bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular genetic diversity of the French-American grapevine hybrids cultivated in North America
Authors: Pollefeys Patrick , Bousquet Jean
Published: December 2003

French-American hybrid grapevines are most popular in eastern and mid-western North America: they are hardy cultivars derived from crosses between the European Vitis vinifera and American wild vines. The aim of this study was to characterize their genetic background using 6 microsatellite (SSR) markers and a set of 33 diagnostic RAPD markers. The latter were reproducible with different PCR thermal cyclers. Two SSR loci were found to be synonymous, VrZAG47 and VVMD27. The DNA profile frequencies estimated for each cultivar were much lower with multi-locus SSR data than that obtained from multi-fragment RAPD data. There was no significant correlation between the multi-locus DNA profile frequencies derived from SSRs and those from RAPDs. Estimates of genetic diversity derived from SSRs were generally higher and the average similarity between cultivars was generally lower than values reported for subgroups of V. vinifera, in accordance with expectations for hybrid cultivars. The phenetic relationships depicted by UPGMA (unweighted pair-group method with arithmetic averaging) and neighbor-joining analyses of microsatellite data were congruent and, to a large extent, in agreement with the known pedigree or history of each cultivar. A major dichotomy was observed between one group where the known genetic background was dominated by the North American Vitis riparia and Vitis labrusca, and another one where the genetic background was dominated by the European V. vinifera. Two Kulhmann varieties thought to be synonymous were found to be different, though closely related.Key words: French-American hybrids, genetic diversity, RAPD, SSR, Vitis.
Distribution of highly repeated DNA sequences in species of the genus Lens Miller
Authors: Galasso Incoronata
Published: December 2003

Multiple-target fluorescence in situ hybridization (FISH) was applied on mitotic chromosomes of seven Lens taxa using two highly repetitive sequences (pLc30 and pLc7) isolated from the cultivated lentil and the multigene families for the 18S–5.8S–25S (pTa71) and 5S rRNA (pTa794) from wheat simultaneously as probes. The number and location of pLc30 and pLc7 sites on chromosomes varied markedly among the species, whereas the hybridization pattern of 5S rDNA and 18S–5.8S–25S rDNA was less variable. In general, each species showed a typical FISH karyotype and few differences were observed among accessions belonging to the same species, except for the accessions of Lens odemensis. The most similar FISH karyotype to the cultivated lentil is that of Lens culinaris subsp. orientalis, whereas Lens nigricans and Lens tomentosus are the two species that showed the most divergent FISH patterns compared with all taxa for number and location of pLc30 and 18S–5.8S–25S rDNA sites.Key words: chromosome identification, comparative FISH karyotype, wild Lens species, genomic relationships.
Development and characterization of recombinant chromosome substitution lines (RCSLs) usingHordeum vulgaresubsp.spontaneumas a source of donor alleles in aHordeum vulgaresubsp.vulgarebackground
Authors: Matus I , Corey A , Filichkin T , Hayes P M , Vales M I , Kling J , Riera-Lizarazu O , Sato K , Powell W , Waugh R
Published: December 2003

The ancestor of barley (Hordeum vulgare subsp. spontaneum) may be a source of novel alleles for crop improvement. We developed a set of recombinant chromosome substitution lines (RCSLs) using an accession of H. vulgare subsp. spontaneum (Caesarea 26-24, from Israel) as the donor and Hordeum vulgare subsp. vulgare 'Harrington' (the North American malting quality standard) as the recurrent parent via two backcrosses to the recurrent parent, followed by six generations of selfing. Here we report (i) the genomic architecture of the RCSLs, as inferred by simple sequence repeat (SSR) markers, and (ii) the effects of H. vulgare subsp. spontaneum genome segment introgressions in terms of three classes of phenotypes: inflorescence yield components, malting quality traits, and domestication traits. Significant differences among the RCSLs were detected for all phenotypes measured. The phenotypic effects of the introgressions were assessed using association analysis, and these were referenced to quantitative trait loci (QTL) reported in the literature. Hordeum vulgare subsp. spontaneum, despite its overall inferior phenotype, contributed some favorable alleles for agronomic and malting quality traits. In most cases, the introgression of the ancestral genome resulted in a loss of desirable phenotypes in the cultivated parent. Although disappointing from a plant breeding perspective, this finding may prove to be a useful tool for gene discovery.Key words: Hordeum vulgare subsp. vulgare, Hordeum vulgare subsp spontaneum, association analysis, QTLs, genetic resources.
Functional genomic analysis of the 61D-61F region of the third chromosome ofDrosophila melanogaster
Authors: Wei Ho-Chun , Shu Huidy , Price James V
Published: December 2003

Assigning functional significance to completed genome sequences is one of the next challenges in biological science. Conventional genetic tools such as deficiency chromosomes help assign essential complementation groups to their corresponding genes. We describe an F2genetic screen to identify lethal mutations within cytogenetic region 61D-61F of the third chromosome of Drosophila melanogaster. One hundred sixteen mutations were identified by their failure to complement both Df(3L)bab-PG and Df(3L)3C7. These alleles were assigned to 14 complementation groups and 9 deficiency intervals. Complementation groups were ordered using existing deficiencies, as well as new deficiencies generated in this study. With the aid of the genomic sequence, genetic and physical maps in the region were correlated by use of PCR to localize the breakpoints of deficiencies within a 268-kb genomic contig (GenBank accession No. AC005847). Six essential complementation groups were assigned to specific genes, including genes encoding a porphobilinogen deaminase and a Sac1-like protein.Key words: Drosophila, functional genomics, porphobilinogen deaminase, synaptojanin.
Visualizing DNA domains and sequences by microscopy: a fifty-year history of molecular cytogenetics
Authors: Jong Hans de
Published: December 2003

This short review presents a historical perspective of chromosome research during the last 50 years. It shows how molecular knowledge and technology of DNA entered cytogenetics step by step making it now daily practice in almost every modern chromosome lab. A crucial milestone in these decades has been the development of in situ protocols by Pardue and Gall, among others, initially only with isotopic labels, and without fluorescence microscopy and sophisticated detection systems. But these very first in situ hybridizations played a decisive role in the discovery of chromosome banding profiles, which were obtained under specific chemical, physical, or enzymatic conditions, thus effecting stainability of specific chromosome regions. In the decades thereafter, numerous technical improvements were achieved leading to complex multi-colour fluorescence in situ hybridization (FISH) protocols for mammals, plants, and insects. Highly improved detection systems of the FISH signals further allowed detection of DNA targets of up to 50 bp, whereas other protocols, which were developed to stretch chromatin fibres to the full length of native DNA, improved spatial resolution of adjacent targets in the light microscope to 1 kb.Key words: historical review, chromosome banding, FISH technology.
DNA and the revolutions of molecular evolution, computational biology, and bioinformatics
Authors: Golding G Brian
Published: December 2003

The discovery of the structure of DNA was a necessary prerequisite for determining the sequence of DNA molecules. Technological advances have now made it possible to sequence DNA rapidly and has resulted in public databases with over 30 billion nucleotides of known sequence. The analysis of these data has lead to new fields of science and to amazing advances in our understanding of evolution.Key words: bioinformatics, computational biology, molecular evolution, DNA, structure, DNA sequence.
Shall we dance or shall we fight? Using DNA sequence data to untangle controversies surrounding sexual selection
Authors: Civetta Alberto
Published: December 2003

Population and evolutionary genetics studies have largely benefitted from advances in DNA manipulation and sequencing, as well as DNA data analysis techniques. Molecular evolution studies of male reproductive genes show a pattern of rapid evolution shaped, in some cases, by an adaptive selective process. Despite the large body of data on male reproductive genes, the female side of the story has remained unexplored. The few cases of female egg receptors analyzed also show rapid evolution. However, to disentangle between competing hypotheses on how selection operates on male × female molecular interaction leading to fertilization, we need to find male and female molecules that are partners in fertilization. A conflict model of sexual selection (similar to a host-parasite model) assumes a male-driven system where females are being forced under suboptimal conditions. This predicts that the amount of divergence at a female receptor depends on the amount of divergence among the male reproductive proteins that it binds (i.e., males are leading). Under a classical model of runaway sexual selection, female protein receptors might be the key to the rapid molecular changes observed in male reproductive proteins and higher divergence should be expected among female receptors than among their respective male binding proteins.Key words: Reproductive genes, DNA sequence data, sexual selection, coadaptation, conflict.
The double-stranded DNA helix in recombination at meiosis
Authors: Moens Peter B
Published: December 2003

The nature of meiotic genetic recombination was resolved at the DNA level by the 1953 Watson and Crick model. What remains to be determined are the roles of the various recombination proteins and the distribution and localization of recombination events in the meiotic prophase nucleus.Key words: Holliday model, Holliday junction, chromosome cores, meiosis, recombinase, checkpoints, gene conversion, cross over.
Unfolding large-scale maps
Authors: Jenkins Glyn
Published: December 2003

This is an account of the development and use of genetic maps, from humble beginnings at the hands of Thomas Hunt Morgan, to the sophistication of genome sequencing. The review charters the emergence of molecular marker maps exploiting DNA polymorphism, the renaissance of cytogenetics through the use of fluorescence in situ hybridisation, and the discovery and isolation of genes by map-based cloning. The historical significance of sequencing of DNA prefaces a section describing the sequencing of genomes, the ascendancy of particular model organisms, and the utility and limitations of comparative genomic and functional genomic approaches to further our understanding of the control of biological processes. Emphasis is given throughout the treatise as to how the structure and biological behaviour of the DNA molecule underpin the technological development and biological applications of maps.Key words: maps, comparative mapping, genome sequencing, functional genomics.
Epigenetics and the renaissance of heresy
Authors: Varmuza Susannah
Published: December 2003

Classic neo-Darwinian theory is predicated on the notion that all heritable phenotypic change is mediated by alterations of the DNA sequence in genomes. However, evidence is accumulating that stably heritable phenotypes can also have an epigenetic basis, lending support to the long-discarded notion of inheritance of acquired traits. As many of the examples of epigenetic inheritance are mediated by position effects, the possibility exists that chromosome rearrangements may be one of the driving forces behind evolutionary change by exerting position effect alterations in gene activity, an idea articulated by Richard Goldschmidt. The emerging evidence suggests that Goldschmidt's controversial hypothesis deserves a serious reevaluation.Key words: epigenetics, position effects, inheritance of acquired traits.
Comment on "Epigenetics and the renaissance of heresy"
Authors: Singh Rama S
Published: December 2003

Lamarckian inheritance (i.e., inheritance of acquired character) and Richard Golschmidt's concept of "systemic mutations" and their role in macroevolution have been two of the most controversial topics in the history of evolutionary biology. The concept of Lamarckian inheritance was put to rest first by Weismann's germplasm theory and experiment and later by the discovery of Mendelian inheritance. Goldschmidt's theory of macroevolution by systemic mutations was put to rest by the discovery of DNA's structure and subsequent demonstration showing allelic variation as the basis for genetic and phenotypic differences observed among organisms. Some authors are using recent demonstrations of epigenetic inheritance in higher organisms to support Lamarckian inheritance and Golschmidt's theory of macroevolution by systemic mutations. In this paper, I show that the recent discoveries related to mutations, such as the so called "directed" mutations in bacteria, and epigenetic inheritance in higher organisms are basically an extension of the notion of "mutation" and thus of the concept of "heritable variation" required for evolution. While the new discoveries of the laws of developmental transformations are enriching our knowledge of the intricate relationship between genotype and phenotype, the findings of epigenetic inheritance do not challenge the basic tenets of the neo-Darwinian theory of evolution, as other than producing new variation no new processes of evolutionary change have been added to the ones we already know — mutation, migration, selection, and drift.Key words: neo-Darwinian theory of evolution, epigenetics, Lamarckian inheritance, systemic mutations, speciation, macroevolution.
Darwin to DNA, molecules to morphology: the end of classical population genetics and the road ahead
Authors: Singh Rama S
Published: December 2003

Molecular reductionism has permeated all of biology and because of successive new technical breakthroughs it has succeeded in unraveling the structural details of genes and genomes. The molecular revolution has reached its reductionist limit, i.e., the study of component parts in isolation, and is ready to come full circle through genomics, proteomics, and gene expression studies back to the phenotype and bring evolutionary biology to confront the Darwinian paradigm, the relationship between gene, organism, and environment. Classical experimental population genetics, dealing with genetic polymorphism and estimation of selection coefficients on a gene-by-gene basis, is coming to an end and a new era of interdisciplinary and interactive biology focusing on dynamic relationships among gene, organism, and environment has begun. In the new population genetics, there will be a shift in focus from single genes to gene networks, from gene-structure to gene-regulation, from additivity to epistasis, and from simple phenotypes to gene-interaction networks and the evolution of complex and modular systems.Key words: genome sequencing, population genetics, gene regulation, gene expression, speciation, norm of reaction, phenotypic plasticity.
DNA, chromosomes, and in situ hybridization
Authors: Schwarzacher Trude
Published: December 2003

In situ hybridization is a powerful and unique technique that correlates molecular information of a DNA sequence with its physical location along chromosomes and genomes. It thus provides valuable information about physical map position of sequences and often is the only means to determine abundance and distribution of repetitive sequences making up the majority of most genomes. Repeated DNA sequences, composed of units of a few to a thousand base pairs in size, occur in blocks (tandem or satellite repeats) or are dispersed (including transposable elements) throughout the genome. They are often the most variable components of a genome, often being species and, occasionally, chromosome specific. Their variability arises through amplification, diversification and dispersion, as well as homogenization and loss; there is a remarkable correlation of molecular sequence features with chromosomal organization including the length of repeat units, their higher order structures, chromosomal locations, and dispersion mechanisms. Our understanding of the structure, function, organization, and evolution of genomes and their evolving repetitive components enabled many new cytogenetic applications to both medicine and agriculture, particularly in diagnosis and plant breeding.Key words: repetitive DNA, genome organization, sequence evolution, telomere, centromere.
Prion protein gene sequence of Canada's first non-imported case of bovine spongiform encephalopathy (BSE)
Authors: Coulthart Michael B , Mogk Rhonda , Rancourt Jason M , Godal Deborah L , Czub Stefanie
Published: December 2003

In May 2003, Canada became the 22nd country outside of the United Kingdom to report a case of bovine spongiform encephalopathy (BSE) in an animal not known to be imported from a country with cattle previously affected by this fatal, transmissible prion disease. Despite extensive testing of thousands of other animals that may have been exposed to contaminated feed at the same time as the affected animal, no evidence has been found for other infections. This finding leaves room for conjectures that the single confirmed case arose spontaneously, perhaps (by analogy with human Creutzfeldt–Jakob disease) as a result of a somatic protein misfolding event or a novel germline mutation. Here we present DNA sequence data from the affected animal's prion protein coding sequence that argue definitively against the latter hypothesis.Key words: bovine spongiform encephalopathy, spontaneous origin, prions, mutation, Canada.
Different methods of membrane domains isolation result in similar 2-D distribution patterns of membrane domain proteins
Authors: Matousek Petr , Hodny Zdenek , Svandova Ivana , Svoboda Petr
Published: December 2003

Membrane domains are highly specialized parts of the cell plasma membrane, carrying on and augmenting the incoming signals. To study their structural and functional properties, it is crucial to find the least damaging mode of their isolation. Using two different cell lines, epithelial HEK cells (clone E2M11) and S49 lymphoma cells, three methods of membrane domain isolation (i.e., detergent extraction, alkaline treatment, and "drastic" homogenization) were tested for similarity and reproducibility by 2-D electrophoresis. Our data show that the protein composition of membrane domains obtained by different isolation methods is similar and that approximately 60% of the spots are present in all membrane domain preparations. Furthermore, the same degree of similarity of 2-D profiles of the most intensively silver stained spots found in membrane domains of the two cell lines derived from different tissues suggests that the composition of a large part of membrane domains proteins is conservative. We suggest that these proteins may either be involved in the organization of membrane domain structure or represent the conservative component of signal transduction machinery.Key words: domains, rafts, GPI-anchored proteins, two-dimensional electrophoresis, proteomics.
Effect of ethanol on cell growth and cholesterol metabolism in cultured Hep G2 cells
Authors: Polo Mónica P , de Bravo Margarita G , de Alaniz María JT
Published: December 2003

The Hep G2 human hepatoma cell line has been recognized as an excellent in vitro human model system. For this reason, this line was used to study the effect of ethanol on HMG-CoA reductase activity concerning cell growth and cholesterol metabolism. Cells were incubated in ethanol-containing medium (0400 mmol/L) for up to 102 h. Ethanol caused an inhibition in the growth rate and in HMG-CoA reductase activity that could be reverted by the removal of ethanol from the culture medium, indicating no cellular damage. These changes cannot be ascribed to the regulatory effect of cholesterol levels, since its content was not modified either in the cells or in the medium. The addition of mevalonate to the culture medium could not revert the growth rate inhibition evoked by ethanol. Moreover, ethanol produced an increment in the cholesterol efflux in [3H]cholesterol-prelabeled cells. We conclude that the decrease in HMG-CoA reductase activity evoked by ethanol treatment on Hep G2 cells would not be the cause but the consequence of the impairment in cellular growth, since this impairment could not be reverted by the addition of mevalonate to the culture medium.Key words: ethanol, cholesterol, HMG-CoA reductase, hepatoma cells, lipid metabolism.
A novel ribonuclease from the veiled lady mushroom Dictyophora indusiata
Authors: Wang Hexing , Ng Tzi Bun
Published: December 2003

A ribonuclease (RNase), exhibiting a molecular mass of 28 kDa and specificity toward polyU and polyA and possessing an N-terminal sequence dissimilar to previously reported mushroom RNases, was isolated from dried fruiting bodies of veiled lady mushroom (Dictyophora indusiata). It demonstrated an RNase activity of 564 U/mg toward yeast transfer RNA. The RNase was adsorbed on DEAE-cellulose, CM-Sepharose, and Q-Sepharose. It demonstrated a pH optimum of 4–4.5 and a temperature optimum of 60 °C. There was a loss of RNase activity at temperatures above 60 °C.Key words: ribonuclease, Dictyophora indusiata, mushroom, purification.
Purification of glysojanin, an antifungal protein, from the black soybean Glycine soja
Authors: Ngai Patrick H.K , Ng T B
Published: December 2003

A monomeric protein, with a molecular mass of 25 kDa and an N-terminal sequence resembling a segment of chitin synthase, was isolated from the seeds of the black soybean Glycine soja. The protein, designated glysojanin, demonstrated potent antifungal activity against the fungi Fusarium oxysporum and Mycosphaerella arachidicola. It inhibited HIV-1 reverse transcriptase with an IC50 of 47 µmol/L, [methyl-3H]thymidine incorporation by mouse spleen cells with an IC50 of 175 µmol/L, and translation in the rabbit reticulocyte lysate with an IC50 of 20 µmol/L. Glysojanin was purified using a procedure that involved ion-exchange chromatography on DEAE-cellulose, affinity chromatography on Affi-gel blue gel, ion-exchange chromatography by fast protein liquid chromatography on Mono S, and gel filtration by fast protein liquid chromatography on Superdex 75.Key words: antifungal protein, seeds, soybean, purification.
The role of connective tissue growth factor, a multifunctional matricellular protein, in fibroblast biology
Authors: Leask Andrew , Abraham David J
Published: December 2003

Connective tissue growth factor (CTGF, CCN2), a member of the CCN family of proteins, is a cysteine-rich proadhesive matricellular protein that plays an essential role in the formation of blood vessels, bone, and connective tissue. As expression of this protein is potently induced by transforming growth factor-β (TGFβ), it has been hypothesized that CTGF mediates several of the downstream actions of TGFβ. In particular, CTGF is profibrotic, as CTGF is overexpressed in fibrotic disease and synergizes with TGFβ to promote sustained fibrosis in vivo. Over the last several years, key data regarding the developmental role and structure and function relationship of CTGF have emerged. In addition, increased information concerning the mechanisms underlying the control of CTGF expression in normal and fibrotic cells and the signal transduction pathways through which CTGF acts on cells has been uncovered. This review summarizes the current state of knowledge regarding CTGF biology.Key words: CTGF, fibrosis, connective tissue, scleroderma.
Observed and simulated effect of rain events on the behaviour of an activated sludge plant removing nitrogen
Authors: Stricker Anne-Emmanuelle , Lessard Paul , Héduit Alain , Chatellier Patrice
Published: December 2003

This study deals with wastewater treatment plant (WWTP) loading and performance when receiving combined sewage. A yearly data set from an activated sludge plant operating at very low food-to-mass ratio (F/M) and being intermittently aerated was analyzed statistically to compare loading and discharge during dry and wet weather. The results show that despite some loading increase, the nitrogen removal performance is only slightly affected by rain, whereas higher soluble COD load discharge is observed. This approach was supplemented with dynamic simulations with the Activated Sludge Model No 1 (ASM1). It was first calibrated on data from an intensive 48-h dry weather sampling campaign at 20 °C. A good fit between simulated and measured variables was obtained after adjusting five parameters of the ASM1. This parameter set was then validated on a wet weather sampling campaign. Once the confidence in the simulations' results was established, several wet-weather scenarios were simulated, with maximum flow and variable pollutant loading. They show that the higher COD load discharge is due to a hydraulic flush of soluble inert compounds, and how the biological potential can be used to treat almost any realistically possible carbon and nitrogen overload.Key words: biological wastewater treatment, activated sludge, rain, combined sewage, nitrogen removal, soluble COD, oxygen demand, ASM1, simulation, calibration.
Interpretation of air quality data using an air quality index for the city of Kanpur, India
Authors: Sharma Mukesh , Pandey Reenu , Maheshwari Mayank , Sengupta B , Shukla B P , Gupta N K , Johri Sulochana
Published: December 2003

An air quality index (AQI) is proposed for the City of Kanpur, India, for simplified public information and data interpretation. A maximum operator concept is used to determine the overall AQI; maximum value of sub-indices (of each pollutant) is taken as the overall AQI. The mathematical functions for calculating sub-indices are proposed based on health criteria of the USEPA and Indian air quality standards. The pollutants included in the AQI are: SO2, SPM (suspended particulate matter), O3, NO2, PM10 (particulate matter with a diameter of 10 μm or less), and CO. The investigations into data interpretation using the AQI for Kanpur city have shown that air quality worsens (very poor to severe) in winter months and also during the early summer months (March, April, and part of May). These months are characterized by dusty winds resulting in high SPM. The air quality generally improves in monsoon and post-monsoon period (good to moderate) as rain washes out the pollutants. Over 95% of the time, sub-index values corresponding to SPM levels were responsible for overall AQI. Key words: air quality index, air quality data interpretation, Kanpur, India.
Pilot-scale study of phosphorus recovery through struvite crystallization – II: Applying in-reactor supersaturation ratio as a process control parameter
Authors: Adnan Ali , Koch Frederic A , Mavinic Donald S
Published: December 2003

A pilot-scale MAP (magnesium ammonium phosphate) crystallizer, which was used to remove/recover phosphorus through struvite formation, achieved ortho-P removal rates of over 90%, for a tested high phosphorus concentration (~220 mg/L). The desired degree of P-removal was achieved by either varying the operating pH or the supersaturation ratio at the inlet. The high P-removals (~90%) were achieved even at a pH of 7.3, which is contrary to the information found in the literature, where generally higher pH values (8.2~9) are recommended. This indicates that alkaline pH is not the only factor that can cause the process fluid to be supersaturated. Using solubility criteria, the in-reactor supersaturation ratio was used to define the metastable zone boundaries. The system performance, both in terms of process efficiency and the quality of the harvested product, was at its best when the in-reactor supersaturation ratio was between 1 and 5. The results showed that there was a narrow working zone for optimized crystallization process and a deviation from the optimal metastable zone always resulted in the plugging of the reactor. Key words: conditional solubility product, crystallization, phosphorus removal, struvite.
PM2.5 characterization and source-receptor relations in South Carolina
Authors: Calhoun D David , Salmon Lynn G , Schauer James J , Christoforou Christos S
Published: December 2003

Ambient PM2.5 aerosol samples were collected at three sites at Clemson University during January and June of 2001. The PM2.5 mass concentrations averaged 12.2 μg/m3 in January and 21.2 μg/m3 in June. Chemical characterization of the samples identified an average of 99% of the fine particulate matter collected in January and 96% in June. The primary ingredients of the PM2.5 aerosol were organic carbon compounds (49% in January and 44% in June) and sulfates (21% in January and 33% in June). Total heavy metals on average contributed 0.3% of the fine aerosol mass. Source-receptor reconciliation was completed for the fine aerosol using a chemical mass balance model, Chemical Mass Balance v. 8 (CMB8). In January, approximately 105% of the measured mass was accounted for, and the major sources were soil dust, ammonium sulfate, and ammonium nitrate. In June, an average of 80% of the measured mass was accounted for, and the major sources were the same as in January, except that the contribution of ammonium nitrate was negligible. A composite source of organic compounds that includes gasoline vehicle exhaust, meat cooking, cigarette smoke, and wood burning, was one of the major sources for both June and January seasons. Key words: PM2.5, CMB8, source receptor modeling.
Application of advanced oxidation methods for landfill leachate treatment – A review
Authors: Wang F , Smith Daniel W , El-Din M Gamal
Published: December 2003

Landfill leachate is a complex wastewater generated when the moisture content or the water content of the landfilled solid waste is larger than its field capacity. The major fraction of old or biologically treated landfill leachate is large recalcitrant organic molecules that are not easily removed during biological treatment. Advanced oxidation using ozone (O3), ozone with hydrogen peroxide (O3/H2O2), ozone with ultraviolet light (O3/UV), hydrogen peroxide with ultraviolet light (H2O2/UV), Fenton process (H2O2/Fe2+), and photo-Fenton process (H2O2/Fe2+/UV) for the treatment of old or biologically treated landfill leachate has been intensively studied in the past decade to improve the removal of these large recalcitrant organic molecules or to transform them into more easily biodegradable substances. The characteristics of landfill leachate and the mechanisms of O3, O3/H2O2, O3/UV, H2O2/UV, H2O2/Fe2+, and H2O2/Fe2+/UV oxidation processes and their applications for landfill leachate treatment are reviewed in this paper. In addition, the influences of ammonia nitrogen (NH3-N), pH, and alkalinity on the advanced oxidation processes applied for treating landfill leachates as well as the methods for the removal of the oxidants residues are also discussed in this paper. Key words: landfill leachate, ozone, hydrogen peroxide, UV, Fenton processes, photo-Fenton processes, refractory organics.
Influence of bacterial strains isolated from lead-polluted soil and their interactions with arbuscular mycorrhizae on the growth of Trifolium pratense L. under lead toxicity
Authors: Vivas A , Azcón R , Biró B , Barea J M , Ruiz-Lozano J M
Published: December 2003

We isolated two bacterial strains from an experimentally lead (Pb)-polluted soil in Hungary, 10 years after soil contamination. These strains represented the two most abundant cultivable bacterial groups in such soil, and we tested their influence on Trifolium pratense L. growth and on the functioning of native mycorrhizal fungi under Pb toxicity in a second Pb-spiked soil. Our results showed that bacterial strain A enhanced plant growth, nitrogen and phosphorus accumulations, nodule formation, and mycorrhizal infection, demonstrating its plant-growth-promoting activity. In addition, strain A decreased the amount of Pb absorbed by plants, when expressed on a root weight basis, because of increased root biomass due to the production of indoleacetic acid. The positive effect of strain A was not only evident after a single inoculation but also in dual inoculation with arbuscular mycorrhizal fungi. Strain A also exhibited higher tolerance than strain B when cultivated under increasing Pb levels in the spiked soil. Molecular identification unambiguously placed strain A within the genus Brevibacillus. We showed that it is important to select the most tolerant and efficient bacterial strain for co-inoculation with arbuscular mycorrhizal fungi to promote effective symbiosis and thus stimulate plant growth under adverse environmental conditions, such as heavy-metal contamination.Key words: arbuscular mycorrhizal symbiosis, Pb-polluted soil, plant-growth-promoting bacteria.
Characterization ofNeisseria meningitidisstrains isolated from invasive meningococcal disease cases in Canada in 2001
Authors: Tsang R S.W , Squires S G , Tam T W.S
Published: December 2003

With the recent introduction of polysaccharide–protein conjugated vaccines for the control of serogroup C meningococal disease and the emergence of different variants of serogroup C meningococci, it is likely the epidemiology of meningococcal disease in many countries may be affected. We have therefore analysed and reported the characteristics of Neisseria meningitidis strains collected in 2001 from the Canadian surveillance program on invasive menin go coccal disease. Only strains collected from normally sterile clinical sites of patients were studied. Of the 289 isolates obtained from individual patients, 173 (59.9%) were serogroup C, 76 (26.3%) were serogroup B, 30 (10.4%) were serogroup Y, and 10 (3.5%) were serogroup W135. Ninety-six percent of the serogroup C isolates belonged to the ET-15 clone, with an additional 2.3% belonging to other electrophoretic types within the ET-37 clonal complex. Different antigenic variants of the endemic serogroup C ET-15 clone were responsible for localized outbreaks in different parts of the country. One novel variant with the antigenic composition of C:2a:P1.1,7 was reported in two provinces, Quebec and Ontario. Eighteen percent of the meningococci isolated from patients in Ontario belonged to serogroup Y, compared with only 8% in the rest of Canada. The current data highlight the importance of strain characterization by serogroup, serotype, and serosubtype antigens in providing useful information for the surveillance of meningococcal disease in Canada.Key words: antigenic, genetic, characterization, meningococci.
Culture-independent phylogenetic analysis of the faecal flora of the rat
Authors: Brooks S P.J , McAllister M , Sandoz M , Kalmokoff M L
Published: December 2003

The dominant faecal flora of the rat was determined using randomly cloned 16S rDNA comparative sequence analysis. A total of 109 near full-length 16S rDNA clones were sequenced, representing 69 unique 16S rRNA phylotypes or operational taxonomic units (OTUs). Estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. Only two of 39 Gram-negative clones aligned with previously cultured species, the remainder fell into a separate lineage within the Bacteroides–Cytophaga phylum. Several clones within this new group were related to 16S rDNA sequences previously identified from mouse faeces. Lactobacilli were the most abundant Gram-positive species, representing 23% of the total clones but only 7% of OTUs. The remaining Gram-positive clones were distributed among the Clostridium coccoides group (9%), the Clostridium leptum subgroup (18%), and throughout the low GC Gram-positive bacteria (13%). The majority of OTUs (63/69 or 91%) were less than 97% homologous to previously cultured bacteria. Faecal samples were also cultured using a variety of anaerobic media. With the exception of the lactobacilli, the cultured isolates demonstrated low species diversity and poorly reflected the population, as defined through comparative sequence analysis.Key words: rat, faeces, 16S rDNA, phylogenetic, cultured bacteria.
Induction, purification, and characterization of two extracellular α-L-arabinofuranosidases from Fusarium oxysporum
Authors: Panagiotou Gianni , Topakas Evagelos , Economou Lina , Kekos Dimitris , Macris Basil J , Christakopoulos Paul
Published: December 2003

In the presence of L-arabinose as sole carbon source, Fusarium oxysporum produces two α-L-arabinofuranosidases (ABFs) named ABF1 and ABF2, with molecular masses of 200 and 180 kDa, respectively. The two F. oxysporum proteins have been purified to homogeneity. The purified enzymes are composed of three equal subunits and are neutral proteins with pIs of 6.0 and 7.3 for ABF1 and ABF2, respectively. With p-nitrophenyl α-L-arabinofuranoside (pNPA) as the substrate, ABF1 and ABF2 exhibited Km values of 0.39 and 0.28 mmol·L–1, respectively, and Vmax values of 1.6 and 4.6 µmol·min–1·(mg of protein)–1, respectively, and displayed optimal activity at pH 6.0 and 50–60 °C. ABFs released arabinose only from sugar beet arabinan and not from wheat soluble and insoluble arabinoxylans. The enzymes were not active on substrates containing ferulic acid ester linked to C-5 and C-2 linkages of pNPA showing that phenolic substituents of pNPA sterically hindered the action of ABFs.Key words: α-L-arabinofuranosidase, enzyme purification, enzyme induction.
Attempts to inhibit ruminal methanogenesis by blocking pyruvate oxidative decarboxylation
Authors: Ungerfeld E M , Rust S R , Burnett R
Published: December 2003

The inhibition of pyruvate oxidative decarboxylation as a means of decreasing ruminal methanogenesis in vitro was studied. In the first experiment, the addition of adenosine and adenine (with and without ribose) to ruminal batch cultures did not decrease methanogenesis. In the second experiment, the addition of oxythiamin decreased methanogenesis by 23%. In the third experiment, three pyruvate derivatives did not inhibit methanogenesis, although hydroxypyruvate improved organic matter fermentation from 57.8% to 64.2%. The additives did not seem to inhibit pyruvate oxidative decarboxylation.Key words: methane, inhibition, rumen, pyruvate decarboxylation, thiamin.
Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway) - denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures
Authors: Wartiainen Ingvild , Hestnes Anne Grethe , Svenning Mette M
Published: December 2003

The methanotrophic community in arctic soil from the islands of Svalbard, Norway (78°N) was analysed by combining group-specific PCR with PCR of the highly variable V3 region of the 16S rRNA gene and then by denaturing gradient gel electrophoresis (DGGE). Selected bands were sequenced for identification. The analyses were performed with DNA extracted directly from soil and from enrichment cultures at 10 and 20 °C. The two genera Methylobacter and Methylosinus were found in all localities studied. The DGGE band patterns were simple, and DNA fragments with single base differences were separated. The arctic tundra is a potential source of extensive methane emission due to climatic warming because of its large reservoirs of stored organic carbon. Higher temperatures due to climatic warming can cause increased methane production, and the abundance and activity of methane-oxidizing bacteria in the arctic soil may be important regulators for methane emission to the atmosphere.Key words: methanotrophic diversity, Svalbard, arctic wetland, denaturing gradient gel electrophoresis.
Phenotypic characteristics and population genetics ofEnterococcus faecaliscultured from patients in Tehran during 2000–2001
Authors: Feizabadi Mohammad Mehdi , Aliahmadi Atusa , Mobasheri Fatemeh , Asgharzadeh Ahmad , Asadi Soroor , Etemadi Gelavizh
Published: December 2003

Conventional bacteriology techniques were used to identify enterococci isolates cultured from patients at different hospitals in Tehran during 2000–2001. The identification was confirmed using species-specific PCR targeting the D-alanyl-D-alanine ligase gene. A total of 59 isolates of Enterococcus faecalis were identified. The rates of resistance to different antibiotics were in the following order: penicillin 84%, ciprofloxacin 42%, high-level gentamicin 30%, nitrofurantoin 14%, imipenem 4%, and chloramphenicol 2%. Resistance to ampicillin was found to be rare among the Iranian isolates of E. faecalis. Multi-locus enzyme electrophoresis was then used to analyze the strains. Forty-five electrophoretic types were obtained when 10 enzyme loci were screened. Although the collection of bacterial isolates was limited in time and location, considerable heterogeneity was found. Analysis of strains for linkage disequilibrium demonstrated that the studied population is not clonal, since the index of association was not significantly different from zero (Ia= 0.0296). Enterococcus faecalis isolates recovered from patients in Tehran were genetically diverse and seemed to possess a high potential for genetic recombinations, though none were resistant to vancomycin.Key words: Enterococcus faecalis, population genetics, MEE analysis, nosocomial infections.
Social allies modulate corticosterone excretion and increase success in agonistic interactions in juvenile hand-raised graylag geese (Anser anser)
Authors: Frigerio Didone , Weiss Brigitte , Dittami John , Kotrschal Kurt
Published: December 2003

In mammals, support by a social partner may reduce stress levels and ease access to resources. We investigated the effects of the passive presence of a nearby social ally on excreted corticosterone immunoreactive metabolites and behaviour in juvenile graylag geese (Anser anser). Two groups of hand-raised juveniles (N1 = 9, N2 = 3) were tested over 1 year by positioning humans of different familiarity (i.e., the human foster parent, a familiar human, a nonfamiliar human, no human) at a standard distance to the focal geese. Their success in agonistic interactions significantly decreased with age and with decreasing familiarity of the accompanying human. The humans present modulated the excretion of corticosterone immunoreactive metabolites, with the strongest effects recorded after fledging when corticosterone metabolites were also positively correlated with agonistic behaviour. This suggests that a human foster parent may provide similar supportive benefits as goose parents do in natural families. We discuss the benefits of social alliances with regard to the integration into the flock, access to resources, and life history.
Captive-born bottlenose dolphin × common dolphin (Tursiops truncatus × Delphinus capensis) intergeneric hybrids
Authors: Zornetzer Heather R , Duffield Deborah A
Published: December 2003

Four bottlenose dolphin (Tursiops truncatus) × long-beaked common dolphin (Delphinus capensis) F1 hybrids were born at SeaWorld California between August 1992 and March 1993 to four different bottlenose dolphin dams. Based on coloration patterns of the neonates at the time of birth, as well as time of conception and blood protein electrophoretic analysis, the sire was determined to be a long-beaked common dolphin that was housed with the dams. Two of the F1 hybrids, a male and a female, are alive today and the female gave birth to a live-born backcross (B1) calf sired by a T. truncatus in October 2000. Morphometric and color pattern descriptions are presented here for the two living captive-born F1 hybrids, as well as for the B1 neonate. We have highlighted characteristics that might be indicative of T. truncatus × D. capensis hybridization, including intermediacy between the parents for tooth counts, color and striping patterns, and certain body proportions of the F1 hybrids. The overall size and appearance of the B1 calf were similar to those of a T. truncatus neonate. This note confirms fertility of these intergeneric hybrids.
Larval development and metamorphic transformation of the feeding system in the kleptoparasitic snailTrichotropis cancellata(Mollusca, Caenogastropoda)
Authors: Parries Shawn C , Page Louise R
Published: December 2003

Trichotropis cancellata Hinds, 1849 has a planktonic larval stage that feeds on microalgae and a benthic stage that feeds both by ctenidial suspension feeding and by stealing food ("kleptoparasitism") from several species of suspension-feeding, tube-dwelling polychaete worms. We used scanning electron microscopy, histological sections, and observations on live animals to document the sequence and timing of morphogenetic events during larval and metamorphic development of T. cancellata. These data were compared with other accounts of gastropod development to test for differences in the timing of developmental events among feeding larvae of two major gastropod clades: the caeno gastropods and heterobranchs. In T. cancellata, as in feeding larvae of previously studied caenogastropods, components of the post-metamorphic body plan differentiate at an earlier stage of larval development (relative to times of hatching and ability to undergo metamorphosis) than in feeding heterobranch larvae. Metamorphosis of T. cancellata was induced by polychaete hosts of this snail's kleptoparasitic benthic stage, and young juveniles of T. cancellata could steal food from these polychaetes within a day after snail metamorphosis began. Rapid onset of kleptoparasitic feeding following metamorphosis of T. cancellata was permitted by development of a specialized feeding structure, the pseudo proboscis, during the larval stage. This novel embellishment of larval development was likely preceded during evolution by selective larval induction by polychaete hosts.
Interacting effects of water temperature and swimming activity on body composition and mortality of fasted juvenile rainbow trout
Authors: Simpkins Darin G , Hubert Wayne A , del Rio Carlos Martinez , Rule Daniel C
Published: December 2003

We assessed changes in proximate body composition, wet mass, and the occurrence of mortality among sedentary and actively swimming (15 cm/s) juvenile rainbow trout (Oncorhynchus mykiss) (120–142 mm total length) that were held at 4.0, 7.5, or 15.0 °C and fasted for 140 days. Warmer water temperatures and swimming activity accentuated declines in lipid mass, but they did not similarly affect lean mass and wet mass. Swimming fish conserved lean mass independent of water temperature. Because lean mass exceeded lipid mass, wet mass was not affected substantially by decreases in lipid mass. Consequently, wet mass did not accurately reflect the effects that water temperature and swimming activity had on mortality of fasted rainbow trout. Rather, lipid mass was more accurate in predicting death from starvation. Juvenile rainbow trout survived long periods without food, and fish that died of starvation appeared to have similar body composition. It appears that the ability of fish to endure periods without food depends on the degree to which lipid mass and lean mass can be utilized as energy sources.