bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and Application of a Real-Time PCR Approach for Quantification of Uncultured Bacteria in the Central Baltic Sea
Authors: Labrenz Matthias , Brettar Ingrid , Christen Richard , Flavier Sebastien , Bötel Julia , Höfle Manfred G.
Published: August 2004

We have developed a highly sensitive approach to assess the abundance of uncultured bacteria in water samples from the central Baltic Sea by using a noncultured member of the “
Epsilonproteobacteria
” related to
Thiomicrospira denitrificans
as an example. Environmental seawater samples and samples enriched for the target taxon provided a unique opportunity to test the approach over a broad range of abundances. The approach is based on a combination of taxon- and domain-specific real-time PCR measurements determining the relative
T. denitrificans-
like 16S rRNA gene and 16S rRNA abundances, as well as the determination of total cell counts and environmental RNA content. It allowed quantification of
T. denitrificans
-like 16S rRNA molecules or 16S rRNA genes as well as calculation of the number of ribosomes per
T. denitrificans
-like cell. Every real-time measurement and its specific primer system were calibrated using environmental nucleic acids obtained from the original habitat for external standardization. These standards, as well as the respective samples to be measured, were prepared from the same DNA or RNA extract. Enrichment samples could be analyzed directly, whereas environmental templates had to be preamplified with general bacterial primers before quantification. Preamplification increased the sensitivity of the assay by more than 4 orders of magnitude. Quantification of enrichments with or without a preamplification step yielded comparable results.
T. denitrificans-
like 16S rRNA molecules ranged from 7.1 × 10
3
to 4.4 × 10
9
copies ml
−1
or 0.002 to 49.7% relative abundance.
T. denitrificans
-like 16S rRNA genes ranged from 9.0 × 10
1
to 2.2 ×10
6
copies ml
−1
or 0.01 to 49.7% relative abundance. Detection limits of this real-time-PCR approach were 20 16S rRNA molecules or 0.2 16S rRNA gene ml
−1
. The number of ribosomes per
T. denitrificans-
like cell was estimated to range from 20 to 200 in seawater and reached up to 2,000 in the enrichments. The results indicate that our real-time PCR approach can be used to determine cellular and relative abundances of uncultured marine bacterial taxa and to provide information about their levels of activity in their natural environment.
Biological Effects of
Trichoderma harzianum
Peptaibols on Mammalian Cells
Authors: Peltola Joanna , Ritieni Alberto , Mikkola Raimo , Grigoriev Pavel A. , Pócsfalvi Gabriella , Andersson Maria A. , Salkinoja-Salonen Mirja S.
Published: August 2004

Trichoderma
species isolated from water-damaged buildings were screened for toxicity by using boar sperm cells as indicator cells. The crude methanolic cell extract from
Trichoderma harzianum
strain ES39 inhibited the boar sperm cell motility at a low exposure concentration (50% effective concentration, 1 to 5 μg [dry weight] ml of extended boar semen
−1
). The same exposure concentration depleted the boar sperm cells of NADH
2
. Inspection of the exposed boar sperm cells by transmission electron microscopy revealed damage to the plasma membrane. By using the black lipid membrane technique, it was shown that the semipurified metabolites (eluted from a SepPak C
18
cartridge) of
T. harzianum
strain ES39 induced voltage-dependent conductivity. The high-performance liquid chromatography-purified metabolites of
T. harzianum
strain ES39 dissipated the mitochondrial membrane potential (Δψ
m
) of human lung epithelial carcinoma cells (cell line A549). The semipurified metabolites (eluted from a SepPak C
18
cartridge) of
T. harzianum
strain ES39 were analyzed by mass spectrometry (MS). Matrix-assisted laser desorption ionization and nanoflow electrospray ionization MS revealed five major peptaibols, each of which contained 18 residues and had a mass ranging from 1,719 to 1,775 Da. Their partial amino acid sequences were determined by collision-induced dissociation tandem MS.
Host Physiology and Pathogenic Variation of
Cochliobolus heterostrophus
Strains with Mutations in the G Protein Alpha Subunit, CGA1
Authors: Degani Ofir , Maor Rudy , Hadar Ruthi , Sharon Amir , Horwitz Benjamin A.
Published: August 2004

Conserved eukaryotic signaling proteins participate in development and disease in plant-pathogenic fungi. Strains with mutations in
CGA1
, a heterotrimeric G protein G alpha subunit gene of the maize pathogen
Cochliobolus heterostrophus
, are defective in several developmental pathways. Conidia from
CGA1
mutants germinate as abnormal, straight-growing germ tubes that form few appressoria, and the mutants are female sterile. Nevertheless, these mutants can cause normal lesions on plants, unlike other filamentous fungal plant pathogens in which functional homologues of
CGA1
are required for full virulence. Δ
cga1
mutants of
C. heterostrophus
were less infective of several maize varieties under most conditions, but not all, as virulence was nearly normal on detached leaves. This difference could be related to the rapid senescence of detached leaves, since delaying senescence with cytokinin also had differential effects on the virulence of the wild type and the Δ
cga1
mutant. In particular, detached leaves may provide a more readily available nutrient source than attached leaves. Decreased fitness of Δ
cga1
as a pathogen may reflect conditions under which full virulence requires signal transduction through CGA1-mediated pathways. The virulence of these signal transduction mutants is thus affected differentially by the physiological state of the host.
Two Morphological Types of Cell Appendages on a Strongly Adhesive Bacterium, Acinetobactersp. Strain Tol 5
Authors: Ishii Shun'ichi , Koki Jun , Unno Hajime , Hori Katsutoshi
Published: August 2004

Two morphological types of appendages, an anchor-like appendage and a peritrichate fibril-type appendage, have been observed on cells of an adhesive bacterium,Acinetobactersp. strain Tol 5, by use of recently developed electron microscopic techniques. The anchor extends straight to the substratum without branching and tethers the cell body at its end at distances of several hundred nanometers, whereas the peritrichate fibril attaches to the substratum in multiple places, fixing the cell at much shorter distances.
Translational Features of Human Alpha 2b Interferon Production in
Escherichia coli
Authors: Valente C. A. , Prazeres D. M. F. , Cabral J. M. S. , Monteiro G. A.
Published: August 2004

The yield of human alpha 2b interferon in
Escherichia coli
was optimized by replacement of low-usage arginine codons located in the mRNA 5′ end. The differences observed among the various gene variants suggest that codon usage, Shine-Dalgarno-like sequences, and mRNA secondary structure contribute to the performance of
E. coli
translation machinery.
Cyanobacterial Protease Inhibitor Microviridin J Causes a Lethal Molting Disruption in
Daphnia pulicaria
Authors: Rohrlack Thomas , Christoffersen Kirsten , Kaebernick Melanie , Neilan Brett A.
Published: August 2004

Laboratory experiments identified microviridin J as the source of a fatal molting disruption in
Daphnia
species organisms feeding on
Microcystis
cells. The molting disruption was presumably linked to the inhibitory effect of microviridin J on daphnid proteases, suggesting that hundreds of further cyanobacterial protease inhibitors must be considered potentially toxic to zooplankton.
Telomeric and interstitial telomeric-like DNA sequences in Orthoptera genomes
Authors: López-Fernández C , Pradillo E , Zabal-Aguirre M , Fernández J L , García de la Vega C , Gosálvez J
Published: August 2004

A (TTAGG)n-specific telomeric DNA probe was hybridized to 11 orthopteroid insect genomes by fluorescence in situ hybridization. Nine different genera, mainly distributed within two evolutionary branches with male chromosome numbers 2n = 23 and 2n = 17 were included in the analysis. Telomere sequences yielded positive signals in every telomere and there was a considerable number of interstitial telomeric-like sequences, mainly located at the distal end of some, but not all, subterminal chromosome regions. One of the species, Pyrgomorpha conica, showed massive hybridization signals associated with constitutive heterochromatin. The results are discussed along two lines: (i) the chromosomal evolutionary trends within this group of insects and (ii) the putative role that ITs may play in a genome when they are considered telomere-derived, but not telomere-functional, DNA sequences.Key words: telomere, insect chromosomes, karyotype evolution, fluorescence in situ hybridization.
Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes
Authors: McKay S J , Trautner J , Smith M J , Koop B F , Devlin R H
Published: August 2004

A defining character of the piscine family Salmonidae is autotetraploidy resulting from a genome-doubling event some 25–100 million years ago. Initially, duplicated genes may have undergone concerted evolution and tetrasomic inheritance. Homeologous chromosomes eventually diverged and the resulting reduction in recombination and gene conversion between paralogous genes allowed the re-establishment of disomic inheritance. Among extant salmonine fishes (e.g. salmon, trout, char) the growth hormone (GH) gene is generally represented by two functional paralogs, GH1 and GH2. Sequence analyses of salmonid GH genes from species of subfamilies Coregoninae (whitefish, ciscos) and Salmoninae were used to examine the evolutionary history of the duplicated GH genes. Two divergent GH gene paralogs were also identified in Coregoninae, but they were not assignable to the GH1 and GH2 categories. The average sequence divergence between the coregonine GH genes was more than twofold lower than the corresponding divergence between the salmonine GH1 and GH2. Phylogenetic analysis of the coregonine GH paralogs did not resolve their relationship to the salmonine paralogs. These findings suggest that disomic inheritance of two GH genes was established by different mechanisms in these two subfamilies.Key words: salmon, phylogeny, growth hormone, disomy, tetraploidy.
Cloning and characterization of a transposable-like repeat in the heterochromatin of the darkling beetle Misolampus goudoti
Authors: Pons Joan
Published: August 2004

A long repeat unit of the PstI family in Misolampus goudoti (Coleoptera, Tenebrionodae) is characterized in this work. The 30 sequenced units have small differences in length (consensus 1169 bp), but very similar nucleotide composition (mean 61.1% A+T). PstI repeats contain a 36-bp-long inverted repeat at both the 5′ and 3′ ends, with a fully conserved 16-bp-long motif similar to those found in class II transposable elements. However, the transposable-like PstI repeats seems to be defective, since they do not encode for any protein related with transposition. Interestingly, energetically stable hairpins resembled the structure of a miniature interspersed transposable element, suggesting that the PstI satellite DNA family in M. goudoti may have originated from an ancestral active transposable element as also described in Drosophila guanche. The presence of transposable-like structure along with the non-detection of gene conversion or unequal crossing-over events suggest that transposition could be one of the putative molecular mechanisms involved in the strong amplification and (or) homogenization of these repeats. A putative transposition of PstI repeats allowing their genomic mobility also could explain why this satellite is widely distributed to all heterochromatic regions, telomeres, pericentromeric regions, and on the Y chromosome, whereas satellites of other tenebrionids lacking transposable-like structures are restricted only to pericentromeric regions.Key words: transposable elements, MITE, satellite DNA, heterochromatin, telomere, beetle, Tenebrionidae.
Assessment of genetic variability of haploids extracted from tetraploid (2n = 4x = 48)Solanum tuberosum
Authors: Ercolano M R , Carputo D , Li J , Monti L , Barone A , Frusciante L
Published: August 2004

The objectives of this study were to assess the genetic variability of haploids (2n = 2x = 24) extracted from tetraploid Solanum tuberosum through 4x × 2x crosses with Solanum phureja. Molecular and phenotypic analyses were performed to fingerprint the genotypes used and to evaluate their potential use in breeding programs. AFLP analysis revealed the presence of specific bands derived from the tetraploid seed parent S. phureja, as well as ex novo originated bands. On average, 210 bands were visualized per genotype, 149 (70%) of which were common to both parental genotypes. The percentage of S. tuberosum specific bands ranged from 25.1% to 18.6%, with an average of 22%. The fraction of genome coming from S. phureja ranged from 1.9% to 6.5%, with an average value of 4%. The percentage of ex novo bands varied from 1.9% to 9.0%. The presence of S. phureja DNA is very interesting because it indicated that S. phureja pollinator is involved in the mechanism of haploid formation. The characterization for resistance to Erwinia carotovora subsp. carotovora and potato virus X (PVX) provided evidence that haploids may express traits that are lacking in the tetraploids they come from, which can be useful for both genetic studies and breeding purposes. It is noteworthy that genotypes combining resistance to both diseases and good pollen stainability were identified. Other possible breeding implications owing to the presence of S. phureja genome in the haploids analyzed are discussed.Key words: AFLP, S. phureja, resistance traits, potato.
Comparative analysis of aBrassicaBAC clone containing several major aliphatic glucosinolate genes with its correspondingArabidopsissequence
Authors: Gao Muqiang , Li Genyi , Yang Bo , McCombie W Richard , Quiros Carlos F
Published: August 2004

We compared the sequence of a 101-kb-long bacterial artificial chromosome (BAC) clone (B21H13) from Brassica oleracea with its homologous region in Arabidopsis thaliana. This clone contains a gene family involved in the synthesis of aliphatic glucosinolates. The A. thaliana homologs for this gene family are located on chromosome IV and correspond to three 2-oxoglutarate-dependent dioxygenase (AOP) genes. We found that B21H13 harbors 23 genes, whereas the equivalent region in Arabidopsis contains 37 genes. All 23 common genes have the same order and orientation in both Brassica and Arabidopsis. The 16 missing genes in the broccoli BAC clone were arranged in two major blocks of 5 and 7 contiguous genes, two singletons, and a twosome. The 118 exons comprising these 23 genes have high conservation between the two species. The arrangement of the AOP gene family in A. thaliana is as follows: AOP3 (GS-OHP)  AOP2 (GS-ALK)  pseudogene  AOP1. In contrast, in B. oleracea (broccoli and collard), two of the genes are duplicated and the third, AOP3, is missing. The remaining genes are arranged as follows: Bo-AOP2.1 (BoGSL-ALKa)  pseudogene  AOP2.2 (BoGSL-ALKb)  AOP1.1  AOP1.2. When the survey was expanded to other Brassica accessions, we found variation in copy number and sequence for the Brassica AOP2 homologs. This study confirms that extensive rearrangements have taken place during the evolution of the Brassicacea at both gene and chromosomal levels.Key words: Brassica oleracea, B. rapa, comparative genomics, glucosinolates.
Conversion of AFLP markers associated with FHB resistance in wheat into STS markers with an extension-AFLP method
Authors: Xu D H , Ban T
Published: August 2004

Amplified fragment length polymorphism (AFLP) has proven a powerful tool for tagging genes or quantitative trait loci (QTLs) of interest in plants. However, conversion of AFLP markers into sequence-tagged site (STS) markers is technically challenging in wheat owing to the complicated nature of its genome. In this study, we developed an "extension-AFLP" method to convert AFLP markers associated with Fusarium head blight (FHB) resistance into STS markers. When an AFLP marker of interest was detected with an EcoRI+3MseI+4-selective primer combination, the PCR product was used as a template for an additional selective amplification with four primer pairs, in which one additional selective base (either A, C, G, or T) was added to the 3' end of one of the two primers. The extended primer pair that produced the targeted band was further extended by adding each of the four selective nucleotide bases for the next round of selective amplification. Extension selective amplification was performed until the target bands became clear enough for subsequent cloning and sequencing. By using the extension-AFLP method, we successfully converted two AFLP markers located on chromosome 3BS and associated with FHB resistance into STS markers. Our results indicated that the extension-AFLP method is an efficient approach for converting AFLP markers into STS markers in wheat. The developed STS markers might be used for marker-assisted selection (MAS) for FHB resistance in wheat breeding programs.Key words: extension-AFLP, wheat, STS, FHB resistance.
Cytogenetic characterization and fae1 gene variation in progenies from asymmetric somatic hybrids between Brassica napus and Crambe abyssinica
Authors: Wang Y P , Snowdon R J , Rudloff E , Wehling P , Friedt W , Sonntag K
Published: August 2004

Sexual progenies of asymmetric somatic hybrids between Brassica napus and Crambe abyssinica were analyzed with respect to chromosomal behavior, fae1 gene introgression, fertility, and fatty-acid composition of the seed. Among 24 progeny plants investigated, 11 plants had 38 chromosomes and were characterized by the occurrence of normal meiosis with 19 bivalents. The other 13 plants had more than 38 chromosomes, constituting a complete chromosomal set from B. napus plus different numbers of additional chromosomes from C. abyssinica. The chromosomes of B. napus and C. abyssinica origin could be clearly discriminated by genomic in situ hybridization (GISH) in mitotic and meiotic cells. Furthermore, meiotic GISH enabled identification of intergenomic chromatin bridges and of asynchrony between the B. napus and C. abyssinca meiotic cycles. Lagging, bridging and late disjunction of univalents derived from C. abyssinica were observed. Analysis of cleaved amplified polymorphic sequence (CAPS) markers derived from the fae1 gene showed novel patterns different from the B. napus recipient in some hybrid offspring. Most of the progeny plants had a high pollen fertility and seed set, and some contained significantly greater amounts of seed erucic acid than the B. napus parent. This study demonstrates that a part of the C. abyssinica genome can be transferred into B. napus via asymmetric hybridization and maintained in sexual progenies of the hybrids. Furthermore, it confirms that UV irradiation improves the fertility of the hybrid and of its sexual progeny via chromosomal elimination and facilitates the introgression of exotic genetic material into crop species.Key words: asymmetric somatic hybrid, Brassica napus, Crambe abyssinica, cytogenetics, fae1 gene.
Segmental duplications within theGlycine maxgenome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes
Authors: Pagel Janice , Walling Jason G , Young Nevin D , Shoemaker Randy C , Jackson Scott A
Published: August 2004

Soybean (Glycine max L. Merr.) is presumed to be an ancient polyploid based on chromosome number and multiple RFLP fragments in genetic mapping. Direct cytogenetic observation of duplicated regions within the soybean genome has not heretofore been reported. Employing flourescence in situ hybridization (FISH) of genetically anchored bacterial artificial chromosomes (BACs) in soybean, we were able to observe that the distal ends of molecular linkage group E had duplicated regions on linkage groups A2 and B2. Further, using fiber-FISH, it was possible to measure the molecular size and organization of one of the duplicated regions. As FISH did not require repetitive DNA for blocking fluorescence signals, we assume that the 200-kb genome region is relatively low in repetitive sequences. This observation, along with the observation that the BACs are located in distal euchromatin regions, has implications for genome structure/evolution and the approach used to sequence the soybean genome.Key words: soybean, genome evolution, FISH, chromosomes, physical mapping.
Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes ofAcricotopus
Authors: Staiber Wolfgang
Published: August 2004

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.
Karyotype characterization of the lake sturgeon, Acipenser fulvescens (Rafinesque 1817) by chromosome banding and fluorescent in situ hybridization
Authors: Fontana Francesco , Bruch Ronald M , Binkowski Fred P , Lanfredi Massimo , Chicca Milvia , Beltrami Nicola , Congiu Leonardo
Published: August 2004

A karyotype analysis using several staining techniques was carried out on the North American lake sturgeon, Acipenser fulvescens. The chromosome number was found to be 2n = 262 ± 6. A representative karyotype of 264 chromosomes was composed of 134 meta- and submetacentrics, 70 telo- and acrocentrics, and 60 microchromosomes. The constitutive heterochromatin, revealed by C banding, was localized in various positions on several chromosomes, including microchromosomes. The signals of fluorescent in situ hybridization (FISH) with a HindIII satellite DNA probe were visible as centromeric heterochromatin blocks on 48 chromosomes. The telomeric repeat (TTAGGG)n detected by FISH was localized at both ends of all chromosomes and two chromosomes were entirely marked. Fluorescent staining with GC-specific chromomycin A3 showed recognizable fluorescent regions, whereas a more uniform base composition was revealed by the AT-specific 4',6-diamidino-2-phenylindole (DAPI). After silver staining, the active nucleolar organizer regions (NORs) were detected on 12 chromosomes. FISH with the 5S probe showed four signals on four small chromosomes. Our data suggest that A. fulvescens is a tetraploid species.Key words: karyotype, C banding, telomeric sequence, fluorochrome staining, satellite DNA, 5S rDNA.
QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativaL.) and African (O. glaberrimaS.) rice
Authors: Li Jiming , Xiao Jinhua , Grandillo Silvana , Jiang Longying , Wan Yizhen , Deng Qiyun , Yuan Longping , McCouch Susan R
Published: August 2004

An interspecific advanced backcross population derived from a cross between Oryza sativa 'V20A' (a popular male-sterile line used in Chinese rice hybrids) and Oryza glaberrima (accession IRGC No. 103544 from Mali) was used to identify quantitative trait loci (QTL) associated with grain quality and grain morphology. A total of 308 BC3F1hybrid families were evaluated for 16 grain-related traits under field conditions in Changsha, China, and the same families were evaluated for RFLP and SSR marker segregation at Cornell University (Ithaca, N.Y.). Eleven QTL associated with seven traits were detected in six chromosomal regions, with the favorable allele coming from O. glaberrima at eight loci. Favorable O. glaberrima alleles were associated with improvements in grain shape and appearance, resulting in an increase in kernel length, transgressive variation for thinner grains, and increased length to width ratio. Oryza glaberrima alleles at other loci were associated with potential improvements in crude protein content and brown rice yield. These results suggested that genes from O. glaberrima may be useful in improving specific grain quality characteristics in high-yielding O. sativa hybrid cultivars.Key words: quantitative trait loci (QTL), grain quality, molecular markers, O. sativa, O. glaberrima.
Colocation between a gene encoding the bZip factor SPA and an eQTL for a high-molecular-weight glutenin subunit in wheat (Triticum aestivum)
Authors: Guillaumie Sabine , Charmet Gilles , Linossier Laurent , Torney Valérie , Robert Nathalie , Ravel Catherine
Published: August 2004

The quality of wheat grain is largely determined by the quantity and composition of storage proteins (prolamins) and depends on mechanisms underlying the regulation of expression of prolamin genes. The endosperm-specific wheat basic region leucine zipper (bZIP) factor storage protein activator (SPA) is a positive regulator that binds to the promoter of a prolamin gene. The aim of this study was to map SPA (the gene encoding bZIP factor SPA) and genomic regions associated with quantitative variations of storage protein fractions using F7recombinant inbred lines (RILs) derived from a cross between Triticum aestivum 'Renan' and T. aestivum 'Récital'. SPA was mapped through RFLP using a cDNA probe and a specific single nucleotide polymorphism (SNP) marker. Storage protein fractions in the parents and RILs were quantified using capillary electrophoresis. Quantitative trait loci (QTLs) for protein were detected and mapped on six chromosome regions. One QTL, located on the long arm of chromosome 1B, explained 70% of the variation in quantity of the x subunit of Glu-B1. Genetic mapping suggested that SPA is located on chromosome arm 1L and is also present in the confidence interval of the corresponding QTL for Glu-B1x on 1BL, suggesting that SPA might be a candidate gene for this QTL.Key words: Triticum aestivum, quantitative trait locus (QTL), single nucleotide polymorphism (SNP), storage protein activator (SPA), high-molecular-weight glutenin subunit (HMW-GS).
AFLP analysis of Cynodon dactylon (L.) Pers. var. dactylon genetic variation
Authors: Wu Y Q , Taliaferro C M , Bai G H , Anderson M P
Published: August 2004

Cynodon dactylon (L.) Pers. var. dactylon (common bermudagrass) is geographically widely distributed between about lat 45°N and lat 45°S, penetrating to about lat 53°N in Europe. The extensive variation of morphological and adaptive characteristics of the taxon is substantially documented, but information is lacking on DNA molecular variation in geographically disparate forms. Accordingly, this study was conducted to assess molecular genetic variation and genetic relatedness among 28 C. dactylon var. dactylon accessions originating from 11 countries on 4 continents (Africa, Asia, Australia, and Europe). A fluorescence-labeled amplified fragment length polymorphism (AFLP) DNA profiling method was used to detect the genetic diversity and relatedness. On the basis of 443 polymorphic AFLP fragments from 8 primer combinations, the accessions were grouped into clusters and subclusters associating with their geographic origins. Genetic similarity coefficients (SC) for the 28 accessions ranged from 0.53 to 0.98. Accessions originating from Africa, Australia, Asia, and Europe formed major groupings as indicated by cluster and principal coordinate analysis. Accessions from Australia and Asia, though separately clustered, were relatively closely related and most distantly related to accessions of European origin. African accessions formed two distant clusters and had the greatest variation in genetic relatedness relative to accessions from other geographic regions. Sampling the full extent of genetic variation in C. dactylon var. dactylon would require extensive germplasm collection in the major geographic regions of its distributional range.Key words: common bermudagrass, AFLP marker, genetic relatedness.
Histone modifications and DNA double-strand break repair
Authors: Moore John D , Krebs Jocelyn E
Published: August 2004

The roles of different histone modifications have been explored extensively in a number of nuclear processes, particularly in transcriptional regulation. Only recently has the role of histone modification in signaling or facilitating DNA repair begun to be elucidated. DNA broken along both strands in the same region, a double-strand break, is damaged in the most severe way possible and can be the most difficult type of damage to repair accurately. To successfully repair the double-strand break, the cell must gain access to the damaged ends of the DNA and recruit repair factors, and in the case of homologous recombination repair, the cell must also find, colocalize, and gain access to a suitable homologous sequence. In the repair of a double-strand break, the cell must also choose between homologous and non-homologous pathways of repair. Here, we will briefly review the mechanisms of double-strand-break repair, and discuss the known roles of histone modifications in signaling and repairing double-strand breaks.Key words: H23A, double strand break repair, histone modification.
Activation domains of gene-specific transcription factors: are histones among their targets?
Authors: Erkine Alexandre M
Published: August 2004

Activation domains of promoter-specific transcription factors are critical entities involved in recruitment of multiple protein complexes to gene promoters. The activation domains often retain functionality when transferred between very diverse eukaryotic phyla, yet the amino acid sequences of activation domains do not bear any specific consensus or secondary structure. Activation domains function in the context of chromatin structure and are critical for chromatin remodeling, which is associated with transcription initiation. The mechanisms of direct and indirect recruitment of chromatin-remodeling and histone-modifying complexes, including mechanisms involving direct interactions between activation domains and histones, are discussed.Key words: activation domain, transcription, chromatin, nucleosome.
New twists on H2A.Z: a histone variant with a controversial structural and functional past
Authors: Dryhurst Deanna , Thambirajah Anita A , Ausió Juan
Published: August 2004

Integration of histone variants into chromatin organization allows for functional specification of chromatin regions. Recent functional analyses of H2A.Z have ascribed to it a multiplicity of complex and often opposing roles in developmental and homeostatic regulation. However, although the manner in which this essential histone variant is able to mediate its effects is not entirely well understood, current work has sought to investigate its mode of action. It is becoming increasingly clear that H2A.Z does not necessarily act independently, but rather, in conjunction with trans-acting factors to elicit chromatin changes. The nature of these structural changes has remained somewhat controversial but nevertheless exemplifies the seemingly multifaceted nature of H2A.Z.Key words: histone H2A.Z, chromatin structure, transcription, heterochromatin.
The long hand of the small RNAs reaches into several levels of gene regulation
Authors: Nolan Tony , Cogoni Carlo
Published: August 2004

Small RNA molecules such as siRNAs and miRNAs represent a new class of molecules that have been implicated in a wide range of diverse gene silencing phenomena. It is now becoming clear that these two similar molecules share several common features in both their biogenesis and their mechanism of action. Thus, the siRNA and miRNA pathways may have evolved from a common ancestral mechanism that has diverged to play important roles in developmental regulation, genomic organisation, and cellular defence against foreign nucleic acids.Key words: miRNA, siRNA, post-transcriptional gene silencing, RNAi, heterochromatin.
Synthetic zinc finger peptides: old and novel applications
Authors: Corbi Nicoletta , Libri Valentina , Onori Annalisa , Passananti Claudio
Published: August 2004

In the last decade, the efforts in clarifying the interaction between zinc finger proteins and DNA targets strongly stimulated the creativity of scientists in the field of protein engineering. In particular, the versatility and the modularity of zinc finger (ZF) motives make these domains optimal building blocks for generating artificial zinc finger peptides (ZFPs). ZFPs can act as transcription modulators potentially able to control the expression of any desired gene, when fused to an appropriate effector domain. Artificial ZFPs open the possibility to re-program the expression of specific genes at will and can represent a powerful tool in basic science, biotechnology and gene therapy. In this review we will focus on old, novel and possible future applications of artificial ZFPs.Key words: synthetic zinc finger, recognition code, artificial transcription factor, chromatin modification, gene therapy.
Telomeres, telomerase, and apoptosis
Authors: Mondello Chiara , Scovassi A Ivana
Published: August 2004

Telomeres are specialized high-order chromatin structures that cap the ends of eukaryotic chromosomes. In vertebrates, telomeric DNA is composed of repetitions of the TTAGGG hexanucleotide, is bound to a set of specific proteins, and is elongated by the reverse transcriptase enzyme telomerase. Telomerase activity is promptly detected in cells with an indefinite replicative potential, such as cancer cells, while is almost undetectable in normal cells, which are characterized by a limited life span. Mounting evidence indicates that the maintenance of telomere integrity and telomerase protect cells from apoptosis. Disruption of the telomere capping function and (or) telomerase inhibition elicit an apoptotic response in cancer cells, while restoration of telomerase activity in somatic cells confers resistance to apoptosis. The possible mechanisms linking telomeres, telomerase and apoptosis are discussed in this review, together with the impact of this field in anticancer research.Key words: telomeres, telomerase, telomeric proteins, apoptosis, tumorigenesis.
Genetic analysis of Canadian isolates of C:2a:P1.2,5 and B:2a:P1.2,5Neisseria meningitidisstrains belonging to the hypervirulent clone of ET-15
Authors: Tyler Shaun , Tsang Raymond
Published: August 2004

Isolates of the hypervirulent Neisseria meningitidis clone ET-15 found to express the serogroup B antigen were investigated and compared with representative members of serogroup B and C isolates. Clonal-clustering methods clearly grouped the B:ET15 isolates with C:ET15 isolates, indicating the only major difference between the two groups was in the capsule expressed. The organization of the cps operon from the B:ET15 isolates was found to be consistent with typical serogroup B isolates and differed from serogroup C isolates only in the sialyl transferase gene present. This suggests that these strains arose via recombination of the sialyl transferase gene. Specific points of recombination could not be identified, however, the majority (64%) of the B:ET15 isolates contained a copy of pseudo-IS1106 downstream of the cps operon indicating the potential for a common ancestral origin. The combination of pulsed-field gel electrophoresis (PFGE) and sequence analysis of targeted regions of the cps operon permitted the differentiation of most B:ET15 isolates indicating that they likely arose from separate genetic events and do not represent the emergence and spread of a new clone. However, two isolates that appeared identical by all methods employed were temporally and geographically related although no epidemiological evidence is available indicating a link between these strains.Key words: Neisseria meningitidis, ET-15, cps operon, capsule switching, IS element.
Enhancement of the antifungal activity ofBacillus subtilisF29-3 by the chitinase encoded byBacillus circulans chiAgene
Authors: Chen Chao-Ying , Wang Yi-Huei , Huang Chien-Jui
Published: August 2004

Bacillus subtilis F293 is an antagonistic bacterium against a wide range of fungal species. In order to determine the effect of chitinase on the antifungal activity of B. subtilis F293, a 2.4-kb DNA fragment containing the chiA gene of Bacillus circulans WL-12 was ligated into a shuttle vector pHY300PLK and transformed into B. subtilis F293. A bioassay conducted on the culture supernatant showed that, in comparison to the B. subtilis control strain, B. subtilis F293 expressing the chiA gene exhibited a greater inhibition of spore germination of Botrytis elliptica, indicating that chitinase could enhance the antifungal function conferred by B. subtilis F293.Key words: Bacillus subtilis, antifungal activity, chiA, Bacillus circulans.
Population patterns and antimicrobial resistance ofAeromonasin urban playa lakes
Authors: Warren William J , Jeter Randall M , Kimbrough Robert C , Zak John C
Published: August 2004

Bacteria belonging to the genus Aeromonas are indigenous to aquatic environments. Once regarded as unimportant human pathogens, reports of opportunistic infections caused by these organisms have appeared increasingly in the medical literature. To estimate the potential for human infection by Aeromonas where limited water resources are being used intensively, we studied the spatial and temporal variation and incidence of antimicrobial resistance among environmental isolates of Aeromonas from two urban playa lakes in Lubbock, Texas. Aeromonas population densities varied seasonally, with the highest densities occurring from mid-April to late October. The greatest range of densities was 100-fold, from 2.50 to 255.17 colony-forming units per 0.1 mL of water sample. Densities also varied with water depth, although the variation did not display a consistent pattern. One hundred fifty-one Aeromonas isolates were divided into 10 species or subspecies groups by using the BIOLOG identification system. Nine isolates displayed resistance to co-trimoxazole, tetracycline, and cefuroxime, and none was resistant to more than one of these antimicrobial agents. In summary, the results of this study showed that the densities of Aeromonas peak in the late spring and again in late summer, times when human activity around the playa lakes is also high. Thus, we infer that human exposure to these potential pathogens varies seasonally. Compared to other published studies, the incidence of antimicrobial-resistant Aeromonas is relatively low in urban playa lakes in Lubbock, Texas. Nevertheless, resistant organisms were detected.Key words: Aeromonas, water, playa, antibiotic resistance, population dynamics.
The fate of a genetically modifiedPseudomonasstrain and its transgene during the composting of poultry manure
Authors: Guan J , Spencer J L , Sampath M , Devenish J
Published: August 2004

The fate of the genetically modified (GM) Pseudomonas chlororaphis strain 3732 RN-L11 and its transgene (lacZ insert) during composting of chicken manure was studied using plate count and nested polymerase chain reaction (PCR) methods. The detection sensitivity of the nested PCR method was 165 copies of the modified gene per gram of moist compost or soil. Compost microcosms consisted of a 100-g mixture of chicken manure and peat, whereas soil microcosms were 100-g samples of sandy clay loam. Each microcosm was inoculated with 4 × 1010CFU of P. chlororaphis RN-L11. In controlled temperature studies, neither P. chlororaphis RN-L11 nor its transgene could be detected in compost microcosms after incubation temperature was elevated to 45 °C or above for one or more days. In contrast, in the compost microcosms incubated at 23 °C, the target organism was not detected by the plate count method after 6 days, but its transgene was detectable for at least 45 days. In compost bins, the target organism was not recovered from compost microcosms or soil microcosms at different levels in the bins for 29 days. However, the transgene was detected in 8 of the 9 soil microcosms and in only 1 of the 9 compost microcosms. The compost microcosm in which transgene was detected was at the lower level of the bin where temperatures remained below 45 °C. The findings indicated that composting of organic wastes could be used to reduce or degrade heat sensitive GM microorganisms and their transgenes.Key words: composting, genetically modified Pseudomonas strain, transgene, polymerase chain reaction.
Le génome des alpha-protéobactéries : complexité, réduction, diversité et fluidité
Authors: Teyssier Corinne , Marchandin Hélène , Jumas-Bilak Estelle
Published: August 2004

The alpha-proteobacteria displayed diverse and often unconventional life-styles. In particular, they keep close relationships with the eucaryotic cell. Their genomic organization is often atypical. Indeed, complex genomes, with two or more chromosomes that could be linear and sometimes associated with plasmids larger than one megabase, have been described. Moreover, polymorphism in genome size and topology as well as in replicon number was observed among very related bacteria, even in a same species. Alpha-proteobacteria provide a good model to study the reductive evolution, the role and origin of multiple chromosomes, and the genomic fluidity. The amount of new data harvested in the last decade should lead us to better understand emergence of bacterial life-styles and to build the conceptual basis to improve the definition of the bacterial species.Key words: alpha-proteobacteria, genome, dynamics, diversity.
Metabolism and life-history correlates in a lowland and highland population of a terrestrial isopod
Authors: Lardies Marco A , Catalán Tamara P , Bozinovic Francisco
Published: August 2004

Ectotherms distributed along environmental gradients often show marked variation in physiological and life-history traits. Different life-history phenotypes may be correlated with variations in maintenance metabolism. We measured life-history traits and metabolic rate (VO2) of the common wood louse (Porcellio laevis Latreille, 1804) from a lowland population and a highland population in northern Chile. We measured VO2at 5, 12, 18, and 25 °C. Wood lice from different altitudes exhibited large variations in life-history traits, which were correlated with changes in VO2. Fecundity of wood lice decreased and egg volume, offspring size, and reproductive output of females increased in highland populations compared with lowland populations. Isopods from the highland had a higher VO2than those from lowland habitats for almost all temperatures. However, when we considered VO2at 5 °C, VO2was lowest in the high-altitude isopods. In addition, since the highest thermal sensitivity values in the VO2–temperature curves were found at the lowest and highest temperature ranges for the highland population rather than for the lowland population, our study did not support the metabolic cold-adaptation hypothesis. We concluded that differences in VO2between the populations contributed to the difference in reproductive output by wood lice from cold and warm habitats.
Responses of wild fishes to alarm chemicals in pristine and metal-contaminated lakes
Authors: McPherson Taryn D , Mirza Reehan S , Pyle Greg G
Published: August 2004

Responses of wild fish populations to alarm chemicals were examined in clean and metal-contaminated lakes in northern Ontario. Approximately 20 groups of three minnow traps were placed randomly in the littoral zone of each study lake. Within each minnow trap group, one trap was treated with a chemical alarm stimulus (Iowa darter (Etheostoma exile (Girard, 1859)) skin extract, prey-guild species, alarm cue present), one with swordtail (Xiphophorus helleri Heckel, 1848) skin extract (phylogenetically distant and allopatric from darters, alarm cue present but not recognized by darters), and one with distilled water (neutral control). Data included the identification and enumeration of fish captured in each trap after a 10-h set. Darters avoided areas labelled with the alarm stimulus relative to controls only in the clean lake; in contaminated lakes, darters did not avoid areas labelled with the alarm stimulus relative to controls. No effects of contamination on chemosensory function were observed for heterospecific non-darter prey-guild or predator-guild species. These findings suggest that chemical alarm systems do exist in nature, and that these systems appear to be affected by the presence of metals. Such pollution-related effects could lead to increased susceptibility of some fish species to predation and to population declines.
Nest stage, wind speed, and air temperature affect the nest defence behaviours of burrowing owls
Authors: Fisher Ryan J , Poulin Ray G , Todd L Danielle , Brigham R M
Published: August 2004

The effect of nest stage on nest defence responses has been fairly well established but the impact of weather conditions has been largely ignored. We examined the effects of nest stage, number of previous visits, wind speed, and air temperature on burrowing owl (Athene cunicularia (Molina, 1782)) defence of nests from a human intruder. We found that burrowing owls changed nest defence tactics from retreat behaviour to more confrontational behaviour once eggs hatched. Aggressiveness was significantly reduced as wind velocity increased and when temperatures were warmer. We found no evidence for a change in owl defence behaviour with the number of previous visits to a nest. Although not statistically significant, there was a tendency for burrowing owls to allow closer approaches and to not retreat as far once eggs had hatched. Wind speed did not have an effect on retreat or approach distances, and owls allowed us to get significantly closer to the nest before retreating when air temperatures were warm. There are a multitude of factors that could affect nesting success and thus fitness of birds, but our study shows that routine climatic events such as warm weather had a measurable impact on how a bird defended its reproductive investment.