bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calcium‐ and polyphosphate‐containing acidocalcisomes in chicken egg yolk
Authors: Ramos Isabela B. , Miranda Kildare , Ulrich Paul , Ingram Peter , LeFurgey Ann , Machado Ednildo A. , de Souza Wanderley , Docampo Roberto 
Published: March 2010

Background information. Poly P (inorganic polyphosphate) is a polymer formed by Pi residues linked by high‐energy phosphoanhydride bonds. The presence of poly P in bacteria, fungi, algae and protists has been widely recognized, but the distribution of poly P in more complex eukaryotes has been poorly studied. Poly P accumulates, together with calcium, in acidic vesicles or acidocalcisomes in a number of organisms and possesses a diverse array of functions, including roles in stress response, blood clotting, inflammation, calcification, cell proliferation and apoptosis.Results. We report here that a considerable amount of phosphorus in the yolk of chicken eggs is in the form of poly P. DAPI (4′,6‐diamidino‐2‐phenylindole) staining showed that poly P is localized mainly in electron‐dense vesicles located inside larger vacuoles (compound organelles) that are randomly distributed in the yolk. These internal vesicles were shown to contain calcium, potassium, sodium, magnesium, phosphorus, chlorine, iron and zinc, as detected by X‐ray microanalysis and elemental mapping. These vesicles stain with the acidophilic dye Acridine Orange. The presence of poly P in organellar fractions of the egg yolk was evident in agarose gels stained with Toluidine Blue and DAPI. Of the total phosphate (Pi) of yolk organelles, 16% is present in the form of poly P. Total poly P content was not altered during the first 4 days of embryogenesis, but poly P chain length decreased after 1 day of development.Conclusions. The results of the present study identify a novel organelle in chicken egg yolk comprising acidic vesicles with a morphology, physiology and composition similar to those of acidocalcisomes, within larger acidic vacuoles. The elemental composition of these acidocalcisomes is proportionally similar to the elemental composition of the yolk, suggesting that most of these elements are located in these organelles, which might be an important storage compartment in eggs.
Cross-species common regulatory network inference without requirement for prior gene affiliation
Authors: Gholami Amin Moghaddas , Fellenberg Kurt 
Published: March 2010

AbstractMotivation: Cross-species meta-analyses of microarray data usually require prior affiliation of genes based on orthology information that often relies on sequence similarity.Results: We present an algorithm merging microarray datasets on the basis of co-expression alone, without any requirement for orthology information to affiliate genes. Combining existing methods such as co-inertia analysis, back-transformation, Hungarian matching and majority voting in an iterative non-greedy hill-climbing approach, it affiliates arrays and genes at the same time, maximizing the co-structure between the datasets. To introduce the method, we demonstrate its performance on two closely and two distantly related datasets of different experimental context and produced on different platforms. Each pair stems from two different species. The resulting cross-species dynamic Bayesian gene networks improve on the networks inferred from each dataset alone by yielding more significant network motifs, as well as more of the interactions already recorded in KEGG and other databases. Also, it is shown that our algorithm converges on the optimal number of nodes for network inference. Being readily extendable to more than two datasets, it provides the opportunity to infer extensive gene regulatory networks.Availability and Implementation: Source code (MATLAB and R) freely available for download at http://www.mchips.org/supplements/moghaddasi_source.tgzContact: kurt@tum.deSupplementary information: Supplementary data are available at Bioinformatics online.
Modeling sample variables with an Experimental Factor Ontology
Authors: Malone James , Holloway Ele , Adamusiak Tomasz , Kapushesky Misha , Zheng Jie , Kolesnikov Nikolay , Zhukova Anna , Brazma Alvis , Parkinson Helen 
Published: March 2010

Abstract
Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users.
Results: We present the Experimental Factor Ontology, designed to meet cross-domain, application focused use cases for gene expression data. We describe our methodology and open source tools used to create the ontology. These include tools for creating ontology mappings, ontology views, detecting ontology changes and using ontologies in interfaces to enhance querying. The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way.
Availability: http://www.ebi.ac.uk/efo
Contact: malone@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Brown Rot on Plum Caused by Monilia polystroma in China
Authors: Zhu X. Q. , Guo L. Y. 
Published: March 2010

In August 2008, mummies of dwarf sweet plum (Prunus aitianli) fruit covered with grayish, conidial tufts were found in an orchard in Mudanjiang City of Heilongjiang in China. Conidial masses were touched with a sterilized wire loop and streaked onto the surface of water agar (WA) plates. After incubating at 22 ± 2°C for 16 to 24 h, individual germinated spores were picked out with a sterilized scalpel blade under a microscope in a laminar flow cabinet, and transferred to potato dextrose agar (PDA) in petri dishes. Mycelium grew an average of 10.7 mm per day on PDA and formed a white-to-grayish colony with irregular, black stroma 12 days after incubation at 22 ± 2°C under 12-h light/12-h dark. The average size of stroma was 8.19 cm2 per petri dish 37 days after incubation in the dark. The conidia were one-celled, hyaline, lemon-shaped, 15.2 (10.8 to 18.9) × 10.9 (8.3 to 16.3) μm, and arranged in branched monilioid chains on inoculated apples. The PCR products of internal transcribed spacer (ITS) region 1 and 2 and 5.8S gene of the ribosomal RNA amplified with primers ITS1 and ITS4 was directly sequenced in both directions using the PCR primers. The sequence of the Monilia polystroma isolate (GenBank Accession No. GU067539) was identical to the reference isolate of M. polystroma (CBS102686), containing five nucleotides that distinguish it from Monilinia fructigena (1,3). The pathogen was identified as M. polystroma on the basis of morphological characteristics (3) and the sequence of internal transcribed spacer (ITS) region 1 and 2 and 5.8S gene of the ribosomal RNA. Pathogenicity was confirmed by inoculating surface-sterilized, mature plum and apple fruit wounded with a nail, with a mycelial plug (5 mm in diameter) of the fungus at each wound. Fruit treated with plain PDA plugs were used as a control. Inoculated fruits were placed in a sterilized moist chamber at room temperature (23 to 28°C). Fifteen plums and nine apples were used in each of two replicated tests. All inoculated fruit developed typical brown rot symptoms 4 days after inoculation, while the control fruit remained healthy. M. polystroma was reisolated from the inoculated fruit and identified by the above methods. M. polystroma was first reported on apple in Japan (3) and it was recently discovered in an apple orchard in Hungary (2). Although the occurrence of Monilinia fructicola, Monilinia laxa, and Monilinia fructigena (teleomorphs of the three Monilia spp.) in China have been documented, to our knowledge, this is the first report of the occurrence of M. polystroma in China. References: (1) C. E. Fulton et al. Eur. J. Plant Pathol. 105:495, 1999. (2) M. Petróczy and L. Palkovics. Eur. J. Plant Pathol. 125:343, 2009. (3) G. C. M. van Leeuwen et al. Mycol. Res. 106:444, 2002.
First Report of ‘Candidatus Liberibacter asiaticus’ Associated with Huanglongbing in Sweet Orange in Ethiopia
Authors: Saponari M. , De Bac G. , Breithaupt J. , Loconsole G. , Yokomi R. K. , Catalano L. 
Published: March 2010

Huanglongbing (HLB) is a serious disease of citrus worldwide. Three different ‘Candidatus Liberibacter’ species are associated with HLB: ‘Ca. Liberibacter asiaticus’, ‘Ca. L. africanus’, and ‘Ca. L. americanus’ (1). ‘Ca. L. africanus’ and its vector, Trioza erytreae, are both heat sensitive, and when present, occur in citrus when temperatures remain below 30 to 32°C. In Africa, ‘Ca. L. africanus’ and T. erytreae have been reported in South Africa, Zimbabwe, Malawi, Burundi, Kenya, Somalia, Ethiopia, Cameroon, and Madagascar (1). Inspection of citrus trees in orchards and budwood sources in nurseries located in the warmer citrus-growing areas of Tigray and North Wollo in northern Ethiopia revealed nearly 100 trees with symptoms of leaf yellowing with a blotchy mottle pattern, dead branches, and decreased fruit quality and yield. Two symptomatic sweet orange budwood trees and three symptomatic orchard plants were sampled in April 2009, along with three healthy-looking sweet orange plants. DNA was extracted from 200 mg of desiccated leaf midribs using the CTAB method (4) and subjected to conventional PCR using the primer pairs A2/J5 (2) and OI2/23S1 (3) that amplify the ribosomal protein gene in the rplKAJL-rpoBC operon and the 16S/23S ribosomal intergenic regions, respectively, of ‘Ca. L. africanus’ and ‘Ca. L. asiaticus’. Positive PCR reactions were obtained for all five symptomatic samples with both primer pairs. PCR amplicons of 703 bp (A2/J5) and 892 bp (OI2/23S) recovered from two of these samples were purified, cloned, and sequenced. BLAST analysis revealed that the nucleotide sequences we obtained for the ribosomal protein (GenBank Accessions Nos. GQ890155 and GQ890156) shared 100% identity with each other and 99% identity with sequences of ‘Ca. L. asiaticus’ from Brazil (DQ471904), Indonesia (AB480161), China (DQ157277), and Florida (CP001677). Similarly, the 16S/23S ribosomal intergenic sequences (GU296538 and GU296539) shared 100% identity with each other and 99% identity with homologous ‘Ca. L. asiaticus’ sequences from Brazil (DQ471903), Indonesia (AB480102), China (DQ778016), and Florida (CP001677) and contained two tRNA genes as occurs in ‘Ca. L. asiaticus’ but not in ‘Ca. L. africanus’ (3). To our knowledge, this is the first report of ‘Ca. L. asiaticus’ in Africa. The presence of ‘Ca. L. asiaticus’ is a threat for warmer citrus-growing areas of Africa that are less favorable for ‘Ca. L. africanus’ and T. erytreae. In areas where ‘Ca. L. asiaticus’ was confirmed, symptomatic trees must be promptly eradicated and surveys to determine spread of the disease and its vectors are necessary. References: (1) J. M. Bove. J. Plant Pathol. 88:7, 2006. (2) A. Hocquellet et al. Mol. Cell. Probes 13:373, 1999. (3) S. Jagoueix et al. Int. J. Syst. Bacteriol. 47:224, 1997. (4) M. G. Murray and W. F Thompson. Nucleic Acids Res. 8:4321, 1980.
First Report of Rhizoctonia solani Causing a Disease of Sunflower in India
Authors: Srinivasan K. , Visalakchi S. 
Published: March 2010

During the spring of 2009, symptoms including leaf yellowing and wilting, root rot, and death of plants were noted in sunflower (Helianthus annuus L.) crops in Dharmapuri District, Tamilnadu, India. In some fields, approximately 30% of the plants were affected. The disease began when plants were approximately 10 weeks old and occurred on scattered or adjacent plants. The presence of white mycelium was observed on necrotic crowns. Symptomatic tissue was surface disinfested in 70% alcohol for 30 s and 0.5% sodium hypochlorite for 1 min and plated onto potato dextrose agar (PDA) (1). One isolate (coded SV001) had near right-angle branching with basal constriction and adjacent septa and sclerotia typical of Rhizoctonia spp. (2). Cream-colored colonies produced irregular, light brown sclerotia that were 3.0 to 7.3 mm (average 3.8 mm) in diameter. Hyphae were 6.8 to 7.0 μm (average 6.9 μm) wide and multinucleate (8 to 15 nuclei per cell). On the basis of hyphal anastomosis with several known AG testers, the fungus was characterized as Rhizoctonia solani Kühn AG-IV (3). One culture was deposited at the Madras University Botany Laboratory, Center for Advanced Studies in Botany, University of Madras, Chennai, India. In a pathogenicity test, R. solani SV001 was grown on PDA for 5 days at 24°C in the dark. Five-millimeter-diameter disks were placed at the base of sunflower plants (cv. Mordan). Four sunflower plants in each of three pots were inoculated; noninoculated plants served as controls. Plants were placed in a glasshouse maintained at 25 to 27°C. Inoculated plants developed yellow foliage and crown rot and root rot symptoms after 7 to 12 days and died in 17 to 20 days. No symptoms were observed on noninoculated plants. The pathogen was reisolated from fragments of necrotic crown tissue of inoculated plants. To our knowledge, this is the first report of R. solani AG-IV causing a disease of sunflower plants in India. References: (1). R. C. Fenille et al. Plant Pathol. 54:325, 2005. (2). J. R. Parmeter et al. Phytopathology 59:1270, 1969. (3) B. Sneh et al. Identification of Rhizoctonia Species. The American Phytopathological Society, St Paul, MN, 1991.
The Protein Kinase SnRK2.6 Mediates the Regulation of Sucrose Metabolism and Plant Growth in Arabidopsis
Authors: Zheng Zhifu , Xu Xiaoping , Crosley Rodney A. , Greenwalt Scott A. , Sun Yuejin , Blakeslee Beth , Wang Lizhen , Ni Weiting , Sopko Megan S. , Yao Chenglin , Yau Kerrm , Burton Stephanie , Zhuang Meibao , McCaskill David G. , Gachotte Daniel , Thompson Mark , Greene Thomas W. 
Published: March 2010

Abstract
In higher plants, three subfamilies of sucrose nonfermenting-1 (Snf1)-related protein kinases have evolved. While the Snf1-related protein kinase 1 (SnRK1) subfamily has been shown to share pivotal roles with the orthologous yeast Snf1 and mammalian AMP-activated protein kinase in modulating energy and metabolic homeostasis, the functional significance of the two plant-specific subfamilies SnRK2 and SnRK3 in these critical processes is poorly understood. We show here that SnRK2.6, previously identified as crucial in the control of stomatal aperture by abscisic acid (ABA), has a broad expression pattern and participates in the regulation of plant primary metabolism. Inactivation of this gene reduced oil synthesis in Arabidopsis (Arabidopsis thaliana) seeds, whereas its overexpression increased Suc synthesis and fatty acid desaturation in the leaves. Notably, the metabolic alterations in the SnRK2.6 overexpressors were accompanied by amelioration of those physiological processes that require high levels of carbon and energy input, such as plant growth and seed production. However, the mechanisms underlying these functionalities could not be solely attributed to the role of SnRK2.6 as a positive regulator of ABA signaling, although we demonstrate that this kinase confers ABA hypersensitivity during seedling growth. Collectively, our results suggest that SnRK2.6 mediates hormonal and metabolic regulation of plant growth and development and that, besides the SnRK1 kinases, SnRK2.6 is also implicated in the regulation of metabolic homeostasis in plants.
Tobraviruses—plant pathogens and tools for biotechnology
Authors: MACFARLANE STUART A. 
Published: March 2010

SUMMARYThe tobraviruses,Tobacco rattle virus(TRV),Pea early‐browning virus(PEBV) andPepper ringspot virus(PepRSV), are positive‐strand RNA viruses with rod‐shaped virus particles that are transmitted between plants by trichodorid nematodes. As a group, these viruses infect many plant species, with TRV having the widest host range. Recent studies have begun to dissect the interaction of TRV with potato, currently the most commercially important crop disease caused by any of the tobraviruses. As well as being successful plant pathogens, these viruses have become widely used as vectors for expression in plants of nonviral proteins or, more frequently, as initiators of virus‐induced gene silencing (VIGS). Precisely why tobraviruses should be so effective as VIGS vectors is not known; however, molecular studies of the mode of action of the tobravirus silencing suppressor protein are shedding some light on this process.
A New Method for the Determination of Carbon Monoxide in Blood
Authors: WKNNESLAND R. 
Published: March 2010

Summary.A new method for the determination of carbon monoxide in blood is described. The blood is brought into an Erlenmeyer flask, mixed with water and its carbon monoxide hemoglobin is converted into acid hematin by addition of sulfuric acid. The carbon monoxide liberated passes into another Erlenmeyer flask, which has been connected with the first one by an airtight rubber cuff and contains a known solution of palladium chloride. A corresponding quantity of the latter is reduced to metallic palladium. Excessive palladium chloride is precipitated by a known quantity of potassium iodide, and the excess of the latter is titrated after the principle of Dupré‐Winkler. The method is well fitted for micro‐analysis.
A Parapharyngeal Method of Hypophysectomy in Babbits
Authors: JACOBSOHN DORA , WESTMAN AXEL 
Published: March 2010

Summary.A technic of hypophysectomy in rabbits is described. The parapharyngeal route is taken and the operation done according to the principles of hypophysectomy in rats, but modified to suit the anatomy of the rabbit. The method has great advantages. It enables direct inspection of the field of operation. The operative risk is slight. The mortality is extremely low.This work has been aided by a grant from « Stiftelsen Therese och Johan Anderssons Minne», Stockholm.
Effect of lesogaberan, a novel GABAB‐receptor agonist, on transient lower oesophageal sphincter relaxations in male subjects
Authors: BOECKXSTAENS G. E. , RYDHOLM H. , LEI A. , ADLER J. , RUTH M. 
Published: March 2010

Aliment Pharmacol Ther 31, 1208–1217SummaryBackground  Transient lower oesophageal sphincter relaxations (TLESRs) are a major mechanism behind gastro‐oesophageal reflux disease (GERD).Aim  To assess the effect of lesogaberan (AZD3355) – a novel peripherally active GABAB receptor agonist – on TLESRs.Methods  Twenty‐four healthy men were enrolled in this single‐blind, placebo‐controlled, randomized, single‐centre, three‐period crossover phase 1 study. Subjects were randomized to receive single oral doses of lesogaberan (0.8 mg/kg), baclofen (40 mg) and placebo, separated by washout periods of ≤7 days. Subjects finished a meal 1 h after the dose. Oesophageal manometry and pH‐metry measurements were taken during the 3 h after the meal.Results  Twenty‐one subjects completed the study. Compared with placebo, lesogaberan 0.8 mg/kg significantly reduced the number of TLESRs by 36% [geometric mean ratio (GMR): 0.64; 95% confidence interval (CI): 0.51–0.82] and significantly reduced the number of acid reflux episodes (mean reduction: 1.6; 95% CI: 0.34–2.9). Lesogaberan also significantly increased lower oesophageal sphincter (LES) pressure by 39% compared with placebo (GMR: 1.39; 95% CI: 1.18–1.64). Comparable results were observed with baclofen. Similar numbers of adverse events were reported by subjects taking lesogaberan and placebo.Conclusion  Compared with placebo, lesogaberan significantly reduced TLESRs and acid reflux episodes and increased LES pressure.
Antacids and dietary supplements with an influence on the gastric pH increase the risk for food sensitization
Authors: Pali‐Schöll I. , Herzog R. , Wallmann J. , Szalai K. , Brunner R. , Lukschal A. , Karagiannis P. , Diesner S. C. , Jensen‐Jarolim E. 
Published: March 2010

SummaryBackground
Elevation of the gastric pH increases the risk for sensitization against food allergens by hindering protein breakdown. This can be caused by acid‐suppressing medication like sucralphate, H2‐receptor blockers and proton pump inhibitors, as shown in recent murine experimental and human observational studies.Objective
The aim of the present study was to assess the sensitization capacity of the dietary supplement base powder and of over‐the‐counter antacids.Methods
Changes of the pH as well as of protein digestion due to base powder or antacids were measured in vitro. To examine the in vivo influence, BALB/c mice were fed codfish extract with one of the acid‐suppressing substances. Read‐out of antibody levels in the sera, of cytokine levels of stimulated splenocytes and of intradermal skin tests was performed.Results
The pH of hydrochloric acid was substantially increased in vitro by base powder as well as antacids in a time‐ and dose‐dependent manner. This elevation hindered the digestion of codfish proteins in vitro. A significant increase in codfish‐specific IgE antibodies was found in the groups fed codfish combined with Rennie® Antacidum or with base powder; the latter also showed significantly elevated IgG1 and IgG2a levels. The induction of an anaphylactic immune response was proven by positive results in intradermal skin tests.Conclusions
Antacids and dietary supplements influencing the gastric pH increase the risk for sensitization against allergenic food proteins. As these substances are commonly used in the general population without consulting a physician, our data may have a major practical and clinical impact. Cite this as: I. Pali‐Schöll, R. Herzog, J. Wallmann, K. Szalai, R. Brunner, A. Lukschal, P. Karagiannis, S. C. Diesner and E. Jensen‐Jarolim, Clinical & Experimental Allergy, 2010 (40) 1091–1098.
Plasma levels of matrix metalloproteinase‐9 in chronic urticaria patients correlate with disease severity and C‐reactive protein but not with circulating histamine‐releasing factors
Authors: Tedeschi A. , Asero R. , Lorini M. , Marzano A. V. , Cugno M. 
Published: March 2010

SummaryBackground
Matrix metalloproteinase‐9 (MMP‐9) is an endopeptidase produced by many inflammatory cells that has been found in increased amounts in plasma from patients with chronic urticaria (CU).Objective
To evaluate plasma levels of MMP‐9 and its tissue inhibitor of metalloproteinase‐1 (TIMP‐1) in CU patients in relation with disease severity, C‐reactive protein (CRP) and circulating histamine‐releasing factors.Methods
Fifty‐two consecutive CU patients were included in the study and disease activity was graded from 0 to 3. Plasma MMP‐9, TIMP‐1 and CRP levels were measured by enzyme immunoassays. Circulating histamine‐releasing factors were assessed using in vivo (autologous serum skin test) and in vitro (basophil histamine release) tests. Seven CU patients were studied both during active disease and during remission. Thirty healthy subjects were used as normal controls.Results
Plasma levels of MMP‐9, TIMP‐1 and CRP were significantly higher in CU patients than in healthy controls (P=0.0001, 0.003 and 0.005, respectively) and a trend towards a higher MMP‐9/TIMP‐1 molar ratio was found (P=0.051). A significant correlation was found between plasma MMP‐9 levels and urticaria severity score (r=0.48, P<0.0001). CRP levels correlated with MMP‐9 levels (r=0.37, P=0.008) and CU severity score (r=0.52, P=0.0001), but not with TIMP‐1 (r=0.13) concentrations. MMP‐9, TIMP‐1 and CRP plasma levels and MMP‐9/TIMP‐1 molar ratio did not differ in patients either with or without an evidence of circulating histamine‐releasing factors. Seven patients evaluated during remission showed a significant reduction of MMP‐9 and CRP plasma levels.Conclusion
Plasma levels of MMP‐9 and its inhibitor TIMP‐1 are increased in CU patients. MMP‐9 levels are associated with disease severity and CRP levels, but not with skin reactivity to autologous serum and with circulating histamine‐releasing factors. These findings suggest that in CU there is an ongoing inflammatory process independent of the presence of circulating histamine‐releasing factors.