Host Distributions of Uncultivated Fecal Bacteroidales Bacteria Reveal Genetic Markers for Fecal Source Identification

The purpose of this study was to examine host distribution patterns among fecal bacteria in the order Bacteroidales, with the goal of using endemic sequences as markers for fecal source identification in aquatic environments. We analyzed Bacteroidales 16S rRNA gene sequences from the feces of eight hosts: human, bovine, pig, horse, dog, cat, gull, and elk. Recovered sequences did not match database sequences, indicating high levels of uncultivated diversity. The analysis revealed both endemic and cosmopolitan distributions among the eight hosts. Ruminant, pig, and horse sequences tended to form host- or host group-specific clusters in a phylogenetic tree, while human, dog, cat, and gull sequences clustered together almost exclusively. Many of the human, dog, cat, and gull sequences fell within a large branch containing cultivated species from the genus Bacteroides. Most of the cultivated Bacteroides species had very close matches with multiple hosts and thus may not be useful targets for fecal source identification. A large branch containing cultivated members of the genus Prevotella included cloned sequences that were not closely related to cultivated Prevotella species. Most ruminant sequences formed clusters separate from the branches containing Bacteroides and Prevotella species. Host-specific sequences were identified for pigs and horses and were used to design PCR primers to identify pig and horse sources of fecal pollution in water. The primers successfully amplified fecal DNAs from their target hosts and did not amplify fecal DNAs from other species. Fecal bacteria endemic to the host species may result from evolution in different types of digestive systems.     

Molecular characterization of a dual inhibitory and mutagenic activity of 5-fluorouridine triphosphate on viral RNA synthesis. Implications for lethal mutagenesis

The basis for a dual inhibitory and mutagenic activity of 5-fluorouracil (5-FU) on foot-and-mouth disease virus (FMDV) RNA replication has been investigated with purified viral RNA-dependent RNA polymerase (3D) in vitro. 5-Fluorouridine triphosphate acted as a potent competitive inhibitor of VPg uridylylation, the initial step of viral replication. Peptide analysis by mass spectrometry has identified a VPg fragment containing 5-fluorouridine monophosphate (FUMP) covalently attached to Tyr3, the amino acid target of the uridylylation reaction. During RNA elongation, FUMP was incorporated in the place of UMP or CMP by FMDV 3D, using homopolymeric and heteropolymeric templates. Incorporation of FUMP did not prevent chain elongation, and, in some sequence contexts, it favored misincorporations at downstream positions. When present in the template, FUMP directed the incorporation of AMP and GMP, with ATP being a more effective substrate than GTP. The misincorporation of GMP was 17-fold faster opposite FU than opposite U in the template. These results in vitro are consistent with the mutational bias observed in the mutant spectra of 5-FU-treated FMDV populations. The dual mutagenic and inhibitory activity of 5-fluorouridine triphosphate may contribute to the effective extinction of FMDV by 5-FU through virus entry into error catastrophe.     

Phylogenetic diversity and molecular detection of bacteria in gull feces

In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rRNA gene clone library was developed and analyzed to determine the identities of fecal bacteria. Analysis of 282 16S rRNA gene clones demonstrated that the gull gut bacterial community is mostly composed of populations closely related to Bacilli (37%), Clostridia (17%), Gammaproteobacteria (11%), and Bacteriodetes (1%). Interestingly, a considerable number of sequences (i.e., 26%) were closely related to Catellicoccus marimammalium, a gram-positive, catalase-negative bacterium. To determine the occurrence of C. marimammalium in waterfowl, species-specific 16S rRNA gene PCR and real-time assays were developed and used to test fecal DNA extracts from different bird (n = 13) and mammal (n = 26) species. The results showed that both assays were specific to gull fecal DNA and that C. marimammalium was present in gull fecal samples collected from the five locations in North America (California, Georgia, Ohio, Wisconsin, and Toronto, Canada) tested. Additionally, 48 DNA extracts from waters collected from six sites in southern California, Great Lakes in Michigan, Lake Erie in Ohio, and Lake Ontario in Canada presumed to be impacted with gull feces were positive by the C. marimammalium assay. Due to the widespread presence of this species in gulls and environmental waters contaminated with gull feces, targeting this bacterial species might be useful for detecting gull fecal contamination in waterfowl-impacted waters.     

Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins

The structural ground underlying the pH-dependency of the dimer-tetramer transition of Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of wild-type and site-directed mutants of recombinant lectins. Synthetic genes coding for the full-length alpha-chains of the seed lectins of Dioclea guianensis (termed r-alphaDguia) and Dioclea grandiflora (termed r-alphaDGL) were designed and expressed in Escherichia coli. This pioneering approach, which will be described in detail in the present paper, yielded recombinant lectins displaying carbohydrate-binding activity, dimer-tetramer equilibria and crystal structures indistinguishable from their natural homologues. Conversion of the pH-stable tetrameric r-alphaDGL into a structure exhibiting pH-dependent dimer-tetramer transition was accomplished through mutations that abolished the interdimeric interactions at the central cavity of the tetrameric lectins. Both the central and the peripheral interacting regions bear structural information for formation of the canonical legume lectin tetramer. We hypothesize that the strength of the ionic contacts at these sites may be modulated by the pH, leading to dissociation of those lectin structures that are not locked into a pH-stable tetramer through interdimeric contacts networking the central cavity loops.     

Endogenous circannual cycles of ovarian activity and changes in prolactin and melatonin secretion in wild and domestic female sheep maintained under a long-day photoperiod

The present study examines the ovulatory activity of wild and domesticated ewes subjected to either a constant photoperiod of long days (16L:8D) or natural changes in daily photoperiod for 16 mo. The aim was to determine whether an endogenous reproductive rhythm controls seasonal reproductive activity in these sheep, and how the photoperiod might affect this. The effects of long-day photoperiods on long-term changes in prolactin and melatonin secretion were also evaluated. The two species showed changes in reproductive activity under the constant photoperiod conditions, suggesting the existence of an endogenous rhythm of reproduction. This rhythm was differently expressed in the two types of ewe (P < 0.05), with the domestic animals exhibiting much greater sensitivity to the effects of long days. A circannual rhythm of plasma prolactin concentration was also seen in both species and under both photoperiod conditions, although in both species the amplitude was always lower in the long-day animals (P < 0.01). The duration of the nocturnal melatonin plasma concentrations reflected the duration of darkness in both species and treatments. The peak melatonin concentration did not differ between seasons either under natural or long-day photoperiods.     

Sap flow as an indicator of transpiration and the water status of young apricot trees

The relationship between water loss via transpiration and stem sap flow in young apricot trees was studied under different environmental conditions and different levels of soil water status. The experiment was carried out in a greenhouse over a 2-week period (November 2–14, 1997) using three-year-old apricot trees (Prunus armeniaca cv. Búlida) growing in pots. Diurnal courses of leaf water potential, leaf conductance and leaf turgor potential also were recorded throughout the experiment. Data from four days of different enviromental conditions and soil water availability have been selected for analysis. On each of the selected days the leaf water potential and the mean transpiration rates were well correlated. The slope of the linear regression of this correlation, taken to indicate the total hydraulic resistance of the tree, confirmed an increasing hydraulic resistance under drought conditions. When the trees were not drought stressed the diurnal courses of sap flow and transpiration were very similar. However, when the trees were droughted, measured of sap flow slightly underestimated actual transpiration. Our heat-pulse measurements suggest the amount of readily available water stored in the stem and leaf tissues of young apricot trees is sufficient to sustain the peak transpiration rates for about 1 hour. This revised version was published online in June 2006 with corrections to the Cover Date.     

Offspring spatial patterns in Picconia excelsa (Oleaceae) in the Canarian laurel forest

We studied the spatial patterns of seedlings and seeds in isolated Picconia excelsa (Oleaceae) trees in the laurel forest of Anaga, Tenerife (Canary Islands). By finding isolated trees we assessed the correlation of seed and seedling bank traits and parent trees by removing the confounding effects of proximity (<100 m radius) of conspecific fruiting trees. We counted all the seedlings per age (height) class within its parental range, and sampled the seed number along transects departing from beneath the parent canopy at regular intervals. We mapped all seedlings per age class and plotted seed and seedling profiles in relation to distance to parent trees. Older Picconia seedlings tended to clump significantly further from parent trees than younger seedlings, which clumped just beneath the parents. We found significant differences among distances to parent tree in numbers of seedlings per age class. The seedling bank area was significantly correlated with maximum distance of seedlings to parent trees. The majority of seeds were deposited within the first 4 m below the parent crown. Seedlings amount at further distances from the trees is larger than seeds/fruits as counted on the ground. Our results suggest that disseminated, older seedlings have occupied germination sites far from the parent tree because there is probably lower seedling–seedling and parent–seedling competition for resources, and perhaps no intraspecific allelopathy and predation/disease.     

Responses of citrus plants to ozone: leaf biochemistry, antioxidant mechanisms and lipid peroxidation.

The effects of ozone upon 3-year-old trees of Clementina mandarin (Citrus clementina Hort. ex Tan.) cv. Marisol exposed for 12 months to ambient (10 nl l(-1)) and high (30 and 65 nl l(-1)) concentrations in open top chambers (OTCs) were investigated. The data showed that in leaves, ozone reduced total chlorophylls, carotenoid and carbohydrate concentration, and increased 1-aminocyclopropane-1-carboxylic acid (ACC) content and ethylene production. In treated plants, the ascorbate leaf pool was decreased, while lipid peroxidation and solute leakage were significantly higher than in ozone-free controls. The data indicated that ozone triggered protective mechanisms against oxidative stress in citrus.     

Compositionally and functionally distinct editosomes in Trypanosoma brucei

Uridylate insertion/deletion RNA editing in Trypanosoma brucei mitochondria is catalyzed by a multiprotein complex, the approximately 20S editosome. Editosomes purified via three related tagged RNase III proteins, KREN1 (KREPB1/TbMP90), KREPB2 (TbMP67), and KREN2 (KREPB3/TbMP61), had very similar but nonidentical protein compositions, and only the tagged member of these three RNase III proteins was identified in each respective complex. Three new editosome proteins were also identified in these complexes. Each tagged complex catalyzed both precleaved insertion and deletion editing in vitro. However, KREN1 complexes cleaved deletion but not insertion editing sites in vitro, and, conversely, KREN2 complexes cleaved insertion but not deletion editing sites. These specific nuclease activities were abolished by mutations in the putative RNase III catalytic domain of the respective proteins. Thus editosomes appear to be heterogeneous in composition with KREN1 complexes catalyzing cleavage of deletion sites and KREN2 complexes cleaving insertion sites while both can catalyze the U addition, U removal, and ligation steps of editing.     

The pcsA gene from Streptomyces diastaticus var. 108 encodes a polyene carboxamide synthase with broad substrate specificity for polyene amides biosynthesis

Two structurally related polyene macrolides are produced by Streptomyces diastaticus var. 108: rimocidin (3a) and CE-108 (2a). Both bioactive metabolites are biosynthesized from the same pathway through type I polyketide synthases by choosing a starter unit either acetate or butyrate, resulting in 2a or 3a formation, respectively. Two additional polyene amides, CE-108B (2b) and rimocidin B (3b), are also produced “in vivo” when this strain was genetically modified by transformation with engineered SCP2*-derived vectors carrying the ermE gene. The two polyene amides, 2b and 3b, showed improved pharmacological properties, and are generated by a tailoring activity involved in the conversion of the exocyclic carboxylic group of 2a and 3a into their amide derivatives. The improvement on some biological properties of the resulting polyenes, compared with that of the parental compounds, encourages our interest for isolating the tailoring gene responsible for the polyene carboxamide biosynthesis, aimed to use it as tool for generating new bioactive compounds. In this work, we describe the isolation from S. diastaticus var. 108 the corresponding gene, pcsA, encoding a polyene carboxamide synthase, belonging to the Class II glutamine amidotransferases and responsible for “in vivo” and “in vitro” formation of CE-108B (2b) and rimocidin B (3b). The fermentation broth from S. diastaticus var. 108 engineered with the appropriate pcsA gene construction, showed the polyene amides to be the major bioactive compounds.