Showing papers on "Ribosomal DNA published in 2006"
TL;DR: It is shown that Tor1 is dynamically distributed in the cytoplasm and nucleus in yeast, indicating that the spatial regulation of TOR complex 1 (TORC1) might be involved in differential control of its target genes.
Abstract: Yeast Tor1 is dynamically distributed in the cytoplasm and nucleus, and its association with the rDNA promoter is important for 35S rRNA synthesis and cell growth. TOR is the target of the immunosuppressant rapamycin and a key regulator of cell growth. It modulates diverse cellular processes in the cytoplasm and nucleus1,2,3,4,5, including the expression of amino acid transporters, ribosomal RNAs and ribosomal proteins. Despite considerable recent progress, little is known about the spatial and temporal regulation of TOR signalling, particularly that leading into the nucleus. Here we show that Tor1 is dynamically distributed in the cytoplasm and nucleus in yeast. Tor1 nuclear localization is nutrient dependent and rapamycin sensitive: starvation or treatment with rapamycin causes Tor1 to exit from the nucleus. Tor1 nuclear localization is critical for 35S rRNA synthesis, but not for the expression of amino acid transporters and ribosomal protein genes. We show further that Tor1 is associated with 35S ribosomal DNA (rDNA) promoter chromatin in a rapamycin- and starvation-sensitive manner; this association is necessary for 35S rRNA synthesis and cell growth. These results indicate that the spatial regulation of TOR complex 1 (TORC1) might be involved in differential control of its target genes. TOR is known as a classic cytoplasmic kinase that mediates the cytoplasm-to-nucleus signalling by controlling the localization of transcription factors. Our data indicate that TOR might be more intimately involved in gene regulation than previously thought.
298 citations
TL;DR: PCR followed by cloning and sequencing may help to identify new pathogens involved in mixed bone infection, and four previously identified bacteria never reported in human infection were detected.
Abstract: The 16S rRNA gene PCR in the diagnosis of bone and joint infections has not been systematically tested. Five hundred twenty-five bone and joint samples collected from 525 patients were cultured and submitted to 16S rRNA gene PCR detection of bacteria in parallel. The amplicons with mixed sequences were also cloned. When discordant results were observed, culture and PCR were performed once again. Bacteria were detected in 139 of 525 samples. Culture and 16S rRNA gene PCR yielded identical documentation in 475 samples. Discrepancies were linked to 13 false-positive culture results, 5 false-positive PCR results, 9 false-negative PCR results, 16 false-negative culture results, and 7 mixed infections. Cloning and sequencing of 16S rRNA gene amplicons in 6 of 8 patients with mixed infections identified 2 to 8 bacteria per sample. Rarely described human pathogens such as Alcaligenes faecalis, Comamonas terrigena, and 21 anaerobes were characterized. We also detected, by 16S rRNA gene PCR, four previously identified bacteria never reported in human infection, Alkanindiges illinoisensis, dehydroabietic acid-degrading bacterium DhA-73, unidentified Hailaer soda lake bacterium, and uncultured bacterium clone HuCa4. Seven organisms representing new potential species were also detected. PCR followed by cloning and sequencing may help to identify new pathogens involved in mixed bone infection.
245 citations
TL;DR: A possible model in which RENT, Tof2, and Lrs4/Csm1 physically clamp rDNA to the cohesin ring, thereby restricting the movement of rDNA sister chromatids relative to each other to inhibit unequal exchange is suggested.
Abstract: Silencing within the yeast ribosomal DNA (rDNA) repeats protects the integrity of this highly repetitive array by inhibiting hyperrecombination and repressing transcription from foreign promoters. Using affinity purification combined with highly sensitive mixture mass spectrometry, we have analyzed the protein interaction network involved in suppressing homologous recombination within the rDNA locus. We show that the Net1 and Sir2 subunits of the RENT (regulator of nucleolar silencing and telophase exit) silencing complex, and Fob1, which recruits RENT to the nontranscribed spacer I (NTS1) region of rDNA, are physically associated with Tof2. In addition to RENT components and Fob1, Tof2 copurified with a two-subunit complex composed of Lrs4 and Csm1. Tof2, Lrs4, and Csm1 are recruited to the NTS1 region by Fob1 and are specifically required for silencing at this rDNA region. Moreover, Lrs4 and Csm1 act synergistically with Sir2 to suppress unequal crossover at the rDNA and are released from the nucleolus during anaphase. Together with previous observations showing that Csm1 physically associates with cohesin, these findings suggest a possible model in which RENT, Tof2, and Lrs4/Csm1 physically clamp rDNA to the cohesin ring, thereby restricting the movement of rDNA sister chromatids relative to each other to inhibit unequal exchange.
164 citations
TL;DR: These strains did not induce any nodule formation when inoculated on the wide host spectrum legume species M. atropurpureum and no nodA gene could be amplified by PCR, however, nifH sequences, most similar to those of Sinorhizobium meliloti, were detected within strains related to the genera Microbacterium, Agromyces, Starkeya and Phyllobacterium.
Abstract: We characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of Tunisia by 16S rDNA polymerase chain reaction (PCR)–restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), 16S rDNA and 16S–23S rDNA internal transcribed spacer sequencing. Phylogenetically, these isolates belong to the branches containing the genera Inquilinus, Bosea, Rhodopseudomonas, Paracraurococcus, Phyllobacterium, Ochrobactrum, Starkeya, Sphingomonas, Pseudomonas, Agromyces, Microbacterium, Ornithinicoccus, Bacillus, and Paenibacillus. These strains did not induce any nodule formation when inoculated on the wide host spectrum legume species M. atropurpureum (Siratro) and no nodA gene could be amplified by PCR. However, nifH sequences, most similar to those of Sinorhizobium meliloti, were detected within strains related to the genera Microbacterium, Agromyces, Starkeya and Phyllobacterium.
158 citations
TL;DR: The great diversity observed in this study emphasizes that tropics are an important reservoir of N2-fixation genes.
153 citations
TL;DR: These 16S rRNA gene sequences provide a reference standard for identification of Leptospira species and confirm previously established relationships within the genus.
Abstract: The genus Leptospira is classified into 13 named species and 4 genomospecies based upon DNA-DNA reassociation studies. Phenotypic tests are unable to distinguish between species of Leptospira, and there is a need for a simplified molecular approach to the identification of leptospires. 16S rRNA gene sequences are potentially useful for species identification of Leptospira, but there are a large number of sequences of various lengths and quality in the public databases. 16S rRNA gene sequences of near full length and bidirectional high redundancy were determined for all type strains of the species of the Leptospiraceae. Three clades were identified within the genus Leptospira, composed of pathogenic species, nonpathogenic species, and another clade of undetermined pathogenicity with intermediate 16S rRNA gene sequence relatedness. All type strains could be identified by 16S rRNA gene sequences, but within both pathogenic and nonpathogenic clades as few as two or three base pairs separated some species. Sequences within the nonpathogenic clade were more similar, and in most cases ≤10 bp distinguished these species. These sequences provide a reference standard for identification of Leptospira species and confirm previously established relationships within the genus. 16S rRNA gene sequencing is a powerful method for identification in the clinical laboratory and offers a simplified approach to the identification of Leptospira species.
152 citations
TL;DR: The results confirm the close relationship of species within the genus Aeromonas and show that a phylogenetic approach including several genes is suitable for improving the complicated taxonomy of the genus.
Abstract: Genetic relationships among bacterial strains belonging to the genus Aeromonas were inferred from 16S rRNA, gyrB and rpoB gene sequences. Twenty-eight type or collection strains of the recognized species or subspecies and 33 Aeromonas strains isolated from human and animal specimens as well as from environmental samples were included in the study. As reported previously, the 16S rRNA gene sequence is highly conserved within the genus Aeromonas, having only limited resolution for this very tight group of species. Analysis of a 1.1 kb gyrB sequence confirmed that this gene has high resolving power, with maximal interspecies divergence of 15.2 %. Similar results were obtained by sequencing only 517 bp of the rpoB gene, which showed maximal interspecies divergence of 13 %. The topologies of the gyrB- and rpoB-derived trees were similar. The results confirm the close relationship of species within the genus Aeromonas and show that a phylogenetic approach including several genes is suitable for improving the complicated taxonomy of the genus.
145 citations
TL;DR: The presence of two to eight rDNA loci in wild common beans from different geographic locations indicates that the 45S rDNA amplification observed in the Andean lineage took place before domestication, and suggests that ectopic recombination between terminal chromosomal regions might be the mechanism responsible for this variation.
Abstract: The extent of 5S and 45S ribosomal DNA (rDNA) variation was investigated in wild and domesticated common beans (Phaseolus vulgaris) chosen to represent the known genetic diversity of the species. 5S and 45S rDNA probes were localized on mitotic chromosomes of 37 accessions by fluorescent in situ hybridization (FISH). The two 5S rDNA loci were largely conserved within the species, whereas a high variation in the number of 45S rDNA loci and changes in position of loci and number of repeats per locus were observed. Domesticated accessions from the Mesoamerican gene pool frequently had three 45S rDNA loci per haploid genome, and rarely four. Domesticated accessions from Andean gene pool, particularly from the race Peru, showed six, seven, eight or nine loci, but seven loci were found in all three races of this gene pool. Between three and eight loci were observed in accessions resulting from crosses between Andean and Mesoamerican genotypes. The presence of two to eight 45S rDNA loci in wild common beans from different geographic locations indicates that the 45S rDNA amplification observed in the Andean lineage took place before domestication. Our data suggest that ectopic recombination between terminal chromosomal regions might be the mechanism responsible for this variation.
143 citations
TL;DR: The bacterial communities associated with 11 different lichen samples (belonging to eight different species) from different habitats were investigated and Paenibacillus and Burkholderia phylotypes seem to be common in lichens.
139 citations
Journal Article•
TL;DR: A molecular method based on DGGE coupled with sequence analysis of 18S rRNA gene to assess fungal diversity on leaves of Magnolia liliifera identified taxa that were not recovered from morphological or cultural studies, but did not detect other taxas that were predominantly isolated using traditional methods.
Abstract: Most fungal diversity studies have previously been based on morphological examination and cultivation methods. In this study we use a molecular method based on DGGE coupled with sequence analysis of 18S rRNA gene to assess fungal diversity on leaves of Magnolia liliifera. To achieve this, we extracted total genomic DNA and used fungal specific primers (NS1 and GCFung) to obtain fungal sequences. PCR-DGGE analysis recovered 14 operational taxonomic units (OTU) from different parts of the studied leaves. Phylogenetically, 8 OTUs belonged to the order Pleosporales and other bitunicate ascomycetes; 2 and 3 were related to the Xylariaceae, (Xylariales) and Hypocreales, respectively; 1 OTU was phylogenetically affiliated with the Rhytismatales. While this molecular approach identified taxa that were not recovered from morphological or cultural studies, it did not detect other taxa that were predominantly isolated using traditional methods. The three different parts of one leaf tested (petioles and midribs, leaf blade lower and upper parts) yielded different fungal taxa that possible indicate tissue-recurrence. The findings are compared with previous studies on the same host where endophytes were investigated using traditional culturing techniques.
137 citations
TL;DR: Maximum parsimony analysis of the three DNA regions revealed four major clades, reflective of sporangial morphology, and a number of species have been proposed to be the elusive intermediate species in the Pythium-to-Phytophthora evolutionary line.
Abstract: Fifty-eight isolates representing 39 Pythium species and 17 isolates representing nine Phytophthora species were chosen to investigate intra- and intergeneric relationships with sequence analysis of three genomic areas. The internal transcribed spacer regions (ITS1 and ITS2), including the 5.8S gene of the ribosomal DNA were PCR amplified with the universal primers ITS1 and ITS4. On the other hand 563 bp of the cytochrome oxidase II (cox II) gene was amplified with the primer pair FM66 and FM58 for Pythium and FM75 and FM78 for Phytophthora. The 658 bp partial beta-tubulin gene was amplified with the forward primer BT5 and reverse primer BT6. Maximum parsimony analysis of the three DNA regions revealed four major clades, reflective of sporangial morphology. Clade 1 was composed of Pythium isolates that bear filamentous to lobulate sporangia. Clade 2 represents Pythium isolates that bear globose to spherical zoosporangia or spherical hyphal swellings. Meanwhile Phytophthora isolates were lumped into Clade 3 wherein the papillate, semipapillate and nonpapillate species occupied separate subclades. Lastly, Clade 4 was composed of Pythium species that bear subglobose sporangia resembling the papillate sporangia observed in Phytophthora. Hence a number of species (Ph. undulata, P. helicoides, P. ostracodes, P. oedochilum and P. vexans) have been proposed to be the elusive intermediate species in the Pythium-to-Phytophthora evolutionary line.
TL;DR: It can be concluded that there is no obvious polyploidization-related tendency to reduce the number of ribosomal DNA loci in the allotetraploid species, when compared with their putative diploid progenitors.
TL;DR: Endophytic fungi were isolated from healthy stems and pods of cacao trees in natural forest ecosystems and agroecosystems in Latin America and West Africa and the role of these fungi within the host and their potential as biological control agents are discussed.
Abstract: Endophytic fungi were isolated from healthy stems and pods of cacao ( Theobroma cacao ) trees in natural forest ecosystems and agroecosystems in Latin America and West Africa. These fungi were collected for screening as a potential source of biocontrol agents for the basidiomycetous pathogens of cacao in South and Central America, Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom). Many of these isolates were morphologically unidentifiable as they failed to form fruiting structures in culture, or only produced arthrosporic stages. Affinities with basidiomycetes were suspected for many of these based on colony morphology. Fifty-nine of these morphologically unidentifiable isolates were selected for molecular identification by DNA extraction and sequence analysis of nuclear ribosomal DNA (rDNA). The large subunit (LSU) was chosen for initial sequencing because this region has been used most often for molecular systematics of basidiomycete fungi, and comprehensive LSU datasets were already available for sequence analyses. Results confirmed that the majority of the isolates tested belonged to the Basidiomycota, particularly to corticoid and polyporoid taxa. With LSU data alone, identification of the isolates was resolved at varying taxonomic levels (all to order, most to family, and many to genus). Some of the isolates came from rarely isolated genera, such as Byssomerulius , whilst the most commonly isolated basidiomycetous endophyte was a member of the cosmopolitan genus Coprinellus (Agaricales). The role of these fungi within the host and their potential as biological control agents are discussed.
TL;DR: It is suggested that, in Nemesia, transposition of rDNA genes may be equally if not more important in chromosome evolution, indicating that rDNA has changed position by transposition.
Abstract: We investigated chromosome evolution in Nemesia using fluorescent in-situ hybridization (FISH) to identify the locations of 5S and 45S (18–26S) ribosomal genes. Although there was conservation between Nemesia species in chromosome number, size and centromere position, there was large variation in both number and position of ribosomal genes in different Nemesia species (21 different arrangements of 45S and 5S rRNA genes were observed in the 29 Nemesia taxa studied). Nemesia species contained between one and three pairs of 5S arrays and between two and four pairs of 45S arrays. These were either sub-terminally or interstitially located and 45S and 5S arrays were often located on the same chromosome pair. Comparison of the positions of rDNA arrays with meiotic chromosome behaviour in interspecific hybrids of Nemesia suggests that some of the changes in the positions of rDNA have not affected the surrounding chromosome regions, indicating that rDNA has changed position by transposition. Chromosome evolution is frequently thought to occur via structural rearrangements such as inversions and translocations. We suggest that, in Nemesia, transposition of rDNA genes may be equally if not more important in chromosome evolution.
TL;DR: The approach combined soil DNA extraction through a bead-beating method modified to increase recovery of fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening of mixed PCR products, and sequencing of unique clones to detect additional diversity and the underlying community structure.
Abstract: We analyzed the communities of soil basidiomycetes in agroecosystems that differ in tillage history at the Kellogg Biological Station Long-Term Ecological Research site near Battle Creek, Michigan. The approach combined soil DNA extraction through a bead-beating method modified to increase recovery of fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening of mixed PCR products, and sequencing of unique clones. Much greater diversity was detected than was anticipated in this habitat on the basis of culture-based methods or surveys of fruiting bodies. With “species” defined as organisms yielding PCR products with ≥99% identity in the 5′ 650 bases of the nuclear large-subunit ribosomal DNA, 241 “species” were detected among 409 unique basidiomycete sequences recovered. Almost all major clades of basidiomycetes from basidiomycetous yeasts and other heterobasidiomycetes through polypores and euagarics (gilled mushrooms and relatives) were represented, with a majority from the latter clade. Only 24 of 241 “species” had 99% or greater sequence similarity to named reference sequences in GenBank, and several clades with multiple “species” could not be identified at the genus level by phylogenetic comparisons with named sequences. The total estimated “species” richness for this 11.2-ha site was 367 “species” of basidiomycetes. Since >99% of the study area has not been sampled, the accuracy of our diversity estimate is uncertain. Replication in time and space is required to detect additional diversity and the underlying community structure.
TL;DR: The finding of a wealth of novel clones related to the Chrysophyceae highlights the utility of a PCR biased towards marine algal plastids as a valuable complement to 18S rDNA based studies of PPE diversity.
Abstract: Marine photosynthetic picoeukaryotes (PPEs), representing organisms <3 µm in size, are major contributors to global carbon cycling. However, the key members of the PPE community and hence the major routes of carbon fixation, particularly in the open ocean environment, are poorly described. Here, we have accessed PPE community structure using the plastid encoded 16S rRNA gene. Plastid 16S rRNA genes were sequenced from 65 algal cultures, about half being PPEs, representing 14 algal classes. These included sequences from 5 classes where previously no such sequences from cultured representatives had been available (Bolidophyceae, Dictyochophyceae, Eustigmatophyceae, Pelagophyceae and Pinguiophyceae). Sequences were also obtained for 6 of the 7 (according to 18S rRNA gene sequence) prasinophyte clades. Phylogenetic analysis revealed plastids from the same class as clustering together. Using all the obtained sequences, as well as plastid sequences currently in public databases, a non-degenerate marine algal plastid-biased PCR primer, PLA491F, was developed to minimize amplification of picocyanobacteria, which often dominate numerically environmental samples. Clone libraries subsequently constructed from the pico-sized fraction from 2 open ocean sites in the Arabian Sea, revealed an abundance of 16S rRNA gene clones phylogenetically related to chrysophytes, whilst prymnesiophyte, clade II prasinophyte (Ostreococcus-like) and pelagophyte clones were also well represented. The finding of a wealth of novel clones related to the Chrysophyceae highlights the utility of a PCR biased towards marine algal plastids as a valuable complement to 18S rDNA based studies of PPE diversity.
TL;DR: DNA sequences for three loci, ITS, Elongation factor 1-alpha (EF-1α) and Actin (ACT) were used to reconsider species boundaries for Mycosphaerella spp.
TL;DR: Diversity analyses demonstrate greater diversity and evenness of bacterial species compared to a skewed representation of species for Archaea and a comparatively less diverse archaeal population.
Journal Article•
TL;DR: Analyses of 18S rDNA and mtDNA sequences underpin the classical taxonomic issues of the X. americanum-group and cast doubt on the degree of speciation within the group.
Abstract: The 18S ribosomal DNA (rDNA) and cytochrome oxidase I region of mitochondrial DNA (mtDNA) were sequenced for 24 Xiphinema americanum-group populations sourced from a number of geographically disparate locations. Sequences were subjected to phylogenetic analysis and compared. 18S rDNA strongly suggested that only X. pachtaicum, X. simile (two populations) and a X. americanum s.l. population from Portugal were different from the other 20 populations studied, whereas mtDNA indicated some heterogeneity between populations. Phylogenetically, based on mtDNA, an apparent dichotomy existed amongst X. americanum-group populations from North America and those from Asia, South America and Oceania. Analyses of 18S rDNA and mtDNA sequences underpin the classical taxonomic issues of the X. americanum-group and cast doubt on the degree of speciation within the X. americanum-group.
TL;DR: Work on rDNA repeat maintenance is summarized, focusing mainly on work done by this group, and it is shown that the maintenance mechanism operates by a collaboration of recombination, sister-chromatid cohesion, and chromatin condensation.
Abstract: Ribosomal RNA gene repeats (rDNA) are one of the most characteristic regions in eukaryotic chromosomes. The repeats consist of more than 100 tandem units occupying large part of the chromosome in most of organisms. Cells are known to deal with this "unusual domain" in a unique manner. In this review, I will summarize work on rDNA repeat maintenance, focusing mainly on work done by our group, and show that the maintenance mechanism operates by a collaboration of recombination, sister-chromatid cohesion, and chromatin condensation.
TL;DR: The identification of novel phylotypes associated with endodontic infections suggests that theendodontium may still harbour a relevant proportion of uncharacterized taxa.
Abstract: A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98% minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65.2%) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10.9%), Spirochaetes (4.3%), Bacteroidetes (6.5%), Actinobacteria (2.2%) and Deferribacteres (2.2%). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.
TL;DR: A model where the deacetylase activity of Sir2 prevents euchromatinization of the rDNA and silences naturally occurring intergenic transcription units whose expression has been associated with disruption of cohesion complexes and repeat amplification at the r DNA is suggested.
Abstract: Silencing at the rDNA, HM loci, and telomeres in Saccharomyces cerevisiae requires histone-modifying enzymes to create chromatin domains that are refractory to recombination and RNA polymerase II transcription machineries. To explore how the silencing factor Sir2 regulates the composition and function of chromatin at the rDNA, the association of histones and RNA polymerase II with the rDNA was measured by chromatin immunoprecipitation. We found that Sir2 regulates not only the levels of K4-methylated histone H3 at the rDNA but also the levels of total histone H3 and RNA polymerase II. Furthermore, our results demonstrate that the ability of Sir2 to limit methylated histones at the rDNA requires its deacetylase activity. In sir2Δ cells, high levels of K4-trimethylated H3 at the rDNA nontranscribed spacer are associated with the expression of transcription units in the nontranscribed spacer by RNA polymerase II and with previously undetected alterations in chromatin structure. Together, these data suggest a model where the deacetylase activity of Sir2 prevents euchromatinization of the rDNA and silences naturally occurring intergenic transcription units whose expression has been associated with disruption of cohesion complexes and repeat amplification at the rDNA.
TL;DR: The aim of this study was to investigate the bacterial diversity associated with the sponge Craniella australiensis using a molecular strategy and isolating Actinomycetes with antimicrobial potentials.
Abstract: Aims: The aim of this study was to investigate the bacterial diversity associated with the sponge Craniella australiensis using a molecular strategy and isolating Actinomycetes with antimicrobial potentials.
Methods and Results: The bacterial diversity associated with South China Sea sponge C. austrialiensis was assessed using a 16S rDNA clone library alongside restriction fragment length polymorphism and phylogenetic analysis. It was found that the C. austrialiensis-associated bacterial community consisted of alpha, beta and gamma-Proteobacteria, Firmicutes, Bacteroidetes as well as Actinobacterium. Actinomycetes were isolated successfully using seawater medium with sponge extracts. According to the BLAST and phylogenetic analysis based on about 600-bp 16S rDNA sequences, 11 of the representative 23 isolates closely matched the Streptomyces sp. while the remaining 12 matched the Actinomycetales. Twenty Actinomycetes have antimicrobial potentials, of which 15 are found to possess broad-spectrum antimicrobial potentials.
Conclusions: The sponge C. austrialiensis-associated bacterial community is very abundant including Proteobacteria, Firmicutes, Bacteroidetes and Actinobacterium while Actinomycetes is not predominant. Artificial seawater medium with sponge extracts is suitable for Actinomycetes isolation. Most of the isolated C. austrialiensis-associated Actinomycetes have a broad spectrum of antimicrobial activity.
Significance and Impact of the Study: This study revealed the diversity of the bacterial community and the isolated Actinomycetes with antimicrobial potentials associated with sponge C. australiensis.
TL;DR: This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano.
Abstract: In this study, ribosomes and genomic DNA were extracted from three sediment depths (0-2, 6-8 and 10-12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, epsilon-Proteobacteria rDNA clones dominated the 0-2 cm clone library whereas gamma-Proteobacteria dominated the 0-2 cm crDNA library suggesting gamma to be among the most active in situ populations detected at 0-2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, alpha-Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano.
TL;DR: P phylogenetic analyses in the Rhizoctonia solani species complex suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solANI species complex is not monophyletic.
TL;DR: The results indicate that AFLP genetic markers offer potential for distinguishing currently recognized North American Biological Species (NABS) of Armillaria in future biological, ecological and taxonomic studies.
Abstract: Phylogenetic and genetic relationships among 10 North American Armillaria species were analysed using sequence data from ribosomal DNA (rDNA), including intergenic spacer (IGS-1), internal transcribed spacers with associated 5.8S (ITS + 5.8S), and nuclear large subunit rDNA (nLSU), and amplified fragment length polymorphism (AFLP) markers. Based on rDNA sequence data, the nLSU region is less variable among Armillaria species than the ITS + 5.8S and IGS-1 regions (nLSU < ITS + 5.8S < IGS-1). Phylogenetic analyses of the rDNA sequences suggested Armillaria mellea, A. tabescens and A. nabsnona are well separated from the remaining Armillaria species (A. ostoyae, A. gemina, A. calvescens, A. sinapina, A. gallica, NABS X and A. cepistipes). Several Armillaria species (A. calvescens, A. sinapina, A. gallica, NABS X and A. cepistipes) clustered together based on rDNA sequencing data. Based on the isolates used in this study, it appears that techniques based on IGS-1, ITS + 5.8S, and/or D-domain/3' ends of nLSU are not reliable for distinguishing A. calvescens, A. sinapina, A. gallica and A. cepistipes. However, AFLP data provided delineation among these species, and AFLP analysis supported taxonomic classification established by conventional methods (morphology and interfertility tests). Our results indicate that AFLP genetic markers offer potential for distinguishing currently recognized North American Biological Species (NABS) of Armillaria in future biological, ecological and taxonomic studies.
TL;DR: The presence of rDNA in mammalian cells always structurally ready for transcription might facilitate a more rapid adjustment of the ribosome production in response to the metabolic needs of the cell.
Abstract: Data on the in situ structural-functional organization of ribosomal genes in the mammalian cell nucleolus are reviewed here. Major findings on chromatin structure in situ come from investigations carried out using the Feulgen-like osmium ammine reaction as a highly specific electron-opaque DNA tracer. Intranucleolar chromatin shows three different levels of organization: compact clumps, fibers ranging from 11 to 30 nm, and loose agglomerates of extended DNA filaments. Both clumps and fibers of chromatin exhibit a nucleosomal organization that is lacking in the loose agglomerates of extended DNA filaments. In fact, these filaments constantly show a thickness of 2-3 nm, the same as a DNA double-helix molecule. The loose agglomerates of DNA filaments are located in the fibrillar centers, the interphase counterpart of metaphase NORs, therefore being constituted by ribosomal DNA. The extended, non-nucleosomal configuration of this rDNA has been shown to be independent of transcriptional activity and characterizes ribosome genes that are either transcribed or transcriptionally silent. Data reviewed are consistent with a model of control for ribosome gene activity that is not mediated by changes in chromatin structure. The presence of rDNA in mammalian cells always structurally ready for transcription might facilitate a more rapid adjustment of the ribosome production in response to the metabolic needs of the cell.
Journal Article•
TL;DR: The molecular-clock hypothesis tested using the likelihood ratio test indicated a highly significant difference in the global evolutionary rate of scleractinian 5.8S rDNA, and rate constancy was rejected for most comparisons between Acropora/Isopora and other coral genera, suggesting that the rates of evolution of 5.5S has accelerated since divergence from the common ancestor of s cleractinian corals.
Abstract: One characteristic of ribosomal DNA (rDNA) sequences in staghorn corals, Acropora spp., is the extremely high levels of intragenomic heterogeneity and interspecific variation. This high genomic diversity is ascribed to incomplete lineage sorting that predated the divergence of species or to recent introgressive hybridization. In order to elucidate whether the high heterogeneity of rDNA is a unique feature of Acropora or a general pattern applicable to scleractinian corals, we examined the molecular evolution of the internal transcribed spacers (ITS) and 5.8S rDNA sequences from 78 species, representing 28 genera, and 12 families of scleractinian corals. Genetic distances (measured by p-distances) and frequency distribution analyses revealed that both extremely high intra- and interspecific heterogeneities of the ITS-5.8S rDNA are specific to the genus Acropora. The 5.8S rDNA phylogeny clearly showed a significantly long branch length leading to the cluster containing the genus Acropora. The molecular-clock hypothesis tested using the likelihood ratio test indicated a highly significant difference in the global evolutionary rate of scleractinian 5.8S rDNA. The relative rate tests showed that the rDNA of Isopora, Caribbean Acropora, and Indo-Pacific Acropora all evolved at constant tempos, indicating that the highly divergent rDNA was present in Acropora before it split into these three lineages. In contrast, rate constancy was rejected for most comparisons between Acropora/Isopora and other coral genera, suggesting that the rates of evolution of 5.8S differed between Acropora/Isopora and the other lineages, and that the evolutionary rate of Acropora/Isopora has accelerated since divergence from the common ancestor of scleractinian corals.
TL;DR: A real-time PCR method that is effective in detecting and identifying the pathogen in seed lots and in whole plants and has great potential for analyzing large numbers of samples without the need for DNA extraction or agarose gel electrophoresis is developed.
Abstract: Panicle blight of rice (Oryza sativa), caused by the bacterium Burkholderia glumae, is one of the most important new diseases in rice production areas of the southern United States. In this study, pathogenic strains were isolated from diseased panicles in Arkansas rice fields and examined using the Biolog GN microplate system, whole cell fatty acid methyl ester analysis (FAME), rep-polymerase chain reaction (PCR) genomic DNA fingerprinting, and 16S-23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) sequence analysis. The B. glumae isolates from Arkansas can be divided into two major groups, but their genetic diversity was relatively low as revealed by 16S-23S rDNA ITS sequence analysis. Since no practical method existed, up to now, for testing the presence of B. glumae in rice seeds, we have developed in this study a real-time PCR method that is effective in detecting and identifying the pathogen in seed lots and in whole plants. The specific PCR primers were designed based on the 16S-23S rDNA ITS sequence of several representative isolates from Arkansas and Japan. This method is highly sensitive, rapid, and reliable, and has great potential for analyzing large numbers of samples without the need for DNA extraction or agarose gel electrophoresis. Although vertical resistance has not been observed among tested rice cultivars, LM-1 and Drew exhibited considerable resistance to B. glumae infection based on disease lesion size and the bacterial growth in planta.
TL;DR: The analysis suggests that concerted evolution has been remarkably ineffective in P. pedestris, and it is proposed that this outcome may be related to the species' exceptionally large genome and the associated low rate of deletion per base pair, which may allow pseudogenes to persist.
Abstract: Eukaryote nuclear ribosomal DNA (rDNA) typically exhibits strong concerted evolution: a pattern in which several hundred rDNA sequences within any one species show little or no genetic diversity, whereas the sequences of different species diverge. We report a markedly different pattern in the genome of the grasshopper Podisma pedestris. Single individuals contain several highly divergent ribosomal DNA groups. Analysis of the magnitude of divergence indicates that these groups have coexisted in the Podisma lineage for at least 11 million years. There are two putatively functional groups, each estimated to be at least 4 million years old, and several pseudogene groups, many of which are transcribed. Southern hybridization and real-time PCR experiments show that only one of the putatively functional types occurs at high copy number. However, this group is scarcely amplified under standard PCR conditions, which means that phylogenetic inference on the basis of standard PCR would be severely distorted. The analysis suggests that concerted evolution has been remarkably ineffective in P. pedestris. We propose that this outcome may be related to the species' exceptionally large genome and the associated low rate of deletion per base pair, which may allow pseudogenes to persist.