bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative analysis of wine yeast gene expression profiles under winemaking conditions
Authors: Varela Cristian , Cárdenas Javier , Melo Francisco , Agosin Eduardo 
Published: April 2005

AbstractWine fermentation is a dynamic and complex process in which the yeast cell is subjected to multiple stress conditions. A successful adaptation involves changes in gene expression profiles where a large number of genes are up‐ or downregulated. Functional genomic approaches are commonly used to obtain global gene expression profiles, thereby providing a comprehensive view of yeast physiology. We used SAGE to quantify gene expression profiles in an industrial strain of Saccharomyces cerevisiae under winemaking conditions. The transcriptome of wine yeast was analysed at three stages during the fermentation process, mid‐exponential phase, and early‐ and late‐stationary phases. Upon correlation with the yeast genome, we found three classes of transcripts: (a) sequences that corresponded to ORFs; (b) expressed sequences from intergenic regions; and (c) messengers that did not match the published reference yeast genome. In all fermentation phases studied, the most highly expressed genes related to energy production and stress response. For many pathways, including glycolysis, different transcript levels were observed during each phase. Different isoenzymes, including hexose transporters (HXT), were differentially induced, depending on the growth phase. About 10% of transcripts matched non‐annotated ORF regions within the yeast genome and could correspond to small novel genes originally omitted in the first gene annotation effort. Up to 22% of transcripts, particularly at late‐stationary phase, did not match any known location within the genome. As the available reference yeast genome was obtained from a laboratory strain, these expressed sequences could represent genes only expressed by an industrial yeast strain. Further studies are necessary to identify the role of these potential genes during wine fermentation. Copyright © 2005 John Wiley & Sons, Ltd.
Rapid enrichment and analysis of yeast phosphoproteins using affinity chromatography, 2D‐PAGE and peptide mass fingerprinting
Authors: Makrantoni Vasso , Antrobus Robin , Botting Catherine H. , Coote Peter J. 
Published: April 2005

AbstractA combination of affinity purification, 2D‐PAGE and peptide mass fingerprinting was employed to study the phosphoprotein complement of Saccharomyces cerevisiae. Protein extracts were first passed through a phosphoprotein affinity column, and the phosphoprotein‐enriched eluate fractions were then separated on 2D gels and visualized by staining with SYPRO Ruby. Proteins were excised from the gels and identified by peptide mass fingerprinting; 11/13 protein spots identified from a gel of the phosphoprotein‐enriched fraction had prior published evidence indicating that they were phosphoproteins. Additional experiments using a specific stain for phosphoproteins, prior incubation of the protein extract with alkaline phosphatase and blotting with monoclonal antibodies to phosphothreonine, phosphoserine and phosphotyrosine demonstrated that the phosphoprotein affinity column was an effective method for enriching phosphoproteins. Further validating the method, growth of yeast in the presence of sorbic acid resulted in altered phosphorylation of 17 proteins, 13 of which had prior published evidence that they were phosphoproteins or had ATP binding activity. Copyright © 2005 John Wiley & Sons, Ltd.
Identification of mouse brain proteins associated with isoform 3 of metallothionein
Authors: Lahti David W. , Hoekman John D. , Tokheim Abigail M. , Martin Bruce L. , Armitage Ian M. 
Published: April 2005

AbstractUsing immunological approaches and mass spectrometry, five proteins associated with metallothionein‐3 in mouse brains have been identified. Metallothionein‐3 and associated proteins were isolated using immunoaffinity chromatography over immobilized anti‐mouse brain MT3 antibody. Proteins in the recovered pool were separated by SDS‐polyacrylamide gel electrophoresis, and distinct bands were excised and the proteins digested using trypsin. Peptides were extracted and analyzed using electrospray ionization mass spectrometry. Initial identification was done comparing the identified peptide mass:charge ratios to the MASCOT database. Confirmation of proteins was accomplished by sequencing of selected peptides using tandem mass spectrometry and comparison to the MASCOT database. The proteins were heat‐shock protein 84 (mouse variant of heat‐shock protein 90), heat‐shock protein 70, dihydropyrimidinase‐like protein 2, creatine kinase, and β actin. Independently using antibodies against metallothionein‐3, creatine kinase, and heat‐shock protein 84 showed that all three proteins were coimmunoprecipitated from whole mouse brain homogenates with each of the three antibodies. Mixing purified samples of metallothionein and human brain creatine kinase also generated a complex that could be immunoprecipitated either by anti‐metallothionein‐3 or anticreatine kinase antibody. These data are consistent with metallothionein‐3 being present in the mouse brain as part of a multiprotein complex providing new functional information for understanding the role of metallothionein‐3 in neuronal physiology.
Enterococcus faecalis phosphomevalonate kinase
Authors: Doun Stephanie S. , Burgner John W. , Briggs Scott D. , Rodwell Victor W. 
Published: April 2005

AbstractThe six enzymes of the mevalonate pathway of isopentenyl diphosphate biosynthesis represent potential for addressing a pressing human health concern, the development of antibiotics against resistant strains of the Gram‐positive streptococci. We previously characterized the first four of the mevalonate pathway enzymes of Enterococcus faecalis, and here characterize the fifth, phosphomevalonate kinase (E.C. 2.7.4.2). E. faecalis genomic DNA and the polymerase chain reaction were used to clone DNA thought to encode phosphomevalonate kinase into pET28b(+). Double‐stranded DNA sequencing verified the sequence of the recombinant gene. The encoded N‐terminal hexahistidine‐tagged protein was expressed in Escherichia coli with induction by isopropylthiogalactoside and purified by Ni++ affinity chromatography, yield 20 mg protein per liter. Analysis of the purified protein by MALDI‐TOF mass spectrometry established it as E. faecalis phosphomevalonate kinase. Analytical ultracentrifugation revealed that the kinase exists in solution primarily as a dimer. Assay for phosphomevalonate kinase activity used pyruvate kinase and lactate dehydrogenase to couple the formation of ADP to the oxidation of NADH. Optimal activity occurred at pH 8.0 and at 37°C. The activation energy was ∼5.6 kcal/mol. Activity with Mn++, the preferred cation, was optimal at about 4 mM. Relative rates using different phosphoryl donors were 100 (ATP), 3.6 (GTP), 1.6 (TTP), and 0.4 (CTP). Km values were 0.17 mM for ATP and 0.19 mM for (R,S)‐5‐phosphomevalonate. The specific activity of the purified enzyme was 3.9 μmol substrate converted per minute per milligram protein. Applications to an immobilized enzyme bioreactor and to drug screening and design are discussed.
A reassessment of the eels of the genus Bathycongrus in the Indo‐west Pacific
Authors: Castle P. H. J. , Smith D. G. 
Published: April 2005

Difficulties in identifying the species of the congrid eel genus Bathycongrus Ogilby, 1898 that frequent the upper slope in the Indo‐west Pacific arise principally because these eels possess very few distinctive external characters. The differences in body proportions between the seven species that are recognized here are not easy to evaluate because of the frequent loss and subsequent regrowth of the tail tip. There are differences in the size and number of vomerine teeth, though these are not readily quantifiable, and in the number of vertebrae. However, the combination of these two characters allows the recognition of large/small‐toothed forms and those with low‐count, mid‐count, and high‐count vertebral numbers. The solution here has been to lump together some of the 16 nominal species.Accordingly, seven Indo‐west Pacific species are recognized in this account. Uranoconger Fowler, 1934 is synonymized with Bathycongrus. Larval characters, especially the number of myomeres, may be of some assistance in resolving the problems of species identification. A key to the species is given.
Molecular Identification of Fomitiporia mediterranea and Eutypa lata/Libertella blepharis in Platanus × acerifolia
Authors: Pilotti M. , Gervasi F. , Brunetti A. 
Published: April 2005

AbstractThe studies of woody organs‐affecting diseases of Platanus × acerifolia can be hampered by the finding of fungi whose identification is difficult with mycological techniques. In a previous study on Platanus × acerifolia affected by severe cankers, Fomitiporia mediterranea/punctata‐like fungi, not associated with fruit bodies and Libertella sp. were recovered. Due to the severity of the associated symptoms, a characterization of fungal ribosomal DNA genes was undertaken in the present study, aimed to specific identification of the pathogens. From DNA of Fomitiporia‐vegetative isolates and Fomitiporia‐fruit body isolates, included in the study for comparison (from fruit body on plane trees typical of F. mediterranea/punctata), and Libertella sp., DNA fragments were amplified in polymerase chain reaction (PCR) with the use of ITS5/ITS4 and 5.8S‐R/LR7 primer pairs. Sequence alignments showed that Fomitiporia‐vegetative/fruit body isolates had highly homologous ITS5/ITS4 sequences, with a nucleotide identity of 98–100%. All the Fomitiporia isolates from plane tree showed 97–100% and 91–94% of nucleotide identity respectively with ITS5/ITS4 sequences of known strains of F. mediterranea and F. punctata, extracted from GenBank. The strong similarity of these identity ranges with those obtained within F. mediterranea (98–100%) and between the two Fomitiporia species (90–94%) confirms the identification of the isolates from plane tree as F. mediterranea. Sequence comparison between Libertella sp. from plane tree and known strains of Eutypa lata/L. blepharis showed 94–99% of nucleotide identity. The comparison with eight additional species of Eutypa showed 90–93% of nucleotide identity. As previously reported for the different taxa within Diatrypaceae, also ITS5/ITS4 sequence of Libertella sp. from plane tree exhibited 11‐bp tandem repeats motifs. Results of sequence alignments, of phylogenetic trees, and of the putative restriction map, identify the Fomitiporia isolates of this work as F. mediterranea, and the isolates of Libertella sp. as E. lata/L. blepharis. For comparative purposes, ITS5/ITS4 sequences of Spongipellis pachyodon and Fomes fomentarius from plane tree, were also obtained in this work.
Chromatographic Characterization and Phytotoxic Activity of Fusarium oxysporum f. sp. albedinis and Saprophytic Strain Toxins
Authors: Amraoui H. , Lazrek H. B. , Sedra M. H. , Sampieri F. , Mansuelle P. , Rochat H. , Hamdaoui A. 
Published: April 2005

AbstractThe bayoud disease, vascular fusariosis of date palm tree (Phoenix dactylifera L.), is caused by the pathogenic fungus Fusarium oxysporum f. sp. albedinis. The characteristic symptoms of the bayoud disease were elicited on detached leaves of F. oxysporum f. sp. albedinis‐susceptible cultivars of date palm trees, which were treated either with the FII (F. oxysporum f. sp. albedinis) fraction purified from the organic extracts of a F. oxysporum f. sp. albedinis liquid culture, or with a solution of fusaric acid. Enniatins, which are secreted by several Fusarium species, were tested at different concentrations and were not capable of inducing symptoms on such detached leaves. The FII (F. oxysporum f. sp. albedinis) fraction was unable to induce necrosis of potato slices, which indicates that it does not contain significant amounts of enniatins. The high‐performance liquid chromatography (HPLC) profiles of the FII (F. oxysporum f. sp. albedinis) fraction showed toxic peaks different from fusaric acid. A fraction, named FII (AZ4), was obtained from culture filtrates of a saprophytic Fusarium strain maintained in the same cultural conditions as for the F. oxysporum f. sp. albedinis. The HPLC profile of the FII (AZ4) fraction did not show the characteristic phytotoxic peaks present in the FII (F. oxysporum f. sp. albedinis) fraction. This finding well agrees with the fact that the FII (AZ4) fraction is not toxic to detached date palm leaves. Moreover, the HPLC profiles of FII fractions obtained from other special forms of F. oxysporum are different the FII (F. oxysporum f. sp. albedinis) profile. The phytotoxic compounds purified from the FII (F. oxysporum f. sp. albedinis) fraction are probably new molecules that may help in understanding the pathogenesis of bayoud disease.
Natural Fusarium Grain Infection Level in Wheat, Barley and Oat after Early Application of Fungicides and Herbicides
Authors: Henriksen B. , Elen O. 
Published: April 2005

AbstractIn Norway, early application of fungicides against cereal leaf diseases (before Zadoks 60) is common practice amongst farmers. Whether this procedure has any effect on Fusarium infection of the mature grain has been little investigated. To evaluate effects on Fusarium grain infection, cereal grains were sampled during 1996, 1997 and 1998 from 12 field trials where early spraying against fungal diseases in spring wheat, spring barley and oats was carried out. Percentage infected grains and frequency of different Fusarium species was analysed in every grain sample. The effect of fungicides, glyphosate and postemergence herbicides on Fusarium grain infection was studied. Significant increase in Fusarium infection was detected in fungicide‐treated plots compared with untreated plots. Fusarium avenaceum and F. tricinctum were the most frequent species detected. The internal ranking of Fusarium species remained the same after spraying. No significant effects were found on the level of Fusarium infection after glyphosate treatment in autumn or herbicide treatment during the growing season.
Morphological, Pathological and Molecular Variability in Colletotrichum capsici, the Cause of Fruit Rot of Chillies in the Subtropical Region of North‐western India
Authors: Sharma P. N. , Kaur M. , Sharma O. P. , Sharma P. , Pathania A. 
Published: April 2005

AbstractFruit rot of chillies (Capsicum annuum L.), caused by Colletotrichum capsici under tropical and subtropical conditions, results in qualitative and quantitative yield losses. Based on variation in cultural and morphological traits of C. capsici populations, 37 isolates were categorized into five groups designated, respectively, as Cc‐I, Cc‐II, Cc‐III, Cc‐IV and Cc‐V. In culture, most of the isolates produced cottony, fluffy or suppressed colonies. However, no significant differences were noticed in shape and size of conidia. The reaction of the 37 isolates on an indigenously developed differential set of Capsicum cultivars indicated the existence of different virulences in Himachal Pradesh (HP) chilli populations. Fifteen pathotypes of the pathogen were characterized from various chilli‐growing regions of HP. Pathotype CCP‐1 was most virulent and attacked all the differential cultivars. The genetic relationship between five morphological groups recognized within C. capsici was investigated using random amplified polymorphic DNA (RAPD) analysis. Molecular polymorphism generated by RAPD confirmed the variation in virulences of C. capsici and different isolates were grouped into five clusters. However, four isolates (Cc‐5, Cc‐33, Cc‐29 and Cc‐37) exhibited identical RAPD haplotypes. The pathological and RAPD grouping of isolates suggested no correlation among the test isolates.
Resistance of Common Bean (Phaseolus vulgaris) to Bacterial Wilt Caused by Curtobacterium flaccumfaciens pv. flaccumfaciens
Authors: Hsieh T. F. , Huang H. C. , Mündel H.‐H. , Conner R. L. , Erickson R. S. , Balasubramanian P. M. 
Published: April 2005

AbstractBacterial wilt caused by Curtobacterium flaccumfaciens pv. flaccumfaciens is an important new disease of common bean (Phaseolus vulgaris) in western Canada. Both yellow and orange variants of the pathogen were found in the region. A controlled environment study was conducted to assess 124 common bean cultivars and lines from eight market classes for resistance to the yellow and orange variants of the pathogen, using the hilum injury/seed inoculation method. Results of the screening tests showed significant (P < 0.05) differences in resistance to bacterial wilt among the cultivars or lines. The great northern line L02E317, the great northern cultivar Resolute and pinto lines L02B662 and 999S‐2A, were highly resistant to both variants of the pathogen, with disease severity indices of 0 on a rating scale of 0 (no wilt symptoms) to 5 (dead seedling). Resistant cultivars or lines were found among black, great northern, pink, pinto, small red and Flor de Mayo bean market classes. The study concludes that new bacterial wilt‐resistant germplasm exists among Canadian bean cultivars and lines, and constitutes a valuable resource for breeding common beans for resistance to both yellow and orange variants of C. flaccumfaciens pv. flaccumfaciens.
Effect of Initial Density of Meloidogyne hapla on its Pathogenic Potential and Reproduction in Three Species of Medicinal Plants
Authors: Park S. D. , Khan Z. , Ryu J. G. , Seo Y. J. , Yoon J. T. 
Published: April 2005

AbstractThe pathogenic potential and reproduction fitness of Meloidogyne hapla on three species of medicinal plants, Angelica koreana, Peucedanum japonicum and Astragalus membranaceus was determined in potted soil under greenhouse conditions. Three weeks old seedlings were inoculated with population density (Pi) of 1000; 2000; 3000; 4000; 5000 and 10000 juveniles (J2)/kg soil. A significant damage was observed in shoot and root length, weight and root‐diameter of these plants by all Pi levels at 90‐day postinoculation. Damage increased with increase in Pi up to 5000 J2/kg soil. At 5000 Pi caused 34.8, 34.1 and 33.3% reduction in root weight of Ang. koreana, P. japonicum and Ast. membranaceus, respectively. Greater root gall severity was observed on Ang. koreana and P. japonicum than on Ast. membranaceus at all Pi levels. At 5000 Pi, root gall severity was 5.0, 5.0, and 3.0 on Ang. koreana, P. japonicum and Ast. membranaceus, respectively. Increasing rate of Pi exponentially reduced reproductive factor (Rf) of M. hapla on all of these medicinal plants. However, Rf was higher on Ang. koreana and P. japonicum than on Ast. membranaceus at all Pi levels. The host status of these medicinal plants renders them unsuitable for their use in crop rotation system in M. hapla‐infested fields.
New South Wales trends in mortality differentials between small rural and urban communities over a 25‐year period, 1970–1994
Authors: Hayes Lillian J. , Quine Susan , Taylor Richard 
Published: April 2005

AbstractObjective:  To identify trends in premature mortality differences between urban and small rural communities in NSW over a 25‐years period. Design:  A longitudinal population‐based study. ABS population and death data by local government area, sex and age for the period 1970 to 1994, were used to derive mortality measures for urban and small rural communities in NSW. Setting:  NSW local government areas categorised by the Rural and Remote Metropolitan Area Classification system as ‘capital city’ (the Sydney Statistical Division) and ‘other rural area’ and ‘other remote area’. Subjects:  All persons aged 0–74 years resident in the aforementioned NSW local government areas between 1970 and 1994 inclusive. Main outcome measure:  Whether premature mortality differentials have widened, narrowed or remained the same over the study period and the magnitude of any identified changes. Result:  There was a decrease in premature mortality rates for men and women in both urban and small rural communities. However, the decline was less in small rural communities, with the differential between small rural and urban areas increasing 2–3% every 5 years. Conclusions:  Differences in age structure, proportion of indigenous and migrant populations between small rural communities and urban NSW can not fully account for the increasing differential. Other possible explanatory factors include socioeconomic status and different exposures and practices in rural areas.
Heart rate variability analysis: a useful assessment tool for diabetes associated cardiac dysfunction in rural and remote areas
Authors: Flynn Allyson C. , Jelinek Herbert F. , Smith Megan 
Published: April 2005

AbstractObjective:  Cardiovascular complications are the main cause of death in people with diabetes. Early, asymptomatic changes are due to autonomic nervous system dysfunction, which if identified can lead to improved health. This study used detrended fluctuation analysis to identify changes in heart rate variability (HRV) associated with short‐time electrocardiograph (ECG) recordings. The aim of the study was to determine whether heart rate variability analysis on short ECG recordings has the potential to be a useful adjunct to clinical practice. Design:  Comparative design with three independent simple random samples. Setting:  University‐based research project. Participants:  Forty‐eight people with no diabetes or cardiovascular complications had a 20 min ECG recorded, which was subsequently analysed using mathematical procedures. All participants also had a lying‐to‐standing autonomic nervous system test. Data was analysed using a Student t‐test.Results:  Heart rate variability expressed as a numeric value (α
1
), is reduced in disease states. We found a significant difference in α
1
(P = 0.03) between the ECG recordings of the diabetes and control groups. In addition lower α
1
values were obtained from people identified with autonomic dysfunction within the diabetes group. Conclusion:  The importance of our findings is that abnormal HRV identifies people with cardiovascular disease, irrespective of diabetes status, that may have autonomic neuropathy. HRV analysis is easily implemented by primary health care providers and has the potential to lead to improved health care by reducing inequity in rural areas and specifically addressing cardiovascular complications associated with diabetes.