover silages. The experiment had a split‐plot design, with three main plots (date of harvest) and six subplots (hybrid) in each of three replicate blocks. Four maize hybrids (Tassilo, Beethoven, Andante and Nescio) were conventional hybrids used in commercial livestock production in Ireland, and two were categorized as high‐biomass hybrids (Atletico and KXA 7211). The three harvest dates – 16 September, 7 October and 28 October – represented early, normal and late harvests respectively. Averaged across hybrids, harvesting on 16 September reduced the DM yield (P < 0·05) and starch concentration (P < 0·01) of whole‐crop and cob, and decreased the neutral detergent fibre (P < 0·05) and acid detergent fibre (P < 0·01) contents of stover. Later harvesting date generally resulted in a more restricted, heterolactic fermentation that was associated with increased dry‐matter (DM) content at ensiling. Whole‐crop and stover from Atletico and KXA 7211 generally had higher DM yields (P < 0·05) and a more extensive fermentation compared to Tassilo, Andante and Nescio. Despite the high‐biomass hybrids having a higher DM yield than conventional hybrids, the high‐biomass hybrids had a lower (P < 0·05) content of cob and a corresponding higher (P < 0·05) content of stover. The changes in proportions of cob and stover in whole‐crop maize with later harvesting significantly influenced its silage digestibility and conservation characteristics.
Evaluating population recovery for sea turtles under nesting beach protection while accounting for nesting behaviours and changes in availability
Authors: Thorson James T. , Punt André E. , Nel Ronel
Published: April 2012

1. Sea turtles and sea birds generally have high conservation importance world‐wide and are often difficult to survey except when present on nesting grounds. Consequently, many such surveys tag nesting individuals and use tag‐resighting models to estimate population size and assess anthropogenic impacts. However, the conventional Cormac–Jolly–Seber (CJS) tag‐resighting model is problematic for these species for three reasons: individuals often return to nesting areas in alternating years because of high energetic costs for nesting, estimated detectability confounds changes in survey efficiency with availability on the surveyed beach, and tag loss is confounded with mortality.

2. We develop a robust design model that uses higher‐order Markovian transitions to approximate skip‐nesting behaviours and incorporates multiple observations for each nesting individual to estimate changes in availability (the probability of returning to the surveyed area rather than alternative nesting areas). We approximate time‐varying effects using a flexible spline method and demonstrate the model using data for leatherback sea turtles Dermochelys coriacea and loggerhead sea turtles Caretta caretta in South Africa.

3. The apparent lack of recovery for leatherback sea turtles after implementing beach protection, as observed in nest count data, is likely to be due to declining detectability caused by decreased availability during population recovery (e.g. habitat expansion). By contrast, loggerhead sea turtles have approximately constant detectability and stable abundance since the 1970s.

4. We find that increased fishing effort has no explanatory power regarding changes in survival for either species.

5. Synthesis and applications. Based on study results, we recommend that future tag‐resighting programmes for sea turtles and birds are accompanied periodically by count surveys beyond the regularly monitored nesting areas to evaluate evidence of range expansion. However, the identification of range expansion in historical data is only possible using model‐based inference and robust design methods such as presented in this study.
Impact of Pleistocene aridity oscillations on the population history of a widespread, vagile Australian mammal, Macropus fuliginosus
Authors: Neaves Linda E. , Zenger Kyall R. , Prince Robert I. T. , Eldridge Mark D. B.
Published: April 2012

Aim  Climatic fluctuations during the Pleistocene have shaped the population structure of many extant taxa. However, few studies have examined widespread species inhabiting the Australian continent, where periods of increased aridity characterized the Pleistocene. Here we investigate the phylogeography and population history of a widespread and vagile southern Australian marsupial, the western grey kangaroo (Macropus fuliginosus).

Location  Southern Australia.

Methods  We examined the variation of the mitochondrial DNA (mtDNA) control region from 511 individuals of M. fuliginosus sampled throughout their transcontinental distribution. Maximum likelihood and Bayesian analyses were used to investigate the phylogeography and coalescence analyses were then used to test hypothesized biogeographical scenarios.

Results  The combined results of the phylogeographical and coalescence analyses revealed a complex evolutionary history. Macropus fuliginosus originated in the south‐west of the continent, with north‐western and south‐western populations subsequently diverging as a result of vicariance events during the mid‐Pleistocene. Subsequent arid phases affected these populations differently. In the north‐west, the expansion and contraction of the arid zone resulted in repeated vicariance events and multiple divergent north‐western mtDNA subclades. In contrast, the south‐western population was less impacted by climatic oscillations but gave rise to a major transcontinental eastward expansion.

Main conclusions  Macropus fuliginosus exhibits the genetic signature of divergence due to unidentified barriers in south‐western Western Australia, while previously identified barriers across southern Australia appear to have had little impact despite evidence of a broad‐scale range expansion prior to the Last Glacial Maximum (LGM). This pattern of localized expansion and contraction is comparable to unglaciated regions in both the Northern and Southern Hemispheres. Furthermore, this study indicates that despite the potential similarities between Northern Hemisphere glaciation and the activation of dune systems in the Australian arid zone, both of which rendered large areas inhospitable, the biotic responses and resultant phylogeographical signatures are dissimilar. Whereas a limited number of major geographically concordant refugia are observed in glaciated areas, the Southern Hemisphere arid zone appears to be associated with multiple species‐specific idiosyncratic refugia.
Patterns in body size and melanism along a latitudinal cline in the wingless grasshopper,Phaulacridium vittatum
Authors: Harris Rebecca , McQuillan Peter , Hughes Lesley
Published: April 2012

Aim We explore geographic variation in body size within the wingless grasshopper,Phaulacridium vittatum, along a latitudinal gradient, and ask whether melanism can help explain the existence of clinal variation. We test the hypotheses that both male and female grasshoppers will be larger and lighter in colour at lower latitudes, and that reflectance and size will be positively correlated, as predicted by biophysical theory. We then test the hypothesis that variability in size and reflectance is thermally driven, by assessing correlations with temperature and other climatic variables.

Location Sixty‐one populations were sampled along the east coast of Australia between latitudes 27.63° S and 43.10° S, at elevations ranging from 10 to 2000 m a.s.l.

Methods Average reflectance was used as a measure of melanism and femur length as an index of body size for 198 adult grasshoppers. Climate variables were generated by BIOCLIM for each collection locality. Hierarchical partitioning was used to identify those variables with the most independent influence on grasshopper size and reflectance.

Results Overall, there was no simple relationship between size and latitude inP. vittatum.Female body size decreased significantly with latitude, while male body size was largest at intermediate latitudes. Rainfall was the most important climatic variable associated with body size of both males and females. Female body size was also associated with radiation seasonality and male body size with reflectance. The reflectance of females was not correlated with latitude or body size, while male reflectance was significantly higher at intermediate latitudes and positively correlated with body size. Analyses of climate variables showed no significant association with male reflectance, while female reflectance was significantly related to the mean temperature of the driest quarter.

Main conclusions Geographic variation in the body size of the wingless grasshopper is best explained in terms of rainfall and radiation seasonality, rather than temperature. However, melanism is also a significant influence on body size in male grasshoppers, suggesting that thermal fitness does play a role in determining adaptive responses to local conditions in this sex.
A 95 kDa protein of Plasmodium vivax and P. cynomolgi visualized by three‐dimensional tomography in the caveola–vesicle complexes (Schüffner's dots) of infected erythrocytes is a member of the PHIST family
Authors: Akinyi Sheila , Hanssen Eric , Meyer Esmeralda V. S. , Jiang Jianlin , Korir Cindy C. , Singh Balwan , Lapp Stacey , Barnwell John W. , Tilley Leann , Galinski Mary R.
Published: April 2012

Plasmodium vivax and P. cynomolgi produce numerous caveola–vesicle complex (CVC) structures within the surface of the infected erythrocyte membrane. These contrast with the electron‐dense knob protrusions expressed at the surface of Plasmodium falciparum‐infected erythrocytes. Here we investigate the three‐dimensional (3‐D) structure of the CVCs and the identity of a predominantly expressed 95 kDa CVC protein. Liquid chromatography – tandem mass spectrometry analysis of immunoprecipitates by monoclonal antibodies from P. cynomolgi extracts identified this protein as a member of the Plasmodium helical interspersed subtelomeric (PHIST) superfamily with a calculated mass of 81 kDa. We named the orthologous proteins PvPHIST/CVC‐8195 and PcyPHIST/CVC‐8195, analysed their structural features, including a PEXEL motif, repeated sequences and a C‐terminal PHIST domain, and show that PHIST/CVC‐8195 is most highly expressed in trophozoites. We generated images of CVCs in 3‐D using electron tomography (ET), and used immuno‐ET to show PHIST/CVC‐8195 localizes to the cytoplasmic side of the CVC tubular extensions. Targeted gene disruptions were attempted in vivo. The pcyphist/cvc‐8195 gene was not disrupted, but parasites containing episomes with the tgdhfr selection cassette were retrieved by selection with pyrimethamine. This suggests that PHIST/CVC‐8195 is essential for survival of these malaria parasites.
Enhanced Cellular Immune Response Elicited by a DNA Vaccine Fused with Ub Against Mycobacterium tuberculosis
Authors: Wang Q.‐M. , Tang Y. , Lei Ch.‐X. , Shi F.‐Zh. , Liu Q.‐H.
Published: April 2012

This study evaluated the immune response elicited by a Ub‐fused Ag85A DNA vaccine against Mycobacterium tuberculosis. BALB/c mice were vaccinated with plasmid DNA encoding Ag85A protein, Ub‐fused Ag85A DNA vaccine (UbGR‐Ag85A) and negative DNA vaccines, respectively. Ag85A DNA vaccine immunization induced a Thl‐polarized immune response. The production of Thl‐type cytokine (IFN‐γ) and proliferative T cell responses was enhanced significantly in mice immunized with UbGR‐Ag85A fusion DNA vaccine, compared with non‐fusion DNA vaccine. Moreover, this fusion DNA vaccine also resulted in an increased relative ratio of IgG2a to IgGl and the cytotoxicity of T cells. IFN‐γ intracellular staining of splenocytes indicated that UbGR‐Ag85A fusion DNA vaccine activated CD4+ and CD8+ T cells, particularly CD8+ T cells. Thus, this study demonstrated that the UbGR‐Ag85A fusion DNA vaccine inoculation could improve antigen‐specific cellular immune responses, which is helpful for protection against TB infection.
Molecular phylogeny of the North American Simulium malyschevi‐group species (Diptera: Simuliidae)
Authors: CONFLITTI IDA M. , SPIRONELLO MICHAEL , CURRIE DOUGLAS C.
Published: April 2012

We investigated species limits and phylogenetic relationships among chromosomally distinct North American members of the Simulium malyschevi species‐group. Maximum parsimony and Bayesian analyses were conducted based on 12S, COII, cyt b and ITS‐1 gene sequences. In terms of species limits, monophyly was highly supported for each chromosomally and morphologically distinct taxon analysed (S. decimatum, S. defoliarti, S. malyschevi, and S. murmanum). In contrast, support for monophyly of morphologically homogeneous S. arcticum complex members was significant only in one case (S. saxosum) and not the other (S. negativum). Considering the overall topology, three principal conclusions were drawn: (i) the status of S. subvariegatum as a member of the S. malyschevi species‐group remains uncertain. This species either was excluded from the malyschevi‐group or formed a sister group with S. malyschevi at the base of the tree; (ii) although S. murmanum and S. decimatum branch after S. malyschevi, the position of the two species relative to each other remains unresolved; and (iii) the structurally homogeneous S. arcticum species complex was not monophyletic due to the inclusion of S. defoliarti. Further investigation may warrant changes to current malyschevi‐group classification. Molecular datasets alone may be insufficient for resolving relationships among particular lineages of black flies.
FTIR spectra of algal species can be used as physiological fingerprints to assess their actual growth potential
Authors: Jebsen Christian , Norici Alessandra , Wagner Heiko , Palmucci Matteo , Giordano Mario , Wilhelm Christian
Published: April 2012

Fourier transform infrared (FTIR) spectra were measured from cells of Microcystis aeruginosa and Protoceratium reticulatum, whose growth rates were manipulated by the availability of nutrients or light. As expected, the macromolecular composition changed in response to the treatments. These changes were species‐specific and depended on the type of perturbation applied to the growth regime. Microcystis aeruginosa showed an increase in the carbohydrate‐to‐protein ratio with decreased growth rates, under nutrient limitation, whereas light limitation induced a decrease of the carbohydrate‐to‐protein ratio with decreasing proliferation rates. The macromolecular pools of P. reticulatum showed a higher degree of compositional homeostasis. Only when the lowest light irradiance and nutrient availability were supplied, an increase of the carbohydrate‐to‐protein FTIR absorbance ratio was observed. A species‐specific partial least squares (PLS) model was developed using the whole FTIR spectra. This model afforded a very high correlation between the predicted and the measured growth rates, regardless of the growth conditions. On the contrary, the prediction based on absorption band ratios generally used in FTIR studies would strongly depend on growth conditions. This new computational method could constitute a substantial improvement in the early warning systems of algal blooms and, in general, for the study of algal growth, e.g. in biotechnology. Furthermore, these results confirm the suitability of FTIR spectroscopy as a tool to map complex biological processes like growth under different environmental conditions.
Partial Characterization of Spiroplasma citri Isolates Associated with Necrotic Yellows Disease of Safflower in Iran
Authors: Khanchezar Amin , Izadpanah Keramat , Salehi Mohammad
Published: April 2012

Spiroplasma citri was associated with a disease of safflower characterized by stunting, yellowing, phloem discoloration and local or general necrosis in the Fars province of Iran. It was identified by ELISA using a locally produced polyclonal antiserum, by PCR with specific primers and isolation in culture medium. The 16S rDNA restriction fragment length polymorphism patterns of safflower isolates were identical with those of the other S. citri isolates. A known isolate of S. citri from periwinkle induced stunting, yellowing, phloem discoloration and wilting in safflower seedlings when transmitted by dodder under greenhouse conditions. A primer pair designed on the basis of S. citri plasmid was more sensitive than those based on spiralin gene or 16S rDNA for the detection of S. citri. Based on the sequence of the spiralin gene, S. citri isolates from safflower as well as other Iranian isolates were variable and grouped into two genetic clusters with 91.9–92.9% identity between groups. This is the first report of association of S. citri with a safflower disease.