Distribution and Diversity of Escherichia coli Populations in the South Nation River Drainage Basin,Eastern Ontario,Canada

We investigated the prevalence and diversity of Escherichia coli strains isolated from surface waters from multiple watersheds within the South Nation River basin in eastern Ontario, Canada. The basin is composed of mixed but primarily agricultural land uses. From March 2004 to November 2007, a total of 2,004 surface water samples were collected from 24 sampling sites. E. coli densities ranged from undetectable to 1.64 × 10⁵ CFU 100 ml⁻¹ and were correlated with stream order and proximity to livestock production systems. The diversity of 21,307 E. coli isolates was characterized using repetitive extragenic palindromic PCR (rep-PCR), allowing for the identification of as many as 7,325 distinct genotypes, without capturing all of the diversity. The community was temporally and spatially dominated by a few dominant genotypes (clusters of more than 500 isolates) and several genotypes of intermediary abundance (clustering between 10 and 499 isolates). Simpson diversity indices, assessed on a normalized number of isolates per sample, ranged from 0.050 to 0.668. Simpson indices could be statistically discriminated on the basis of year and stream order, but land use, discharge, weather, and water physical-chemical properties were not statistically important discriminators. The detection of Campylobacter species was associated with statistically lower Simpson indices (greater diversity; P < 0.05). Waterborne E. coli isolates from genotypes of dominant and intermediary abundance were clustered with isolates obtained from fecal samples collected in the study area over the same period, and 90% of the isolates tested proved to share genotypes with fecal isolates. Overall, our data indicated that the densities and distribution of E. coli in these mixed-use watersheds were linked to stream order and livestock-based land uses. Waterborne E. coli populations that were distinct from fecal isolates were detected and, on this basis, were possibly naturalized E. coli strains.Escherichia coli is ubiquitously distributed in fecal material from humans and warm-blooded animals (38). The detection of E. coli in water is an implicit indicator of recent fecal contamination and therefore of the risk of cooccurrence of enteric pathogens that can cause illness in susceptible populations (62). Many jurisdictions evaluate and mandate compliance with drinking and recreational water quality standards on the basis of the presence and abundance of E. coli (14, 44). For example, Canadian recreational water quality standards stipulate that E. coli densities in excess of a geometric mean of 200 CFU per 100 ml indicate that the water is unsuitable for swimming and bathing (23).In a background of increasing occurrence of microbial contamination of surface water, a variety of methods for elucidating the sources of fecal contamination have been developed, and these microbial source tracking (MST) methods are recommended components of fecal pollution abatement strategies (16, 57). So-called library-dependent MST methods compare environmental isolates to collections of isolates obtained from likely sources of fecal pollution in the area of investigation. The host source is distinguished on the basis of the similarity of environmental isolates to reference fecal isolates. Comparison can be undertaken on the basis of genomic fingerprinting methods, including repetitive extragenic palindromic PCR (rep-PCR), ribotyping, or pulsed-field gel electrophoresis (PFGE) (13, 17, 31, 54, 57). A variety of studies using these methods have revealed enormous diversity in the fecal and environmental E. coli populations. For example, 461 distinct PFGE genotypes and 175 distinct enterobacterial repetitive intergenic consensus (ERIC)-PCR genotypes were detected in a collection of 555 E. coli strains isolated from river water in Texas (10). As many as 291 and 94 rep-PCR genotypes were distinguished in collections of 643 river isolates and 353 beach water E. coli isolates, respectively (43). Significant diversity was also revealed using multilocus enzyme electrophoresis (MLEE) and multilocus sequence typing (MLST) on 185 E. coli isolates from freshwater beaches, where an average of 40 alleles per locus were detected (59). Almost 60% of 657 E. coli isolates in a fecal reference collection had unique (i.e., detected in only one individual) fingerprints determined by rep-PCR (32). Extensive diversity of E. coli was also observed in soils in temperate climates, where the growth and persistence of “naturalized” populations without any known fecal input have been found (7, 28, 30). Naturalized populations have been dominated by the B1 phylogroup and may have adapted in ways that enhance their survival in temperate secondary habitats (59). The temporal and spatial diversity of E. coli may not be a significant factor in coarse-source (e.g., human versus animal) classification of E. coli by means of ribotyping procedures (48). Ultimately, the characterization and understanding of the diversity of populations of selected microorganisms in surface watercourses affected by multiple sources of fecal pollution (as in agricultural watershed settings, for example) may be more critical for assessing the specific impacts of contamination-mitigating measures than previously thought. For instance, restricting the access of cattle on pasture to adjacent water by implementing vegetative buffering along watercourses creates habitat for varied wildlife, which then contribute to fecal pollution. In this context, the diversity in populations of indicator bacteria could be useful for better understanding how changes in landscape use influence fecal source inputs.As part of a research program evaluating the impact of agriculture on water quality and the efficacy of better agricultural management practices to mitigate agricultural pollution, we have conducted a multiyear study of the microbiological water quality for a suite of different-sized watersheds in the South Nation River basin in eastern Ontario, Canada (41, 46, 61). Land use in this river basin is mixed, consisting primarily of agricultural activities, light urban development, and interspersed wildlife habitat. Surface water systems in the study region differ widely in their contributing areas and therefore in their discharges (61).In the work undertaken here, we sought to determine the spatial and seasonal variability in the density and the structure of populations of E. coli in surface waters within the South Nation River basin. The specific objectives of the study were (i) to characterize the seasonal distribution and abundance of E. coli in different watershed settings within the river basin, (ii) to evaluate the spatial distribution of E. coli densities and diversity with respect to upstream land use activities, (iii) to use rep-PCR to elucidate the dominant E. coli genotypes and the diversity of E. coli populations and to explore linkages to pathogen presence, season, and environmental and land use variables, and (iv) using rep-PCR, to evaluate the concordance between waterborne isolates and fecal isolates obtained from within the study area. The study is distinguished by an intensive 4-year sampling of numerous (n = 24) sites that differed in their stream order and proximal land use activity; the number of E. coli isolates (≈21,000) included in the analysis; and the use of two distinct rep-PCR fingerprinting methods (ERIC and BOXA1R) to characterize the isolates. Furthermore, we used classification and Regression Tree (CART) analysis to evaluate relationships between the abundance and diversity of E. coli in water samples and environmental and land use variables.     

Application of solid–liquid TPPBs to the production of L‐phenylacetylcarbinol from benzaldehyde using Candida utilis

The biotransformation of benzaldehyde and glucose to L ‐phenylacetylcarbinol (PAC) using Candida utilis was demonstrated in a solid–liquid two‐phase partitioning bioreactor (TPPB) with the aim of reducing substrate, product, and by‐product toxicity via sequestration. Previous work in the field had used octanol as the sequestering phase of liquid–liquid TPPBs but was limited by the toxic effects of octanol on C. utilis. To improve solvent selection in any future studies, the critical log P of C. utilis was determined in the current study to be 4.8 and can be used to predict biocompatible solvents. Bioavailability tests showed alkanes and alkenes to be non‐bioavailable. As polymers are biocompatible and non‐bioavailable, a wide range of commercially available polymers was screened and it was demonstrated that polymer softness plays a key role in absorptive capability. The polymer Hytrel G3548L was selected as the second phase to sequester benzaldehyde, PAC, and benzyl alcohol, with partition coefficients of 35, 7.5, and 10, respectively. With a 9% by volume partitioning phase, 13.6 g/L biomass of C. utilis achieved an overall PAC concentration of 11 g/L, a 1.9‐fold improvement over the single‐phase case. Benzyl alcohol concentration was 4.5 g/L, a 1.6‐fold reduction. The volumetric productivity was 0.85 g/L h, a 1.2‐fold improvement over the single‐phase system. These results demonstrate a promising starting point for solid–liquid TPPBs for PAC production. Biotechnol. Bioeng. 2010;107:633–641. © 2010 Wiley Periodicals, Inc.     

Amoebae and algae can prolong the survival of Campylobacter species in co-culture

Several species of free-living amoebae can cause disease in humans. However, in addition to the direct pathogenicity of e.g. Acanthamoebae and Naegleria species, they are recognized as environmental hosts, indirectly involved in the epidemiology of many pathogenic bacteria. Although several studies have demonstrated intracellular survival of many different bacteria in these species, the extent of such interactions as well as the implications for the epidemiology of the bacterial species involved, are largely unknown and probably underestimated. In this study, we evaluated eight different unicellular eukaryotic organisms, for their potential to serve as environmental hosts for Campylobacter species. These organisms include four amoebozoas (Acanthamoeba polyphaga, Acanthamoeba castellanii, Acanthamoeba rhysodes and Hartmanella vermiformis), one alveolate (Tetrahymena pyriformis), one stramenopile (Dinobryon sertularia), one eugoenozoa (Euglena gracilis) and one heterolobosea (Naegleria americana). Campylobacter spp. including Campylobacter jejuni, Campylobacter coli and Campylobacter lari are the most common cause of gastroenteritis in the western world. Survival and replication of these three species as well as Campylobacter hyointestinalis were assessed in co-cultures with the eukaryotic organisms. Campylobacter spp. generally survived longer in co-cultures, compared to when incubated in the corresponding growth media. The eukaryotic species that best promoted bacterial survival was the golden algae D. sertularia. Three species of amoebozoas, of the genus Acanthamoeba promoted both prolonged survival and replication of Campylobacter spp. The high abundance in lakes, ponds and water distribution networks of these organisms indicate that they might have a role in the epidemiology of campylobacteriosis, possibly contributing to survival and dissemination of these intestinal pathogens to humans and other animals. The results suggest that not only C. jejuni, but a variety of Campylobacter spp. can interact with different eukaryotic unicellular organisms.     

DDB2, an Essential Mediator of Premature Senescence

Reactive oxygen species (ROS) is critical for premature senescence, a process significant in tumor suppression and cancer therapy. Here, we reveal a novel function of the nucleotide excision repair protein DDB2 in the accumulation of ROS in a manner that is essential for premature senescence. DDB2-deficient cells fail to undergo premature senescence induced by culture shock, exogenous oxidative stress, oncogenic stress, or DNA damage. These cells do not accumulate ROS following DNA damage. The lack of ROS accumulation in DDB2 deficiency results from high-level expression of the antioxidant genes in vitro and in vivo. DDB2 represses antioxidant genes by recruiting Cul4A and Suv39h and by increasing histone-H3K9 trimethylation. Moreover, expression of DDB2 also is induced by ROS. Together, our results show that, upon oxidative stress, DDB2 functions in a positive feedback loop by repressing the antioxidant genes to cause persistent accumulation of ROS and induce premature senescence.DDB2 is encoded by the nucleotide excision repair (NER) XPE gene (17, 24, 33). Unlike other NER gene-deficient cells or xeroderma pigmentosum (XP) cells, the XPE cells exhibit only a mild deficiency in NER (55). However, because of its high affinity for cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts, several studies implicated DDB2 in the early damaged-DNA recognition step of NER (61). However, a direct role of DDB2 in NER is a point of controversy (28, 41, 57). Lower organisms (yeasts), in which other XP genes are conserved, apparently do not encode a DDB2 homolog (55, 64). We showed that DDB2 associates with Cul4, a component of an E3 ubiquitin ligase complex that is now known to involve the DDB2 binding protein DDB1 as its adapter (48). The Cul4-DDB1 E3 ligase associates with a number of substrate-specific adapter proteins to target substrates for ubiquitination (30, 35). DDB2 is believed to be one of those substrate adapters, which allows Cul4-DDB1 to target specific proteins. Two studies suggested that the Cul4A-DDB1-DDB2 complex could participate in the ubiquitination of histones, indicating a role of DDB2 in chromatin remodeling (23, 59). Other investigators suggested a role of Cul4A-DDB1-DDB2 in the ubiquitination of XPC (15, 52). We recently found that DDB2 is involved also in targeting p21 for proteolysis and demonstrated that DDB2 stimulated NER by regulating the level of p21 (51).It was shown elsewhere that DDB2^−/− mouse embryonic fibroblasts (MEFs) are resistant to UV-induced apoptosis (20, 21). Recently, we extended those observations by demonstrating that DDB2^−/− MEFs or DDB2-deficient human cells are resistant to apoptosis induced by a variety of DNA-damaging agents (50). Moreover, DDB2^−/− MEFs are deficient in E2F1-induced apoptosis. The resistance to apoptosis is linked also to high-level accumulation of p21 because deletion of p21 restored apoptosis. The polyubiquitination of p21 is significantly reduced in DDB2-deficient cells (50), suggesting that after DNA damage DDB2 plays a key role in polyubiquitinating p21. Also, we observed evidence for a physical association between DDB2 and p21, which was increased in UV-irradiated cells (50), indicating that DDB2 plays a direct role in targeting p21 for proteolysis after DNA damage. These observations provided evidence that DDB2, in addition to stimulating NER, plays a significant role in terminating DNA damage checkpoint, allowing cells with extensive DNA damage to undergo apoptosis.In addition to its role in the inhibition of cell cycle and apoptosis, p21 has been implicated also in cellular senescence, as its level increases in senescent cells (7). Cellular senescence is defined as a proliferative arrest of a cell after a limited number of cell divisions while the cell remains metabolically and synthetically active (6, 63). Senescence can be triggered by both extrinsic factors such as oncogenic stress, DNA damage, oxidative stress, and culture shock and intrinsic factors such as telomere regression in human cells (19). When grown in cell culture medium, human diploid fibroblasts undergo 60 to 80 population doublings, after which they cease proliferation as a result of telomere erosion and enter into the stage of replicative senescence characterized by enlarged and flattened morphology, increased granularity, and enhanced senescence-associated β-galactosidase (SA-β-Gal) activity (13). In contrast, telomere length does not limit the ability of the murine fibroblasts to proliferate in culture. It was shown that the supraphysiological level of oxygen or reactive oxygen species (ROS) under which the cells are grown led murine fibroblasts to senesce (39). ROS accumulation or oxidative stress induces the senescent phenotype in response to oncogenic stress as well as in response to DNA-damaging agents (56). These pathways have been termed premature senescence, which recapitulates molecular features of replicative senescence. Premature senescence induced by oncogene expression is a significant mechanism of tumor suppression involving the Ink4a/Arf locus (47). Moreover, DNA damage-induced premature senescence is significant, as many anticancer drugs have been shown to induce premature senescence of tumor cells (12, 44).Because DDB2^−/− MEFs express p21 at a high level, we expected those cells to undergo premature senescence at an earlier passage than the wild-type (WT) MEFs. Surprisingly, we found that DDB2^−/− MEFs escape senescence at a very high frequency. Moreover, DDB2^−/− MEFs or DDB2-deficient human cells are resistant to premature senescence induced by a variety of agents, including oncogenic stress, exogenous oxidative stress, and DNA damage. The lack of premature senescence in the presence of high-level p21, especially after DNA damage, suggests that DDB2 functions in the senescence program through a mechanism that is downstream of the p21 pathway senescence. Here we show that DDB2 participates in the senescence program by inducing persistent accumulation of ROS.     

Discovery of highly potent and efficacious MC4R agonists with spiroindane N-Me-1,2,4-triazole privileged structures for the treatment of obesity

We report an SAR study of MC4R analogs containing spiroindane heterocyclic privileged structures. Compound 26 with N-Me-1,2,4-triazole moiety possesses exceptional potency at MC4R and potent anti-obesity efficacy in a mouse model. However, the efficacy is not completely mediated through MC4R. Additional SAR studies led to the discovery of compound 32, which is more potent at MC4R. Compound 32 demonstrates MC4R mediated anti-obesity efficacy in rodent models.     

Actomyosin tube formation in polar body cytokinesis requires Anillin in C. elegans

Polar body extrusion (PBE) is the specialized asymmetric division by which oocytes accomplish reduction in ploidy and retention of cytoplasm. During maternal gametogenesis, as in male meiosis and mitosis, cytokinesis is accomplished by a ring rich in active Rho, myosin, and formin-nucleated F-actin [1-7]. However, unlike mitosis, wherein the contractile ring encircles the cell equator, the polar body ring assembles as a discoid cortical washer. Here we show that in Caenorhabditis elegans, the meiotic contractile ring transforms during closure from a disc above the spindle to a cylinder around the spindle midzone. The meiotic midbody tube comprises stacked cytoskeletal rings. This topological transition suggests a novel mechanism for constriction of an initially discoid cytokinetic ring. Analysis of mouse PBE indicates that midbody tube formation is a conserved process. Depletion of the scaffold protein anillin (ANI-1) from C. elegans results in large and unstable polar bodies that often fuse with the oocyte. Anillin is dispensable for contractile ring assembly, initiation, and closure but is required for the meiotic contractile ring to transform from a disc into a tube. We propose that cytoskeletal bundling by anillin promotes formation of the midbody tube, which ensures the fidelity of PBE.     

Representing ontogeny through ontology: A developmental biologist's guide to the gene ontology

Developmental biology, like many other areas of biology, has undergone a dramatic shift in the perspective from which developmental processes are viewed. Instead of focusing on the actions of a handful of genes or functional RNAs, we now consider the interactions of large functional gene networks and study how these complex systems orchestrate the unfolding of an organism, from gametes to adult. Developmental biologists are beginning to realize that understanding ontogeny on this scale requires the utilization of computational methods to capture, store and represent the knowledge we have about the underlying processes. Here we review the use of the Gene Ontology (GO) to study developmental biology. We describe the organization and structure of the GO and illustrate some of the ways we use it to capture the current understanding of many common developmental processes. We also discuss ways in which gene product annotations using the GO have been used to ask and answer developmental questions in a variety of model developmental systems. We provide suggestions as to how the GO might be used in more powerful ways to address questions about development. Our goal is to provide developmental biologists with enough background about the GO that they can begin to think about how they might use the ontology efficiently and in the most powerful ways possible. Mol. Reprod. Dev. 77: 314–329, 2010. © 2009 Wiley‐Liss, Inc.     

Mycorrhizal colonizations of ferns and lycophytes on the island of La Réunion in relation to nutrient availability

Very little is known about the degree and ecological correlates of mycorrhization of lycophytes and ferns, although mycorrhizae are believed to be crucial for the majority of land plants. We screened the degree of mycorrhizal colonization for all 75 fern species recorded in nine survey plots across a wide range of soil conditions on the island of La Réunion, including five plots on lava flows of different age. Overall, 66% of all samples had mycorrhizae, but ground-dwelling species had significantly higher colonization levels (78%) than epiphytes (58%). Among ground-dwelling species, 98% of the individuals belonged to species with mycorrhizae, which was significantly higher than at the species level. Most samples had glomeromycetes as fungal partners, but septate endophytes were found in 41% of the colonized samples. While we found no significant relationship between the percentage of fern species with mycorrhizae per plot and seven ecological parameters, the percentage of fern individuals with mycorrhizal colonizations per plot significantly increased on shallow soils with high pH values and high base-saturation. This supports the idea that mycorrhizal colonizations confer an ecological advantage to colonized individuals, and that this advantage is more pronounced on nutrient-deficient sites. Our study thus provides evidence for an ecological advantage of mycorrhizae for ferns, but raises the question why, despite this advantage, species level mycorrhization among ferns (68%) is so much lower than the average for land plants (85%).     

A small GTPase molecular switch regulates epigenetic centromere maintenance by stabilizing newly incorporated CENP-A

Epigenetic mechanisms regulate genome activation in diverse events, including normal development and cancerous transformation. Centromeres are epigenetically designated chromosomal regions that maintain genomic stability by directing chromosome segregation during cell division. The histone H3 variant CENP-A resides specifically at centromeres, is fundamental to centromere function and is thought to act as the epigenetic mark defining centromere loci. Mechanisms directing assembly of CENP-A nucleosomes have recently emerged, but how CENP-A is maintained after assembly is unknown. Here, we show that a small GTPase switch functions to maintain newly assembled CENP-A nucleosomes. Using functional proteomics, we found that MgcRacGAP (a Rho family GTPase activating protein) interacts with the CENP-A licensing factor HsKNL2. High-resolution live-cell imaging assays, designed in this study, demonstrated that MgcRacGAP, the Rho family guanine nucleotide exchange factor (GEF) Ect2, and the small GTPases Cdc42 and Rac, are required for stability of newly incorporated CENP-A at centromeres. Thus, a small GTPase switch ensures epigenetic centromere maintenance after loading of new CENP-A.