bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region
Authors: Han F , Kilian A , Chen J P , Kudrna D , Steffenson B , Yamamoto K , Matsumoto T , Sasaki T , Kleinhofs A
Published: April 2011

In the course of map-based cloning of the barley stem rust resistance gene Rpg1, we identified a rice bacterial artificial chromosome (BAC) containing the Rpg1 flanking markers. Based on the excellent gene order colinearity between barley and rice in this region, we expected that this rice BAC would contain the barley Rpg1 homologue. In order to identify the putative rice homologue, we sequenced ca. 35 kb of the rice BAC at random and then an additional 33 kb of contiguous sequence between the two most closely spaced Rpg1 flanking markers. Sequence analysis revealed a total of 15 putative genes, 5 within the 33-kb contiguous region. A rice Rpg1 homologue was not identified, although a gene encoding a hypothetical polypeptide with similarity to a membrane protein could not be eliminated as a candidate. Surprisingly, four of the genes identified in the 33-kb contiguous rice sequence showed a high degree of similarity with genes on Arabidopsis chromosome 4. The genome regions harboring these genes showed some relatedness, but many rearrangements were also evident. These data suggest that some genes have remained linked even over the long evolutionary separation of Arabidopsis and rice, as has also been reported for mammals and invertebrates.Key words: genes, genome, rice, synteny, sequence.
Development of a CAPS marker for the Pvr4 locus: A tool for pyramiding potyvirus resistance genes in pepper
Authors: Caranta Carole , Thabuis Arnaud , Palloix Alain
Published: April 2011

The Pvr4 resistance gene in pepper confers a complete resistance to the three pathotypes of potato virus Y (PVY) and to pepper mottle virus (PepMoV). In order to use this gene in a marker-assisted selection (MAS) program and to permit the pyramiding of several potyvirus resistance genes in the same cultivar, tightly linked amplified fragment length polymorphism (AFLP) markers were obtained by the bulked segregant analysis method. Eight linked AFLP markers were mapped in an interval from 2.1 ± 0.8 to 13.8 ± 2.9 cM around this locus. The closest codominant AFLP marker was converted into a codominant CAPS (cleaved amplified polymorphic sequence) marker using data from the alignment of the two allele sequences. We have further characterized the relevance of the CAPS marker for MAS programs in different pepper breeding lines.Key words: amplified fragment length polymorphism markers, bulked segregant analysis, Capsicum annuum, marker-assisted selection, potyvirus resistance.
Genomic relationships between maize and its wild relatives
Authors: Takahashi C , Marshall J A , Bennett M D , Leitch I J
Published: April 2011

Recent molecular studies confirm the long-held theory that maize is a tetraploid, but the identity of the ancestral diploid species remains an enigma. The various hypotheses were investigated using genomic in situ hybridization (GISH). Total genomic DNA from 10 wild relatives of maize were used as probes onto maize chromosomes to see if this could identify the ancestral genome donors in maize. While none of the taxa hybridized to a subset of chromosomes, genomic DNA from Zea mays ssp. mexicana, Z. mays ssp. parviglumis, Z. diploperennis, Tripsacum dactyloides and Coix lacryma-jobi all showed a similar hybridization pattern consisting of a dispersed signal over all maize chromosomes. Moreover, the first four species also showed highly localized subtelomeric signal on the long arms of maize chromosomes 5, 6 ,7, and 8. In contrast, three Sorghum species tested (S. bicolor, S. halapense, and S. versicolor) only showed hybridization at the nucleolar organizer region. In light of recent data on retrotransposon occurrence in maize, the results may provide insights into the timing of speciation of Zea, Tripsacum, and Coix. Data obtained from the tetraploid Z. perennis strongly supported its taxonomic separation from the diploid Z. diploperennis.Key words: Zea, GISH, evolution, Tripsacum, Sorghum.
TheHalocus of wheat: Identification of a polymorphic region for tracing grain hardness in crosses
Authors: Turner M , Mukai Y , Leroy P , Charef B , Appels R , Rahman S
Published: April 2011

The grain softness proteins or friabilins are known to be composed of three main components: puroindoline a, puroindoline b, and GSP-1. cDNAs for GSP-1 have previously been mapped to group-5 chromosomes and their location on chromosome 5D is closely linked to the grain hardness (Ha) locus of hexaploid wheat. A genomic DNA clone containing the GSP-1 gene (wGSP1-A1) from hexaploid wheat has been identified by fluorescent in situ hybridization as having originated from the distal end of the short arm of chromosome 5A. A genomic clone containing the gene (wGSP1-D1) was also isolated from Aegilops tauschii, the donor of the D genome to bread wheat. There are no introns in the GSP-1 genes, and there is high sequence identity between wGSP1-A1 and wGSP1-D1 up to 1 kb 5' and 300 bp 3' to wGSP1-D1. However, regions further upstream and downstream of wGSP1-D1 share no significant sequence identity to corresponding sequences in wGSP1-A1. These regions therefore identified potentially valuable sequences for tracing the Ha locus through assaying polymorphic DNA sequences. The sequence from 300 to 500 bp 3' to wGSP1-D1 (wGSP1-D13) was mapped to the Ha locus in a mapping population. wGSP1-D13 was also tightly linked to genes for puroindoline a and puroindoline b which have been previously mapped to be at the Ha locus. In addition wGSP1-D13 was used to detect RFLPs between near isogenic soft and hard Falcon lines and in a random selection of soft and hard wheats.Key words: wheat, grain hardness, chromosome 5, puroindoline, GSP-1.
Chromosomal location and genetic mapping of the mismatch repair gene homologsMSH2,MSH3, andMSH6in rye and wheat
Authors: Korzun V , Börner A , Siebert R , Malyshev S , Hilpert M , Kunze R , Puchta H
Published: April 2011

The efficiency of homeologous recombination is influenced by mismatch repair genes in bacteria, yeast, and mammals. To elucidate a possible role of these genes in homeologous pairing and cross-compatibility in plants, gene probes of wheat (Triticum aestivum) specific for the mismatch repair gene homologues MSH2, MSH3, and MSH6 were used to map them to their genomic positions in rye (Secale cereale). Whereas MSH2 was mapped to the short arm of chromosome 1R, MSH3 was mapped to the long arm of chromosome 2R and MSH6 to the long arm of chromosome 5R. Southern blots with nullisomic-tetrasomic (NT) lines of wheat indicated the presence of the sequences on the respective homeologous group of wheat chromosomes. Additionally, an MSH6-specific homologue could also be detected on homoeologous group 3 of wheat. However, in the well-known, highly homoeologous pairing wheat mutant ph1b the MSH6-specific sequence is not within the deleted part of chromosome 5BL, indicating that the pairing phenotype is not due to a loss of one of the mismatch repair genes tested.Key words: mismatch repair genes, chromosomal location, RFLP mapping, wheat, rye.
Broad-sense sexual selection, sex gene pool evolution, and speciation
Authors: Civetta A , Singh R S
Published: April 2011

Studies of sexual selection have traditionally focused on explaining the extreme sexual dimorphism in male secondary sexual traits and elaborate mating behaviors displayed by males during courtship. In recent years, two aspects of sexual selection have received considerable attention in the literature: an extension of the sexual selection concept to other traits (i.e., postcopulatory behaviors, external and internal genital morphology, gametes, molecules), and alternative mechanistic explanations of the sexual selection process (i.e., coevolutionary runaway, good-genes, sexual conflicts). This article focuses on the need for an extension of sexual selection as a mechanism of change for courtship and (or) mating male characters (i.e., narrow-sense sexual selection) to all components of sexuality not necessarily related to courtship or mating (i.e., broad-sense sexual selection). We bring together evidence from a wide variety of organisms to show that sex-related genes evolve at a fast rate, and discuss the potential role of broad-sense sexual selection as an alternative to models that limit speciation to strict demographic conditions or treat it simply as an epiphenomenon of adaptive evolution.Key words: sexual selection, sex-related genes, speciation.
Efficiency of RFLP, RAPD, and AFLP markers for the construction of an intraspecific map of the tomato genome
Authors: Saliba-Colombani Vera , Causse Mathilde , Gervais Laurent , Philouze Jacqueline
Published: April 2011

We have constructed a tomato genetic linkage map based on an intraspecific cross between two inbred lines of Lycopersicon esculentum and L. esculentum var. cerasiforme. The segregating population was composed of 153 recombinant inbred lines. This map is comprised of one morphological, 132 RFLP (restriction fragment length polymorphism, including 16 known-function genes), 33 RAPD (random amplified polymorphic DNA), and 211 AFLP (amplified fragment length polymorphism) loci. We compared the 3 types of markers for their polymorphism, segregation, and distribution over the genome. RFLP, RAPD, and AFLP methods revealed 8.7%, 15.8%, and 14.5% informative bands, respectively. This corresponded to polymorphism in 30% of RFLP probes, 32% of RAPD primers, and 100% of AFLP primer combinations. Less deviation from the 1:1 expected ratio was obtained with RFLP than with AFLP loci (8% and 18%, respectively). RAPD and AFLP markers were not randomly distributed over the genome. Most of them (60% and 80%, respectively) were grouped in clusters located around putative centromeric regions. This intraspecific map spans 965 cM with an average distance of 8.3 cM between markers (of the framework map). It was compared to other published interspecific maps of tomato. Despite the intraspecific origin of this map, it did not show any increase in length when compared to the high-density interspecific map of tomato. Key words: Lycopersicon esculentum, molecular linkage map, RFLP, AFLP, intraspecific cross.
Microsatellite loci in the phytoparasitic nematodeGlobodera
Authors: Thiéry M , Mugniéry D
Published: April 2011

A Globodera pallida genomic library, population Guiclan (Pa2/3), was screened for TG and TC microsatellite motifs. Screening of 50 000 clones revealed 48 positive matches. After sequencing, primers were designed to amplify 14 microsatellite loci. The specificity of the loci was tested with DNA templates of other populations of G. pallida, and also on other species of Globodera. Appearance of amplification products on several of these DNA templates showed that the microsatellite flanking regions are relatively conserved between G. pallida populations as well as between Globodera species. Evidence for allele polymorphism between individuals was demonstrated by using nine loci primers, in G. pallida population Guiclan and from a population of a closely related species G. "mexicana". Some alleles appeared to be species specific. Key words: Globodera, microsatellites, nematodes, phytoparasite, allele frequency.
Molecular phylogeny of mangroves VI. Intraspecific genetic variation in mangrove species Excoecaria agallocha L. (Euphorbiaceae)
Authors: Lakshmi M , Parani M , Ram Nivedita , Parida Ajay
Published: April 2011

Genomic DNA from 84 individuals of Excoecaria agallocha from seven mangrove populations were analysed for random amplified polymorphic DNAs (RAPDs) using 16 random 10-mer primers. Polymorphism within populations varied from 20% to 31%. At the interpopulation level, 111/149 (74%) of RAPDs were polymorphic. Restriction fragment length polymorphism (RFLP) analysis of 21 individuals (3 individuals randomly selected from the 7 populations) using 30 probe-enzyme combinations revealed a high level of interpopulation polymorphism (62.2%) indicating interpopulation genetic divergence. The polymorphic RAPDs and RFLPs were pooled, and clustering was carried out based on mean similarity for individual populations. The dendrogram showed groupings of populations from the West and East Coasts of India into separate clusters, at 60% similarity level. Further, RAPD and RFLP analysis of male and female plants showed approximately the same level of variation in both sexes, and no sex-linked markers were found. These results demonstrate that considerable intrapopulation and interpopulation genetic variations exist in E. agallocha, and that lack of genetic variation is not the reason for the morphological uniformity observed across the range of the species. Key words: mangroves, Excoecaria agallocha, molecular markers, RAPD, RFLP, genetic variation.
Development of a PCR marker for rapid identification of the Bt-10 gene for common bunt resistance in wheat
Authors: Laroche André , Demeke Tigst , Gaudet Denis A , Puchalski Byron , Frick Michelle , McKenzie R
Published: April 2011

In western Canada, the Bt-10 resistance gene in wheat (Triticum aestivum) is effective against all the known races of common bunt caused by Tilletia tritici and T. laevis. The genotypes of 199 F2 plants, originated from a cross between BW553 containing Bt-10 and the susceptible spring wheat cultivar 'Neepawa,' were established in greenhouse and field inoculation studies. A ratio of 1:2:1 resistant : heterozygous : susceptible was observed for bunt reaction, indicating that Bt-10 was expressed in a partially dominant fashion. A polymorphic DNA fragment, amplified using RAPD, and previously shown to be linked to Bt-10 was sequenced and SCAR (sequence characterized amplified region) primers devised. However, SCAR primers failed to amplify the polymorphic fragment. Restriction of PCR products with DraI revealed a polymorphic fragment of 490 bp resulting from a single base pair difference between lines possessing Bt-10 and those lacking the gene. As per the base pair difference, FSD and RSA primers were designed to generate a 275-bp polymorphic DNA fragment. Both 275- and 490-bp polymorphic fragments were present in all of the 22 cultivars known to carry Bt-10, and absent in all 16 cultivars lacking Bt-10. A 3:1 ratio was observed for presence: absence of the 275-bp marker in the F2 population. Using Southern analysis, the 490-bp fragment was effective in differentiating homozygous resistant plants from those heterozygous for Bt-10, based on its presence and the hybridization signal strength. A 1:2:1 resistant : heterozygous : susceptible ratio was also observed for the molecular marker and corresponded to 88% of the phenotypes deduced from the original F2 population. The molecular marker was estimated to be between 1.1 cM and 6.5 cM away from the Bt-10 resistance gene, based on the segregation analysis. Segregation analyses of Bt-10 and the 275-bp marker, evaluated in three different Canada Prairie Spring (CPS) wheat populations, demonstrated a segregation ratio of 3:1 for the molecular marker in two of the populations. These results demonstrated that the PCR marker system using the FSD and RSA primer pair permitted a rapid and reliable identification of individual lines carrying the Bt-10 gene for resistance to common bunt.

Key words: resistance gene, genetic segregation, molecular marker, RAPD analysis.
Chromosomal location of AFLP markers in common wheat utilizing nulli-tetrasomic stocks
Authors: Huang Xiuqiang , Zeller Friedrich J , Hsam Sai LK , Wenzel Gerhard , Mohler Volker
Published: April 2011

Amplified fragment length polymorphism (AFLP) markers with a total of 256 EcoRI + ANN- MseI + CNN primer combinations were investigated employing the common wheat cultivar Triticum aestivum 'Chinese Spring.' On average, 103 fragments per primer combination were amplified, ranging from a maximum of 226 fragments to a minimum of 18 fragments. The primer combinations E + AAA - M + CNN and E + ATT - M + CNN produced very few distinct fragments. By using 15 randomly chosen EcoRI + ANN - MseI + CNN primer combinations, 928 AFLP markers were allocated to wheat chromosomes, of which 131 were assigned to specific chromosome arms. These AFLP markers were locus-specific and randomly distributed on the different chromosomes. In addition, 6 and 41 AFLP markers were simultaneously absent in two nulli-tetrasomics (NTs) of both homoeologous and non-homoeologous groups, respectively, whereas additional fragments were detected in N1BT1A, N5AT5D, and N6BT6A lines.

Key words: aneuploid, chromosome assignment, Triticum aestivum.
TAS49a dispersed repetitive sequence isolated from subtelomeric regions ofNicotianatomentosiformischromosomes
Authors: Horáková Mirka , Fajkus Jirí
Published: April 2011

We have isolated and characterized a new repetitive sequence, TAS49, from terminal restriction fragments of Nicotiana tomentosiformis genomic DNA by means of a modified vectorette approach. The TAS49 was found directly attached to telomeres of N. tabacum and one of its ancestors, N. tomentosiformis, and also at inner chromosome locations. No association with telomeres was detected neither in N. otophora nor in the second tobacco ancestor, N. sylvestris. PCR and Southern hybridization reveal similarities in the arrangement of TAS49 on the chromosomes of 9 species of the genus Nicotiana, implying its occurrence as a subunit of a conserved complex DNA repeat. TAS49 belongs to the family of dispersed repetitive sequences without features of transposons. The copy number of TAS49 varies widely in the genomes of 8 species analyzed being lowest in N. sylvestris, with 3300 copies per diploid genome. In N. tomentosiformis, TAS49 forms about 0.56% of the diploid genome, corresponding to 17 400 copies. TAS49 units are about 460 bp long and show about 90% of mutual homology, but no significant homology to DNA sequences deposited in GenBank and EMBL. Although genomic clones of TAS49 contain an open reading frame encoding a proline-rich protein similar to plant extensins, no mRNA transcript was detected. TAS49 is extensively methylated at CpG and CpNpG sites and its chromatin forms nucleosomes phased with a 170 ± 8 bp periodicity.

Key words: repetitive DNA sequence, subtelomere, plant, Nicotiana.
Cloning of two glutamate dehydrogenase cDNAs fromAsparagus officinalis: Sequence analysis and evolutionary implications
Authors: Pavesi Angelo , Ficarelli Antonella , Tassi Francesca , Restivo Francesco Maria
Published: April 2011

Two different amplification products, termed c1 and c2, showing a high similarity to glutamate dehydrogenase sequences from plants, were obtained from Asparagus officinalis using two degenerated primers and RT-PCR (reverse transcriptase polymerase chain reaction). The genes corresponding to these cDNA clones were designated aspGDHA and aspGDHB. Screening of a cDNA library resulted in the isolation of cDNA clones for aspGDHB only. Analysis of the deduced amino acid (aa) sequence from the full-length cDNA suggests that the gene product contains all regions associated with metabolic function of NAD glutamate dehydrogenase (NAD-GDH). A first phylogenetic analysis including only GDHs from plants suggested that the two GDH genes of A. officinalis arose by an ancient duplication event, pre-dating the divergence of monocots and dicots. Codon usage analysis showed a bias towards A/T ending codons. This tendency is likely due to the biased nucleotide composition of the asparagus genome, rather than to the translational selection for specific codons. Using principal coordinate analysis, the evolutionary relatedness of plant GDHs with homologous sequences from a large spectrum of organisms was investigated. The results showed a closer affinity of plant GDHs to GDHs of thermophilic archaebacterial and eubacterial species, when compared to those of unicellular eukaryotic fungi. Sequence analysis at specific amino acid signatures, known to affect the thermal stability of GDH, and assays of enzyme activity at non-physiological temperatures, showed a greater adaptation to heat-stress conditions for the asparagus and tobacco enzymes compared with the Saccharomyces cerevisiae enzyme.

Key words: Asparagus officinalis, glutamate dehydrogenase, complementary DNA, enzyme thermostability, principal coordinate analysis, evolution.
Cloning and characterization ofVine-1, a LTR-retrotransposon-like element inVitis viniferaL., and otherVitisspecies
Authors: Verriès C , Bès C , This P , Tesnière C
Published: April 2011

We report the organization of a grapevine chimeric gene Adhr-Vine-1, composed by an Adhr gene, into which a retroelement, Vine-1, was inserted. Sequence analysis revealed that Adhr is a member of the Adh multigene family, but does not correspond to any other grapevineAdh described to date. Vine-1, albeit defective, is the most complete LTR (long terminal repeat)-retrotransposon-like element described in Vitis vinifera L. It is 2392 bp long, with two almost identical LTRs (287 bp) in the same orientation, and flanked by direct repeats of a 5 bp host DNA. This element presents other features, characteristic of retroviruses and retrotransposons including inverted repeats, a primer binding site, and a polypurine tract. It has a single open reading frame (ORF) of 581 amino acids, potentially encoding for a gag protein and parts of the protease and integrase proteins. Vine-1 is most likely related to the copia-like type family, but with no significant similarity to any previously described plant retrotransposon or inserted element, nor to any eukaryotic element described to date. Vine-1 element has been found in Adhr at the same location in different V. vinifera cultivars, but not in some other analyzed Vitis species. These data suggest that Vine-1 insertion in Adhr is specific to V. vinifera, and has occurred after the Adh isogene separation, but prior to cultivar development. Sequences related to Vine-1 were revealed in multiple copies in the V. vinifera genome and, to a lesser extent, in other analyzed Vitis species. The polymorphism observed prompts us to question the role played by transposition in the evolution of the Vitis genus.

Key words: alcohol dehydrogenase, LTR, polymorphism, retrotransposon, Vitis vinifera L.
Chromosomal location of a Triticum timopheevii - derived powdery mildew resistance gene transferred to common wheat
Authors: Järve K , Peusha H O , Tsymbalova J , Tamm S , Devos K M , Enno T M
Published: April 2011

A dominant powdery mildew resistance gene introduced from Triticum timopheevii in line 146-155-T of common wheat, Triticum aestivum, was located on chromosome 6B by monosomic analysis. Restriction fragment length polymorphism (RFLP) and microsatellite analyses detected the presence of a T. timopheevii segment, translocated to chromosome 6B, with breakpoints between the loci Xpsr8/Xpsr964 on 6BS and Xpsr154/Xpsr546 on 6BL. The novel powdery mildew resistance gene, which has been designated Pm27, was shown to cosegregate with the microsatellite locus Xpsp3131, which is located on the introgressed T. timopheevii segment. The molecular data confirm the location of Pm27 on the translocated 6B chromosome.

Key words: monosomic analysis, RFLP, microsatellites, Pm27.
Morphology and content of dry matter and some elements in cells and stalks of Nevskia from an eutrophic lake
Authors: Heldal Mikal , Tumyr Ole
Published: April 2011

Pelagic colonies of Nevskia-like stalked bacteria were found in water samples from Lake Hjortlandsstemma at 8–12 m depth during the autumn circulation. In the samples studied, Nevskia was quite abundant and found together with a planktonic Gallionella. The apical cells of Nevskia were 0.5–0.7 μm wide and 1.5–3 μm long, curved rods with laterally excreted stalks and without measurable amounts of iron in the cells. The stalks were short and, in some instances, were composed of six to eight strands of fibrils. The stalks were also encrusted with iron, aluminum, and other elements. Dry matter content of the cells was 260–350 pg per cell. The organic material excreted as stalks was estimated to be 500–1200 fg per cell. The Nevskia described here is morphologically related to the genus Gallionella.
Characterization of the surface layer protein from Azotobacter vinelandii
Authors: Bingle Wade H. , Doran James L. , Page William J.
Published: April 2011

The regular surface array protein (S protein) of Azotobacter vinelandii was extracted from outer membrane fragments with distilled water and further purified by gel filtration chromatography. The protein was shown to behave anomalously on sodium dodecyl sulfate polyacrylamide gels producing a number of conformational isomers. The amino acid composition of S protein was similar to that of other surface array proteins, particularly in its lack of cysteine. The theoretical monomelic molecular weight of S protein was calculated to be 60 218 based on the total amino acid composition and the apparent molecular weight determined by sodium dodecyl sulfate – polyacrylamide gel electrophoresis. Circular dichroism spectra indicated that S protein was composed of approximately 35% β sheet structure, negligible α helix, with the remainder of the polypeptide backbone aperiodic in nature. The effect of the divalent cations Ca2+ and Mg2+ on the conformation of S protein was examined by circular dichroism spectroscopy; however, no conformational change was detected in response to the presence of these species nor did S-protein monomer aggregate into multimers in the presence of these cations. Purified S-protein monomer was inactive in divalent cation mediated reassembly of the S layer onto the surface of distilled water washed cells. A larger multimeric form present only in fresh preparations appeared to be the active species involved in in vitro reassembly of the A. vinelandii surface array.
Transfert de la flore caecale du hamster à la souris C3H axénique: utilisation de ce modèle pour étudier la flore de barrière anti-Clostridium difficile
Authors: Su W. J. , Bourlioux P. , Bournaud M. , Besnier M. O. , Fourniat J.
Published: April 2011

The purpose of this work was the research and development of an experimental model to study anti-Clostridium difficile caecal microflora in the hamster. First the existence of this "barrier" was verified in conventional hamsters. Then, the caecal flora from these animals was orally transferred to C3H germfree mice. The barrier effect was maintained in the axenic mice. The comparative bacteriological analysis of hamster and mouse feces did not reveal important variations in the dominant anaerobic flora (P < 0.01). After treatment with erythromycin, the barrier effect was maintained and while the disappearance of Escherichia coli was observed, the dominant anaerobic flora persisted. After dilution (10−2) and subsequent heating (70 °C, 10 min) of caecal contents, the inhibitory activity against C. difficile was maintained although the number of aerobic and aerotolerant bacteria was reduced. The isolation from caecal microflora of anaerobic strains implicated in the resistance to colonization is presently underway in Freter anaerobic chambers. [Translated by the journal]
The fatty acid composition of the conidia and mycelia of the fungus Aspergillus nidulans
Authors: Evans Joseph L. , Moclock Michael A. , Gealt Michael A.
Published: April 2011

The total fatty acids were characterized from conidia, exponential phase, and stationary phase Aspergillus nidulans. Several quantitative and qualitative variations were observed. Most notable was the approximately 15-fold increase in linolenate observed during the 1st day of incubation and its subsequent total disappearance by day 4.
Effect of chemical seed treatments on symptoms caused by seed-borne barley stripe mosaic virus in Vantage barley
Authors: Miller R. Vincent , Carroll Thomas W. , Sands David C.
Published: April 2011

A protocol was developed for testing chemical treatments for activity against seed-borne barley stripe mosaic virus. Vantage barley seeds infected with the MI-3 strain of the virus were allowed to imbibe dimethylsulfoxide solutions of test compounds. Of 49 compounds tested, alone or in combination with butylated hydroxyanisol, 18 reduced the number of plants expressing viral symptoms by up to 50%. Using an enzyme-linked immunosorbent assay to detect barley stripe mosaic virus, less than 2% of the asymptomatic plants arising from five chemical treatments were found to contain detectable virus antigen. In some treatments, reductions in the number of emerged plants with virus symptoms were correlated with reduced emergence.
Community dynamics of a mixed-bacterial culture growing on petroleum hydrocarbons in batch culture
Authors: Van Hamme Jonathan D , Odumeru Joseph A , Ward Owen P
Published: April 2011

The effects of various hydrocarbon substrates, and a chemical surfactant capable of enhancing crude-oil biodegradation, on the community structure of a mixed-bacterial inoculum were examined in batch culture. Of 1000 TSA-culturable isolates, 68.6% were identified at the genus level or better by phospholipid fatty acid analysis over 7-day time course experiments. Cultures were exposed to 20 g/L Bow River crude oil with and without 0.625 g/L Igepal CO-630 (a nonylphenol ethoxylate surfactant), 5 g/L saturates, 5 g/L aromatics, or 125 g/L refinery sludge. A group of six genera dominated the cultures: Acinetobacter, Alcaligenes, Ochrobactrum, Pseudomonas/Flavimonas, Stenotrophomonas, and Yersinia. Species from four of the genera were shown to be capable of hydrocarbon degradation, and counts of hydrocarbon degrading and total heterotrophic bacteria over time were nearly identical. Pseudomonas/Flavimonas and Stenotrophomonas normally dominated during the early portions of cultures, although the lag phase of Stenotrophomonas appears to have been increased by surfactant addition. Acinetobacter calcoaceticus was the most frequently isolated microorganism during exposure to the saturate fraction of crude oil. Regardless of substrate, the culture medium supported a greater variety of organisms during the latter portions of cultures. Understanding the community structure and dynamics of mixed bacterial cultures involved in treatment of heterogeneous waste substrates may assist in process development and optimization studies.Key words: mixed culture, phospholipid fatty acid analysis, petroleum hydrocarbons, community structure.
Detection of adenoviruses and enteroviruses in tap water and river water by reverse transcription multiplex PCR
Authors: Cho Hong Baek , Lee Seung-Hoon , Cho Jang-Cheon , Kim Sang-Jong
Published: April 2011

A reverse transcription (RT) multiplex polymerase chain reaction (PCR) assay was developed to simultaneously detect adenoviruses and enteroviruses, both of which have attracted much attention as molecular indices of viral pollution in environmental samples. The method involves a reverse transcription step, followed by a multiplex nested PCR in which the combination of primers amplifies cDNA from enteroviruses and adenoviruses. The sensitivity of this assay was found to be similar to that of each monoplex PCR or RT-PCR assay, and to be consistent regardless of relative concentrations of adenoviruses and enteroviruses. To assess suitability and environmental application of the RT multiplex PCR assay, a total of 12 river water samples and 4 tap water samples were analyzed by RT multiplex PCR, each monoplex PCR or RT-PCR, and cell culture assay on the Buffalo Green Monkey kidney cell line. The sensitivity of the RT multiplex PCR was also found to be similar to that of each monoplex PCR in environmental samples. This suggests the RT multiplex PCR assay could be applied to the routine monitoring of viral pollution in environ mental waters.Key words: adenoviruses, enteroviruses, multiplex PCR, tap water.
Bacterial metabolism of fluorene, dibenzofuran, dibenzothiophene, and carbazole
Authors: Bressler David C , Fedorak Phillip M
Published: April 2011

Fluorene and its three heteroatomic analogs, dibenzofuran, dibenzothiophene, and carbazole, are environmental contaminants in areas impacted by spills of creosote. In addition, dibenzofuran has been used as an insecticide, and it is formed from the photolysis of chlorinated biphenyl ethers. Many biodegradation studies of dibenzofuran have considered it as a model for chlorinated dibenzofurans, which are of greater environmental concern. This paper reviews the bacterial degradation of fluorene and its analogs. These compounds are susceptible to three different modes of initial oxidation: (i) the naphthalene-like attack, in which one of the aromatic rings is oxidized to a dihydrodiol; (ii) an angular dioxygenase attack, in which the carbon bonded to the methylene group in fluorene or to the heteroatoms in the analogs, and the adjacent carbon in the aromatic ring are both oxidized; and (iii) the five-membered ring attack, in which the methylene carbon atom in fluorene or the sulfur atom in dibenzothiophene is oxidized. The metabolites, enzymology, and genetics of these transformation are summarized. Literature data are presented, indicating that the electronegativity of the atom connecting the two aromatic rings influences the attack of the angular dioxygenase. In dibenzofuran and carbazole, the connecting atoms, O and N respectively, have high electronegativities, and these compounds serve as substrates for angular dioxygenases. In contrast, the connecting atoms in dibenzothiophene and fluorene, S and C respectively, have lower electronegativities, and these atoms must be oxidized before the angular dioxygenases attack these compounds.Key words: angular dioxygenase, carbazole, dibenzofuran, dibenzothiophene, fluorene.
Nutrition and phylogeny of predacious yeasts
Authors: Lachance Marc-André , Pupovac-Velikonja Ana , Natarajan Sabrina , Schlag-Edler Birgit
Published: April 2011

Yeast predation was studied with respect to the range of its distribution among ascomycetous yeasts, the range of yeast species that can be affected, and nutritional aspects of the phenomenon. The yeasts identified as predators belong to the Saccharomycopsis clade as defined on the basis of rDNA sequence relatedness. The 11 recognized species in the clade, plus three undescribed but related Candida species, were shown to be incapable of utilizing sulfate as sole source of sulfur, and all but two (Saccharomycopsis capsularis andSaccharomycopsis vini) were observed to penetrate and kill other yeasts under some conditions. Other unrelated sulfate transport-deficient yeasts (strains in the genera Pichia and Candida and the two known species of Starmera) are not predacious. The predacious species vary considerably as to the optimal environmental conditions that favour predation. Some are inhibited by the presence of rich nitrogenous nutrients, organic sulfur compounds, or higher concentrations of ammonium nitrogen, whereas other species may be stimulated under the same conditions. An attempt was made to correlate prey susceptibility to the excretion of substances that stimulate the growth of predators, but no correlation was detected between the two phenomena. The range of susceptible prey covers both ascomycetes and basidiomycetes, and includes Schizosaccharomyces pombe, which was previously thought to be immune. The achlorophyllous alga Prototheca zopfii is not killed by predacious yeasts, but the initial steps of penetration have been observed in some cases. Predacious species attack other predacious species, and in some cases, young cultures may penetrate older cultures of the same strain.Key words: predacious yeasts, sulfate transport deficiency, Saccharomycopsis.
Occurrence of pathogenic microorganisms in the Saint Lawrence River (Canada) and comparison of health risks for populations using it as their source of drinking water
Authors: Payment Pierre , Berte Aminata , Prévost Michèle , Ménard Bruno , Barbeau Benoît
Published: April 2011

A 300-km portion of the Saint Lawrence hydrological basin in the province of Québec (Canada) and 45 water treatment plants were studied. River water used by drinking water treatment plants was analyzed (6-L sample volumes) to determine the level of occurrence of bacterial indicators (total coliforms, fecal coliforms, and Clostridium perfringens) and pathogens (Giardia lamblia, Cryptosporidium, human enteric viruses). Pathogens and bacterial indicators were found at all sites at a wide range of values. Logistic regression analysis revealed significant correlations between the bacterial indicators and the pathogens. Physicochemical and treatment practices data were collected from most water treatment plants and used to estimate the level of removal of pathogens achieved under cold (0°C-4°C) and warm (20°C-25°C) water temperature conditions. The calculated removal values were then used to estimate the annual risk of Giardia infection using mathematical models and to compare the sites. The estimated range of probability of infection ranged from 0.75 to less than 0.0001 for the populations exposed. Given the numerous assumptions made, the model probably overestimated the annual risk, but it provided comparative data of the efficacy of the water treatment plants and thereby contributes to the protection of public health.Key words: public health, drinking water, health risk, pathogen occurrence.
Mutational analysis of the C-terminal anchoring domains ofStreptococcus mutansP1 antigen: Role of the LPXTGX motif in P1 association with the cell wall
Authors: Lee Song F , Gao Lingqiu
Published: April 2011

The salivary agglutinin-interacting adhesin P1 of Streptococcus mutans is anchored to the cell wall via the carboxy (C) terminus, which contains a wall-associated domain, a conserved LPXTGX motif, a hydrophobic domain, and a charged tail. To further investigate the role of the C-terminal anchoring regions in cell wall sorting and anchoring, mutational analysis was performed on P1 in this study. Three truncated P1 mutants and seven site-directed mutants were generated by a polymerase chain reaction-based technique. The mutated P1 genes were returned to the P1-negative S. mutans SM3352 for expression and localization studies by ELISA and Western immunoblotting. The results showed that P1 mutants with deletion of the hydrophobic domain and charged tail, or deletion of the charged tail alone resulted in the secretion of P1 to the culture medium. Results from cellular fractionation experiments with the truncated mutants showed that P1 was not trapped in the membrane or cytoplasm. The site-directed mutants showed normal distribution of P1 to the cell surface as compared to the wild-type. However, when cell walls prepared from the site-directed mutants were boiled with SDS, P1 could be removed readily from the mutants with Thr residue in the LPNTGV motif, altered to either Ser (T1531S) or Phe (T1531F); the mutant with Thr and Gly residues altered to two Phe residues (TG1531-1532FF), and the LPNTGV-deleted mutant (LPNTGV-). In contrast, the wild-type P1 and the other three site-directed P1 mutants (P1529V, N1530I, and G1532F) could not be removed by boiling SDS. When the cell wall P1s from the wild-type, mutants P1529V, N1530I, and G1532F were reacted with an antibody directed against the hydrophobic domain and charged tail, no reaction was detected. However, P1s from mutants T1531S, T1531F, TG1531-1532FF, and LPNTGV-were recognized by the antibody, indicating that the inability of these mutated P1s to firmly link to the cell wall was the result of failure in proteolytic cleavage of the hydrophobic domain and charged tail. In summary, the results suggest that the charged tail plays a decisive role in sorting P1 to the cell surface, while the LPXTGX motif determines the nature of P1-cell wall association. The Thr residue of the LPXTGX motif is required for enzymatic processing to link P1 to the cell wall, presumably via a covalent bond.Key words: antigen P1, cell wall proteins, Streptococcus mutans, protein anchoring, site-directed mutagenesis.
Biodiversity of killer activity in yeasts isolated from the Brazilian rain forest
Authors: Buzzini Pietro , Martini Alessandro
Published: April 2011

The occurrence of killer activity against a panel composed of 22 industrially and (or) medically important yeasts was investigated in 438 yeast and yeast-like cultures belonging to 96 species, isolated from different environments of the Brazilian rain forest. Altogether, 26% of ascomycetes, 56% of basidiomycetes, and 42% of yeast-like cultures exhibited killer activity against at least one of the panel yeasts. More than 15 species never reported before as toxin producers were found, with Pseudozyma antarctica, Trichosporon asteroides, and Geotrichum klebahnii, showing the broader activity spectra. Plasmid curing did not cure the killer phenotypes of Candida maltosa, Debaryomyces hansenii, G. klebahnii, Tr. asteroides, Cryptococcus laurentii, and Ps. antarctica.Key words: yeasts, killer activity, tropical environments.
Host cell invasion and intracellular residence byAeromonas salmonicida: Role of the S-layer
Authors: Garduño Rafael A , Moore Anne R , Olivier Gilles , Lizama Angela L , Garduño Elizabeth , Kay William W
Published: April 2011

Virulent strains of the fish pathogen Aeromonas salmonicida, which have surface S-layers (S+), efficiently adhere to, enter, and survive within macrophages. Here we report that S+bacteria were 10- to 20-fold more adherent to non-phagocytic fish cell lines than S-layer-negative (S-) mutants. When reconstituted with exogenous S-layers, these S-mutants regained adherence. As well, latex beads coated with purified S-layers were more adherent to fish cell lines than uncoated beads, or beads coated with disorganized S-layers, suggesting that purified S-layers were sufficient to mediate high levels of adherence, and that this process relied on S-layer structure. Gentamicin protection assays and electron microscopy indicated that both S+and S-A. salmonicida invaded non-phagocytic fish cells. In addition, these fish cells were unable to internalize S-layer-coated beads, clearly suggesting that the S-layer is not an invasion factor. Lipopolysaccharide (which is partially exposed in S+bacteria) appeared to mediate invasion. Surprisingly, A. salmonicida did not show net growth inside fish cells cultured in the presence of gentamicin, as determined by viable bacterial cell counts. On the contrary, bacterial viability sharply decreased after cell infection. We thus concluded that the S-layer is an adhesin that promotes but does not mediate invasion of non-phagocytic fish cell lines. These cell lines should prove useful in studies aimed at characterizing the invasion mechanisms of A. salmonicida, but of limited value in studying the intracellular residence and replication of this invasive bacterium in vitro.Key words: Aeromonas salmonicida, invasion, S-layer, lipopolysaccharide, capsule, intracellular bacteria, furunculosis.
Inoculation of somatic embryos of sweet potato with an arbuscular mycorrhizal fungus improves embryo survival and plantlet formation
Authors: Bressan Wellington , Siqueira de Carvalho Carlos Henrique , Sylvia David M
Published: April 2011

Responses of somatic embryos of sweet potato (Ipomoea batata (L.) Poir., cv. White Star) at different developmental stages to in vitro inoculation with Glomus etunicatum (Becker and Gerdemann) (isolate INVAM FL329) were evaluated. Somatic embryos were grown in glass tubes containing sterilized vermiculite and sand. A layer of natrosol plus White's medium was used as a carrier for arbuscular mycorrhizal (AM) fungal spores. Survival of embryos inoculated with AM fungi was significantly (P < 0.05) greater than that of noninoculated embryos at the rooted-cotyledonary-torpedo and rooted-elongated-torpedo developmental stages. Mycorrhizae significantly (P < 0.05) increased plantlet formation only when inoculation occurred at the rooted-elongated-torpedo developmental stage. The growth stage at which the embryos were inserted into the glass tubes exerted a significant influence upon plantlet formation, and plantlet formation was further enhanced by inoculation with G. etunicatum. Plantlet formation was greatest at the rooted-elongated-torpedo stage. These results demonstrate that inoculation of somatic embryos with AM fungi improves embryo survival and plantlet formation, and could enhance use of somatic embryos as synthetic seeds.Key words: mycorrhiza, Glomus etunicatum, somatic embryos.
Amylase hyper-producing haploid recombinant strains ofThermomyces lanuginosusobtained by intraspecific protoplast fusion
Authors: Rubinder K , Chadha B S , Singh S , Saini H S
Published: April 2011

Amylase hyper-producing, catabolite-repression-resistant, recombinant strains were produced by intraspecific protoplast fusion of thermophilic fungus Thermomyces lanuginosus strains, using well-characterized, morphological, and 2-deoxy-D-glucose resistant markers. The fusant heterokaryons exhibited enhanced amylase activities as compared to the amylase hyper-producing parental strain (T2). Diploids derived from heterokaryons segregated to stable haploid recombinant strains. In the haploid strain (Tlh 4q), approximately 5-fold higher specific activities of α-amylase and glucoamylase in the culture filtrate were observed as compared to the wild-type strain (W0).Key words: Thermomyces lanuginosus, protoplast fusion, amylase hyper-producing strain, catabolite repression.
Identification and characterization of nuclease activities in anaerobic environmental samples
Authors: Ruiz Thomas R , Andrews Sarah , Smith Geoffrey B
Published: April 2011

DNA-degrading activity from anaerobic samples of bovine ruminal fluid, primary anaerobic digestor wastewater, freshwater sediments, and marine sediments was observed in the presence of 5 mM EDTA. Nuclease activity experiments involved exposing salmon chromosomal DNA to the environmental samples in 50 mM pH 7.2 buffer, incubating at 37°C, and subjecting the products to electrophoresis. The same stock and concentration of EDTA used in these assays (5 mM) completely inhibited commercial grade DNase. Nuclease activity in two of the samples, ruminal fluid and wastewater, was further characterized. DNA degradation in the ruminal sample was significantly reduced when EDTA or citrate concentrations were increased to 50 mM or above. DNA degradation activity in ruminal fluid was associated with material that passed through a 0.22-µm filter, but wastewater activity was associated with material retained by a 3-µm filter. Degradation activity in the wastewater was resistant to heat pretreatment, whereas the rumen activity was heat-labile (70°C, 60 min). These results demonstrated the biochemical complexity of these two environments and that high molecular weight DNA has a short half-life in these anaerobic environments.Key words: nucleic acid degradation, ruminal fluid, wastewater.
Substrate-dependent differential expression ofHumicola griseavar.thermoideacellobiohydrolase genes
Authors: Poças-Fonseca Marcio J , Silva-Pereira Ildinete , Rocha Bruno B , Azevedo Maristella de O
Published: April 2011

Transcription of fungal cellulase genes may be affected by substrate induction. We studied the expression of Humicola grisea var. thermoidea cellobiohydrolase genes (cbh1.1 and cbh1.2) under induction by several soluble and insoluble carbon sources. Using the RT-PCR technique, the cbh1.2 transcript was detected in all the conditions assayed along the growth curve. Catabolite repression, which frequently occurs in other fungal cellulolytic systems, was not observed. On the other hand, cbh1.1 transcription was shown to be driven by insoluble and complex lignocellulosic substrates. In summary, the cbh1.2 gene product is constitutively produced, while cbh1.1 seems to respond to a distinct regulatory mechanism.Key words: Humicola, cellobiohydrolase genes, gene expression, carbon sources, lignocellulosic substrates.