ribosomal RNA

Hybridization probes produced from DNA sequences have proven to be a powerful tool in the rapid and sensitive analysis of natural microbial communities. By using function-specific probes, such as those identifying genes coding for photosynthesis, the potential a microbial community has for performing a given function may be rapidly determined. Gene probes have also been used in the idelatification and isolation of a specific catabolic genotype in less than one-fourth the time required for the conventional culture enrichment technique. Species-specific probes constructed from portions of genes coding for ribosomal RNA have been used for the rapid identification and enumeration of bacterial species in environmental samples. The use of reassociation kinetics as a measure of community diversity and complexity is also discussed. The successful application of this technique to community analysis may reduce the time required from 1 year, for conventional analysis, to 2 weeks.

Trypanosome infections in their natural hosts are frequently di.cult to detect by microscopy\ and culture methods are unreliable and not suitable for all species of Trypanosoma[ A nested PCR strategy for detecting and identifying Trypanosoma species\ suitable for detecting both known and unknown trypanosomes\ is presented[ Thirty!two blood samples from 12 species of Australian birds and mammals were screened by a nested PCR for the presence of Trypanosoma sp[ ssrRNA[ Three infections were detected\ one in an eastern grey kangaroo "Macropus giganteus#\ one in a common wombat "Vombatus ursinus# and one in a platypus "Ornithorhynchus anatinus#[ The kangaroo and wombat are new host records for Trypanosoma sp[^the platypus parasite was Trypanosoma binneyi[ The three parasites could be distinguished by restriction fragment length polymorphisms of the ampli_ed fragment of the ssrRNA gene[ The kangaroo and wombat parasites were also isolated in a semi!solid blood agar medium[ The culture forms of the kangaroo trypanosome had an expanded~agellar sheath in which structures similar to hemidesmosomes were detected by EM[ The nested PCR was at least as sensitive as culture\ and analysis of the PCR products gave parasite!speci_c _ngerprints[ Therefore this method could be suitable for rapidly screening host animals for the presence of trypanosomes and identifying the infecting strain[ Þ 0888 Australian Society for Parasitology[ Published by Elsevier Science Ltd[ All rights reserved[ Keywords] Macropus giganteus^Ornithorhynchus anatinus^Ortholfersia macleayi^Trypanosoma binneyi^Trypanosoma cruzi^Vombatus ursinus^Guanidine thiocyanate

DNA sequence comparisons of two mitochondrial DNA genes were used to infer phylogenetic relationships among four species of mullids. Approximately 238 bp of the mitochondrial 16S ribosomal RNA (rRNA) and 261 bp of the cytochrome b (cytb) genes were sequenced from representatives of three mullid genera (Mullus, Upeneus, Pseudopeneus), present in the Mediterranean Sea. Trees were constructed using three methods: maximum likelihood (ML), neighbor joining (NJ) and parsimony (MP). The results of the analyses of these data together with published data of the same mtDNA segments of two other perciform species (Sparus aurata, Perca fluviatilis), support the previous taxonomic classification of the three genera examined, as well as the classification of the two red mullet species in the same genus. # : S 0 3 0 5 -1 9 7 8 ( 0 1 ) 0 0 0 3 7 -0

Positioning of the mRNA codon towards the 18S ribosomal RNA in the A site of human 80S ribosomes has been studied applying short mRNA analogs containing either the stop codon UAA or the sense codon UCA with a per£uoroaryl azide group at the uridine residue. Bound to the ribosomal A site, a modi¢ed codon crosslinks exclusively to the 40S subunits under mild UV irradiation. This result is inconsistent with the hypothesis RNA 7, 1683^1692] which requires direct contact between the large rRNA and the stop codon of the mRNA as recognition step at translation termination. Both sense and stop codons crosslink to the same A1823/ A1824 invariant dinucleotide in helix 44 of 18S rRNA. The data point to the resemblance between the ternary complexes formed at elongation (sense codonW Waminoacyl-tRNAW WAA dinucleotide of 18S rRNA) and termination (stop codonW WeRF1W WAA dinucleotide of 18S rRNA) steps of protein synthesis and support the view that eRF1 may be considered as a functional mimic of aminoacyl-tRNA. ß

Several DNA fragments carrying tRNA genes have been cloned from EcoRI endonuclease digests of Escherichia coZi DNA. Using cloned DNA, the sequence of the region around the distal gene for tRNAlASP(F(or G)) in the E. coZi ribosomal RNA operon [rrnF(or G)] has been determined. In the distal portion of rrnF(or G), the genes for 23S, 5S rRNA and tRN41P(F(or G)) are located in that order and separated by intergenic spacers of 93 and 52 base pairs, respectively. A possible hairpin structure, with its center between the 22nd and 23rd base pair downstream from the 3'-end of the tRNAAsP(F(or G)) gene, followed by a sequence of eight thymidine residues was identified as the transcription termination signal for rrnF(or G). The termination is rhoindependent, at least in vitro, and occurs within the region of the contiguous thymidine residues. A possible promoter for a protein gene is present about 50 base pairs downstream from the rrnF(or G) terminator.

The analytical performance of 9 different PCR primer sets designed to detect Escherichia coli and Shigella in water has been evaluated in terms of ubiquity, specificity, and analytical detection limit. Of the 9 PCR primer sets tested, only 3 of the 5 primer sets targeting uidA gene and the primer set targeting tuf gene amplified DNA from all E. coli strains tested.

Based on the sequence diversity of the Plasmodium 18S ribosomal RNA (rRNA), we designed oligonucleotide primers for polymerase chain reaction (PCR) to yield different size fragments for P. falciparum and P. vivax. The primers for the PCR procedure were chosen such that the 5' primer was Plasmodium-conserved while the 3" primers were species-specific. Using primer cocktails and cloned plasmid DNAs containing the 18S rRNA genes or parasite genomic DNA as targets, we show that the PCR procedure yields 1-4-kb and 0.5-kb DNA fragments for P. falciparum and P. vivax, respectively. Limited field testing of this procedure demonstrated the utility of a ribosomal gene based species-specific malaria diagnosis.

Oligonucleotide probes targeting ribosomal RNA can be designed with high specificity to target microbial populations at different phylogenetic levels if the cellular abundance of ribosomal RNA is sufficiently high. In contrast, polyclonal antibody probes cannot be produced with the same specificity for various phylogenetic groups, but they have the potential to detect slow growing microorganisms, populations with low metabolic activities, or even non-viable cells. We combined a polyclonal antibody stain with a ribosomal RNA targeted oligonucleotide probe for the single cell detection of species of the genus Gordona. Gordona species typically require long generation times, often exhibit filamentous growth, and are commonly encountered in activated sludge foams. Our results suggest that the ribosomal RNA content of individual cells of Gordona in activated sludge is highly variable. Therefore, the combined use of an immunostain and an oligonucleotide probe targeting ribosomal RNA can determine the identity of single cells and provide an approximation of their activity. This approach should result in improved detection limits while maintaining high specificity. z

Clonal cultures of Alexandrium species collected from a shrimp pond on the northern coast of Vietnam were established and morphologically identified as Alexandrium minutum. Nucleotide sequences of domains 1 and 2 of the large subunit ribosomal (LSU) rRNA gene showed high sequence similarity to A. minutum isolates from Malaysia. Paralytic shellfish toxin profile of the clones was characterized by the dominance of GTX4, GTX1, and NEO. GTX3, GTX2, and dcSTX were also present in trace amount. Toxin content varied among the strains and growth stages, ranged from 3.0 to 12.5 fmol cell À1 . In addition to these known toxin components, a new gonyautoxin derivative was detected by HPLC, eluting between GTX4 and GTX1. The peak of this compound disappeared under non-oxidizing HPLC condition but unchanged either after treated with 0.05 M ammonium phosphate/10% mercaptoethanol or 0.1N HCl hydrolysis. LCMS ion scanning showed a parental ion of [M + H] + at m/z 396, [M À SO 3 ] + at m/z 316, and [M À SO 4 ] + at m/z 298. Based on these results, the derivative was identified as deoxy-GTX4-12ol, and this represents the first report of this toxin analogue. #

The newly developed cultivars of soybean in Africa, known as Tropical Glycine cross (TGx), are nodulated by bradyrhizobia indigenous to African soils, here designated Bradyrhizobium spp. (TGx). Isolates of Bradyrhizobium spp. (TGx) obtained from nodules of TGx soybeans that were inoculated with soils from 65 locations in six African countries were characterized and grouped into 11 phylogenetic clusters on the basis of RFLP of the 16S rRNA gene. Five restriction enzymes (RsaI, HinfI, MspI, CfoI and HaeIII) established RFLP groups within these Bradyrhizobium spp. (TGx) isolates, which were used to construct a phylogenetic tree showing their genetic relationship with other Bradyrhizobium species. RFLP analysis indicated that Bradyrhizobium spp. (TGx) is a heterogeneous group with some isolates related to Bradyrhizobium japonicum and Bradyrhizobium elkanii strains and some to Bradyrhizobium spp. (misc.) reference strains isolated from a variety of tropical legumes. The heterogeneity within the large phylogenetic clusters was further examined through analysis of randomly amplified polymorphic DNA (RAPD) using GCrich PCR primers. The RAPD analysis showed additional heterogeneity in the Bradyrhizobium spp. (TGx) phylogenetic clusters, which was not revealed by separations based on RFLP analysis. The Bradyrhizobium spp. (TGx) isolates were classified into effective and ineffective types based on their symbiotic performance on TGx soybean. The isolates were randomly distributed throughout the phylogenetic clusters regardless of their symbiotic effectiveness on TGx soybean.

Each difference between the genome sequences of Escherichia coli B strains REL606 and BL21(DE3) can be interpreted in light of known laboratory manipulations plus a gene conversion between ribosomal RNA operons. Two treatments with 1-methyl-3-nitro-1-nitrosoguanidine in the REL606 lineage produced at least 93 single-base-pair mutations (∼ 90% GC-to-AT transitions) and 3 single-base-pair GC deletions. Two UV treatments in the BL21(DE3) lineage produced only 4 single-base-pair mutations but 16 large deletions. P1 transductions from K-12 into the two B lineages produced 317 single-base-pair differences and 9 insertions or deletions, reflecting differences between B DNA in BL21(DE3) and integrated restriction fragments of K-12 DNA inherited by REL606. Two sites showed selective enrichment of spontaneous mutations. No unselected spontaneous singlebase-pair mutations were evident. The genome sequences revealed that a progenitor of REL606 had been misidentified, explaining initially perplexing differences. Limited sequencing of other B strains defined characteristic properties of B and allowed assembly of the inferred genome of the ancestral B of Delbrück and Luria. Comparison of the B and K-12 genomes shows that more than half of the 3793 proteins of their basic genomes are predicted to be identical, although ∼ 310 appear to be functional in either B or K-12 but not in both. The ancestral basic genome appears to have had ∼4039 coding sequences occupying ∼ 4.0 Mbp. Repeated horizontal transfer from diverged Escherichia coli genomes and homologous recombination may explain the observed variable distribution of single-base-pair differences. Fifteen sites are occupied by phage-related elements, but only six by comparable elements at the same site. More than 50 sites are occupied by IS elements in both B and K, 16 in common, and likely founding IS elements are identified. A signature of widespread cryptic phage P4-type mobile elements was identified. Complex deletions (dense clusters of small deletions and substitutions) apparently removed nonessential genes from ∼30 sites in the basic genomes.

The genus Haemonchus consists of blood-sucking parasitic nematodes in the abomasum of ruminants. Members of this genus are responsible for extensive production losses, particularly of small ruminants in the tropics but are also found in temperate regions. In this study, we examined the internal transcribed spacers-1 and -2 of rRNA in Haemonchus spp. The rRNA region spanning the internal transcribed spacers-1, -2 and the 5.8S rRNA gene was amplified by PCR from each of 10 worms from Swedish sheep, a Swedish goat and Kenyan sheep. The fragments were sequenced and examined with respect to genetic differences fixed among the three isolates. These and additional worms were further analysed with Pyrosequencinge technology. This technique allowed us to rapidly analyse 110 individuals in three putative polymorphic nucleotide positions that were initially identified with dideoxy sequencing. The geographical isolates could to a large extent be genetically distinguished, but none of the polymorphic positions were consistent among all individuals within each isolate. Furthermore an alignment of our sequences and a consensus sequence published for Haemonchus contortus revealed two differences in positions 123 and 196 in internal transcribed spacers-2. Although these positions were previously reported as heterogenic, no polymorphism was detected among the 30 worms sequenced in the present study. Modelling of the internal transcribed spacers-2 secondary structure based on our data also identified a new putative long-range interaction. The isolates are best described as populations. In conclusion, consistent differences were not identified and the studied isolates are therefore best described as discrete populations. This study also reveals for the first time the potential of Pyrosequencinge technology as a tool in the analysis of nematode population genetics. q

Microbial community structure of a lab scale thermophilic aerobic wastewater treatment reactor was analyzed by a combination of culture-independent methods. Quinone profile method provides for chemical analysis of respiratory quinone molecular species, which corresponds to bacterial groups. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA partial sequences (PCR-DGGE) clarifies community changes at species level, as DGGE can separate DNA fragments of different sequences. Certain phylogenetic groups of bacterial cells can be labeled by fluorescence in situ hybridization (FISH). Quinone profile showed a predominant presence of MK-7. PCR-DGGE revealed that constituents of the community were unchanged during the stable phase. FISH demonstrated the existence of the relatives of Bacillus lentus and B. thermocloacae in considerable proportions. The community was mainly composed of Bacillaceae, and obligate thermophilic and mesophilic Bacillus appeared in spite of the temperature fluctuation from 351C to 601C. The combination of these culture-independent methods revealed the community precisely enough to evaluate the reactor performance.

Three aerobic lignin-degrading bacterial strains were isolated from palm oil plantation soils. The bacterial isolates were screened using a selective nutrient medium of minimum salt media (MSM), with kraft lignin as lignin substrate and methylene blue as the ligninolytic dye indicator. The newly isolated bacterial strains SHC1, SHC2, and SHC3 were found to have the potential to tolerate high concentrations of kraft lignin and produced all three main ligninolytic enzymes (lignin peroxidase, manganese peroxidase, and laccase); these strains may therefore be useful in the degradation of lignin in oil palm empty fruit bunch biomass. The production of ligninolytic enzymes was carried out by means of submerged fermentation for 7 days using 2 mm of oil palm empty fruit bunch (OPEFB) fiber as a substrate. These bacterial isolates were characterized using biochemical tests from Biolog and identified using 16S rRNA gene sequencing analysis, which identified the strains SHC1, SHC2, and SHC3 as Bacillus sp., Ochrobactrum sp., and Leucobacter sp., respectively with 99% sequence similarity. Bacillus sp. SHC1 produced the highest manganese peroxidase (MnP) of 2313.4 U/L on the third day and the highest lignin peroxidase (LiP) of 209.30 U/L on the fifth day of fermentation. The optimum pH and temperature for the production of ligninolytic enzymes by Bacillus sp. SHC1 were pH 8 and 30 °C.

Humankind's innate curiosity makes us wonder whether life is or was present on other planetary bodies such as Mars. The EuroGeoMars 2009 campaign was organized at the Mars Desert Research Station (MDRS) to perform multidisciplinary astrobiology research. MDRS in southeast Utah is situated in a cold arid desert with mineralogy and erosion processes comparable to those on Mars. Insight into the microbial community composition of this terrestrial Mars analogue provides essential information for the search for life on Mars: including sampling and life detection methodology optimization and what kind of organisms to expect. Soil samples were collected from different locations. Culture-independent molecular analyses directed at ribosomal RNA genes revealed the presence of all three domains of life (Archaea, Bacteria and Eukarya), but these were not detected in all samples. Spiking experiments revealed that this appears to relate to low DNA recovery, due to adsorption or degradation. Bacteria were most frequently detected and showed high alpha-and beta-diversity. Members of the Actinobacteria, Proteobacteria, Bacteroidetes and Gemmatimonadetes phyla were found in the majority of samples. Archaea alpha-and beta-diversity was very low. For Eukarya, a diverse range of organisms was identified, such as fungi, green algae and several phyla of Protozoa. Phylogenetic analysis revealed an extraordinary variety of putative extremophiles, mainly Bacteria but also Archaea and Eukarya. These comprised radioresistant, endolithic, chasmolithic, xerophilic, hypolithic, thermophilic, thermoacidophilic, psychrophilic, halophilic, haloalkaliphilic and alkaliphilic micro-organisms. Overall, our data revealed large difference in occurrence and diversity over short distances, indicating the need for high-sampling frequency at similar sites. DNA extraction methods need to be optimized to improve extraction efficiencies.

This paper describes a method of transferring fragments of DNA from agarose gels to cellulose nitrate filters. The fragments can then be hybridized to radioactive RNA and hybrids detected by radioautography or fluorography. The method is illustrated by analyses of restriction fragments complementary to ribosomal RNAs from Esoherichia coli and Xenopus lacvis, and from several mammals.

Libraries of plasmid clones covering the entire chloroplast (cp) genome of the common wheat, Triticum aestivum cv. Chinese Spring were constructed and assembled into contig-clones. From these, we obtained the complete nucleotide sequence of wheat chloroplast DNA -a 134,540 bp circular DNA (DDBJ accession no. AB042240) containing four species of ribosomal RNA, 30 genes for 20 species of transfer RNA, and 71 protein coding genes. Additionally, we detected five unidentified open reading frames conserved among grasses. Plasmid clones are available on request.

Theileria parva is the causative agent of Corridor disease in cattle in South Africa. The African buffalo (Syncerus caffer) is the reservoir host, and, as these animals are important for eco-tourism in South Africa, it is compulsory to test and certify them disease free prior to translocation. A T. parva-specific real-time polymerase chain reaction (PCR) test based on the small subunit ribosomal RNA (18S rRNA) gene is one of the tests used for the diagnosis of the parasite in buffalo and cattle in South Africa. However, because of the high similarity between the 18S rRNA gene sequences of T. parva and Theileria sp. (buffalo), the latter is also amplified by the real-time PCR primers, although it is not detected by the T. parva-specific hybridization probes. Preliminary sequencing studies have revealed a small number of sequence differences within the 18S rRNA gene in both species but the extent of this sequence variation is unknown. The aim of the current study was to sequence the 18S rRNA genes of T. parva and Theileria sp. (buffalo), and to determine whether all identified genotypes can be correctly detected by the real-time PCR assay. The reverse line blot (RLB) hybridization assay was used to identify T. parva and Theileria sp. (buffalo) positive samples from buffalo blood samples originating from the Kruger National Park, Hluhluwe-iMfolozi Park, the Greater Limpopo Transfrontier Park, and a private game ranch in the Hoedspruit area. Theileria parva and Theileria sp. (buffalo) were identified in 42 % and 28 %, respectively, of 252 samples, mainly as mixed infections. The full-length 18S rRNA gene of selected samples was amplified, cloned and sequenced. From a total of 20 sequences obtained, 10 grouped with previously published T. parva sequences from GenBank while 10 sequences grouped with a previously published Theileria sp. (buffalo) sequence. All these formed a monophyletic group with known pathogenic Theileria species. Our phylogenetic analyses confirm the distinction between Theileria sp. (buffalo) and T. parva and indicate the existence of a single group of T. parva and two Theileria sp. (buffalo) 18S rRNA gene variants in the African buffalo. Despite the observed variation in the full-length parasite 18S rRNA gene sequences, the area in the V4 hypervariable 3 region where the RLB and real-time PCR hybridization probes were developed was relatively conserved. The T. parva specific real-time PCR assay was able to successfully detect all T. parva variants and, although amplicons were obtained from Theileria sp. (buffalo) DNA, none of the Theileria sp. (buffalo) 18S rRNA sequence variants were detected by the T. parva-specific hybridization probes.

Isolation and purification of biologically active RNA from filamentous fungi is difficult because of the complex cell wall and the presence of intracellular ribonucleases in these microorganisms. We have developed a procedure for the rapid isolation of intact RNA from the various morphological forms of the filamentous fungus Mucor circinelloides. Fractionation of fungus RNA by agarose gel electrophoresis revealed distinct bands of ribosomal RNA. The integrity of the RNA was further substantiated by Northern blot analysis by probing it with the 1.9-kb and 2.5-kb EcoR1 fragments of the putative transcription factor gene (MTF1) and the 25S ribosomal RNA gene, respectively. The RNA isolated by this procedure appears to be relatively pure since it has a ratio of absorbance at 260 / 280 of 1.7-1.8. This procedure should be useful for isolating RNA from other filamentous fungi and therefore, will serve as an important tool for the molecular analysis of these organisms.

Background: Sets of Giemsa-stained, blood smear slides with systematically verified composite diagnoses would contribute substantially to development of externally validated quality assurance systems for the microscopic diagnosis of malaria.

Despite extensive phylogenetic analysis of small subunit ribosomal RNA (SSUrRNA) genes, the deep-level relationships among kinetoplastids remain poorly understood, limiting our grasp of their evolutionary history, especially the origins of their bizarre mitochondrial genome organizations. In this study we examine the SSUrRNA data in the light of a new marker-cytoplasmic heat shock protein 90 (hsp90) sequences. Our phylogenetic analyses divide kinetoplastids into four main clades. Clades 1-3 include the various bodonid kinetoplastids. Trypanosomatids comprise the fourth clade. SSUrRNA analyses give vastly different and poorly supported positions for the root of the kinetoplastid tree, depending on the out-group and analysis method. This is probably due to the extraordinary length of the branch between kinetoplastids and any out-group. In contrast, almost all hsp90 analyses place the root between clade 1 (including Dimastigella, Rhynchomonas, several Bodo spp., and probably Rhynchobodo) and all other kinetoplastids. Maximum likelihood and maximum likelihood distance analyses of hsp90 protein and second codonposition nucleotides place trypanosomatids adjacent to Bodo saltans and Bodo cf. uncinatus (clade 3), as (weakly) do SSUrRNA analyses. Hsp90 first codon-plus second codon-position nucleotide analyses return a slightly different topology. We show that this may be an artifact caused, in part, by the different evolutionary behavior of first-and second-codon positions. This study provides the most robust evidence to date that trypanosomatids are descended from within bodonids and that B. saltans is a close relative of trypanosomatids. A total reevaluation of the highlevel systematics within kinetoplastids is needed. We confirm that the interlocking network organization of kinetoplast DNA seen in trypanosomatids is a derived condition within kinetoplastids but suggest that open-conformation minicircles may have arisen early in kinetoplastid evolution. Further understanding of the evolution of kinetoplast structure and RNA editing is hampered by a paucity of data from basal (i.e., clade 1) bodonids.

of the small rRNA genes and partial sequences of the large rRNA genes were obtained by PCR amplification from a variety of vertebrate trypanosomes. The trypanosome species and hosts included Trypunosomu auium from a bird, T. rotatorium from an amphibian. T. boissoni from an elasmobranch, T. triglae from a marine teleost and T. carassii from a freshwater teleost. Phylogenetic relationships among these species and other representatives of the family Trypanosomatidae were inferred using maximum likelihood, maximum parsimony and evolutionary parsimony.

The morphological based taxonomy of highly derived parasite groups is likely to poorly reflect their evolutionary relationships. The taxonomy of the monogenean family Capsalidae, which comprises approximately 180 species of flatworm parasites that predominantly attach to external surfaces of chondrichthyan and teleost fishes, is based mainly on six morphological characters. The phylogenetic history of the family is largely unknown. We reconstructed the phylogenetic relationships of 47 species in 20 genera from eight of the nine subfamilies, from nucleotide sequences of three unlinked nuclear genes, 28S ribosomal RNA, Histone 3 and Elongation Factor 1 a. Our phylogeny was well corroborated, with 75% of branches receiving strong support from both Bayesian posterior probabilities and maximum likelihood bootstrap proportions and all nodes showed positive partitioned likelihood support for each of the three genes. We found that the family was monophyletic, with the Gyrodactylidae and Udonellidae forming the sister group. The Capsalinae was monophyletic, however, our data do not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Entobdella, Listrocephalos, Neobenedenia and Tristoma, but Benedenia and Neoentobdella were polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on the molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification shows little correspondence with the phylogenetic relationships within the family.

BACKGROUND & AIMS: An association between water sources and the prevalence of Helicobacter pylori infection in Peruvian children was shown previously. The aim of this study was to confirm the presence of H. pylori in drinking water in the same community. METHODS: Forty-eight drinking water samples from different locations in pueblo jovenes (new towns) near Lima were collected. Samples were frozen until technology advanced to the point to the point at which H. pylori might be reliably detected. Immunomagnetic beads coated with anti-H. pylori immunoglobulin Gs were used to concentrate H. pylori, and two polymerase chain reaction assays based on different H. pylori genes were used. One was a polymerase chain reaction for the detection of the H. pylori adhesin subunit encoding gene, and the second was a previously validated H. pylori 16S ribosomal RNA reverse transcriptase- polymerase chain reaction. RESULTS: The expected 375-base pair fragment from the adhesin gene was amplified from 24 water samples. The expected 500-base pair fragment of the 16S ribosomal RNA and the 375-base pair fragment of the adhesin gene were amplified from 11 of the samples. CONCLUSIONS: These results confirm the presence of H. pylori in drinking water in Peru and are consistent with conclusions from a previous epidemiological study of the same population. This provides additional evidence for waterborne transmission of H. pylori in some environments. (Gastroenterology 1996 Apr;110(4):1031-5)

In sediments, methane-oxidizing bacteria live in opposing gradients of methane and oxygen. In such a gradient system, the fluxes of methane and oxygen are controlled by diffusion and consumption rates, and the rate-limiting substrate is maintained at a minimum concentration at the layer of consumption. Opposing gradients of methane and oxygen were mimicked in a specific cultivation set-up in which growth of methanotrophic bacteria occurred as a sharp band at either c. 5 or 20 mm below the air-exposed end. Two new strains of methanotrophic bacteria were isolated with this system. One isolate, strain LC 1, belonged to the Methylomonas genus (type I methantroph) and contained soluble methane mono-oxygenase. Another isolate, strain LC 2, was related to the Methylobacter group (type I methantroph), as determined by 16S rRNA gene and pmoA sequence similarities. However, the partial pmoA sequence was only 86% related to cultured Methylobacter species. This strain accumulated significant amounts of formaldehyde in conventional cultivation with methane and oxygen, which may explain why it is preferentially enriched in a gradient cultivation system.

Abstract}The feasibility of codigestion of the organic fraction of municipal solid waste, primary sludge, and waste activated sludge was evaluated in mesophilic (378C), laboratory-scale digesters. In a first experiment, different startup strategies were compared using four digesters, operated under continuously mixed conditions. After two weeks, the experiment was continued under minimally mixed conditions. Results demonstrated that reducing the level of

4b There was limitation in the choice of average grain counts used for radioautographic analysis, because at higher averages, some mitochondria were obscured by their associated grains. At the average grain counts used in our analyses, small populations of highly labeled or of unlabeled mitt)ehondria could be detected, but mixtures of labeled populations with small differences in their average grain counts would not be resolved.

Art. 5º -Todos são iguais perante a lei, sem distinção de qualquer natureza, garantindo -se aos brasileiros e aos estrangeiros residentes no País a inviolabilidade do direito à vida, à liberdade, à igualdade, à segurança e à propriedade, nos termos seguintes:

A series of 2′′-O-substituted ether analogues of paromomycin were prepared based on new site-selective functionalizations. X-ray cocrystal complexes of several such analogues revealed a new mode of binding in the A-site rRNA, whereby rings I and II adopted the familiar orientation and position previously observed with paromomycin, but rings III and IV were oriented differently. With few exceptions, all of the new analogues showed potent inhibitory activity equal or better than paromomycin against a sensitive strain of S. aureus. Single digit µM MIC values were obtained against E. coli, with some of the ether appendages containing polar or basic end groups. Two analogues showed excellent survival rate in a mouse septicemia protection assay. Preliminary histopathological analysis of the kidney showed no overt signs of toxicity, while controls with neomycin and kanamycin were toxic at lower doses. . Paromomycin C2′′ ethers complexed for X-ray study. Left: superposition of paromomycin (blue) with tobramycin (green) from their respective X-ray complexes; Right: structures of active C2′′ ethers (6-8) cocrystallized with A-site oligonucleotides.

T2-family acidic endoribonucleases are represented in all genomes. A physiological role for RNase T2 has yet to be defined for metazoa. RNASET2 mutation in humans is linked with a leukoencephalopathy that arises in infancy characterized by cortical cysts and multifocal white matter lesions. We now show localization of RNASET2 within lysosomes. Further, we demonstrate that loss of rnaset2 in mutant zebrafish results in accumulation of undigested rRNA within lysosomes within neurons of the brain. Further, by using high field intensity magnetic resonance microimaging, we reveal white matter lesions in these animals comparable to those observed in RNASET2deficient infants. This correlates with accumulation of Amyloid precursor protein and astrocytes at sites of neurodegeneration. Thus we conclude that familial cystic leukoencephalopathy is a lysosomal storage disorder in which rRNA is the best candidate for the noxious storage material.

Most of the 29 living species of Potamididae show a close association with mangroves. The trees provide the snails with shelter, protection from predators, a solid substrate and sometimes food. Using sequences from three genes (nuclear 18S rRNA and 28S rRNA, mitochondrial COI) we derive a molecular phylogeny and recognize six living genera (Terebralia, Telescopium, Tympanotonos, Cerithidea, Cerithideopsis, Cerithideopsilla). The oldest modern genera (Terebralia, Cerithideopsis) appeared in the Tethyan realm in the Middle Eocene, shortly after the origin of mangrove trees. Whereas most potamidid genera are now restricted to either the Indo-West Pacific (IWP) or to the eastern Pacific plus Atlantic (EPA), sister clades of Cerithideopsis survive in both realms. Based on a reinterpretation of the fossil record (particularly of the monotypic Tympanotonos and extinct Potamides), and parsimonious reconstruction of ancestral habitats, we suggest that the living potamidids are an adaptive radiation that has always been closely associated with mangroves. The specialized tree-climbing groups Cerithidea and Cerithideopsis were independently derived from mud-dwelling ancestors. Cerithideopsilla cingulata (a species complex in the IWP) and 'Potamides' conicus (in the Mediterranean and Indian Ocean) form a single clade within the genus Cerithideopsilla. This refutes the hypothesis that 'P.' conicus is the sole relict of the Tethyan Potamides that has occurred in the Mediterranean region since the Palaeocene. Instead, the phylogeny and fossil record suggest that an ancestor of Cerithideopsilla conica with planktotrophic larvae dispersed from the IWP to the Mediterranean in the Middle Miocene, that its direct development evolved in the Mediterranean during the Pliocene, and that it reinvaded the Indian Ocean during the Plio-Pleistocene.

Marine nematodes, which play an important role in many ecosystems, include a number of apparently cosmopolitan taxa that exhibit broad biogeographic ranges even though there is no obvious dispersal phase in their lifecycle. In this study, standard taxonomic approaches to marine nematode identiWcation in conjunction with multivariate statistical analysis of morphometric data were compared with molecular techniques. Specimens of the marine nematode Terschellingia longicaudata that had been identi-Wed by their morphological features were investigated from a range of localities (East and West Atlantic, Bahrain, Malaysia) and habitats (estuarine, intertidal, subtidal) using molecular approaches based on the ampliWcation and sequencing of the small subunit ribosomal RNA (18S rRNA). The study revealed that the majority of the morphologically deWned T. longicaudata specimens share a single 18S rRNA sequence and apparently belong to a single taxon distributed from the British Isles to Malaysia. In addition, 18S rRNA analysis also revealed two additional sequences. One of these sequences was found in both the British Isles and Mexico, the other was recorded only from British waters. Individuals collected in Bahrain and identi-Wed from their morphology as T. longicaudata had two highly divergent 18S rRNA sequences. Separate morphological and morphometric approaches to identiWcation of specimens from the same sites that had been formalinpreserved did not support evidence of multiple genotypes revealed previously by molecular analysis. Current taxonomy based on morphological characters detected using light-microscopy may be unable to discriminate possible species complexes. Biodiversity of marine nematodes may often be underestimated due to the presence of morphologically cryptic species complexes. High-throughput techniques such as DNA barcoding would aid in species identiWcation but may require thorough analysis of multiple nuclear and mitochondrial molecular markers. Communicated by S. Uthicke.

Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive evidence of different genes providing significantly different estimates of phylogeny in higher organisms" (p. 156; Huelsenbeck et al., 1996, Trends Ecol. Evol. 11:152-158). Our research indicates that the previous discrepancy of phylogenetic results between the 18S rRNA gene and other genes is caused mainly by (1) the misalignment of the sequences, (2) the inappropriate use of the frequency parameters, and (3) poor sequence quality. When the sequences are aligned with the aide of the secondary structure of the 18S rRNA molecule and when the frequency parameters are estimated either from all sites or from the variable domains where substitutions have occurred, the 18S rRNA sequences no longer support the grouping of the avian species with the mammalian species. [alignment; 18S rRNA; RNA secondary structure; Indel; molecular phylogenetics; tetrapod phylogeny.]