De novo sequencing of the Hypericum perforatum L. flower transcriptome to identify potential genes that are related to plant reproduction sensu lato

Background: St. John's wort (Hypericum perforatum L.) is a medicinal plant that produces important metabolites with antidepressant and anticancer activities. Recently gained biological information has shown that this species is also an attractive model system for the study of a naturally occurring form of asexual reproduction called apomixis, which allows cloning plants through seeds. In aposporic gametogenesis, one or multiple somatic cells belonging to the ovule nucellus change their fate by dividing mitotically and developing functionally unreduced embryo sacs by mimicking sexual gametogenesis. Although the introduction of apomixis into agronomically important crops could have revolutionary implications for plant breeding, the genetic control of this mechanism of seed formation is still not well understood for most of the model species investigated so far. We used Roche 454 technology to sequence the entire H. perforatum flower transcriptome of whole flower buds and single flower verticils collected from obligately sexual and unrelated highly or facultatively apomictic genotypes, which enabled us to identify RNAs that are likely exclusive to flower organs (i.e., sepals, petals, stamens and carpels) or reproductive strategies (i.e., sexual vs. apomictic). Results: Here we sequenced and annotated the flower transcriptome of H. perforatum with particular reference to reproductive organs and processes. In particular, in our study we characterized approximately 37,000 transcripts found expressed in male and/or female reproductive organs, including tissues or cells of sexual and apomictic flower buds. Ontological annotation was applied to identify major biological processes and molecular functions involved in flower development and plant reproduction. Starting from this dataset, we were able to recover and annotate a large number of transcripts related to meiosis, gametophyte/gamete formation, and embryogenesis, as well as genes that are exclusively or preferentially expressed in sexual or apomictic libraries. Real-Time RT-qPCR assays on pistils and anthers collected at different developmental stages from accessions showing alternative modes of reproduction were used to identify potential genes that are related to plant reproduction sensu lato in H. perforatum. Conclusions: Our approach of sequencing flowers from two fully obligate sexual genotypes and two unrelated highly apomictic genotypes, in addition to different flower parts dissected from a facultatively apomictic accession, enabled us to analyze the complexity of the flower transcriptome according to its main reproductive organs as well as for alternative reproductive behaviors. Both annotation and expression data provided original results supporting the hypothesis that apomixis in H. perforatum relies upon spatial or temporal mis-expression of genes acting during female sexual reproduction. The present analyses aim to pave the way toward a better understanding of the molecular basis of flower development and plant reproduction, by identifying genes or RNAs that may differentiate or regulate the sexual and apomictic reproductive pathways in H. perforatum

Assessing Design and Funding Methods of Water Infrastructure for Saskatchewan First Nations

Many water systems on First Nations in Saskatchewan are at risk of not being able to consistently meet water quality guidelines, which negatively impacts human health. It was the goal of my thesis to assess design and funding methods for water infrastructure projects on First Nations. It was important that this research was informed by community values and priorities gained from discussions with Elders, interviews with water treatment officers, and activities with elementary and high school students. A scoping review looked for existing literature on water infrastructure projects that involved the community in the design process, termed ‘co-design’. Of 1,551 articles searched, only 13 were found using the search terms (and synonyms): “water”, “co-design”, “Indigenous communities”, “infrastructure”, and “Canada”. A common definition of co-design and clear process is required to trend towards community informed design. Co-design as a process for water infrastructure in Indigenous communities encompasses the cultural, traditional, and spiritual values associated with water from the community’s worldview along with the environmental and technical conditions from an engineering standpoint. The increased involvement for this process requires extra funding, which is difficult in communities that are already restricted by rigid funding frameworks. Communities prefer a centralized system (piped water) to reduce the likelihood of contamination and water quantity rationing. The preference for a centralized system is prevented by a funding formula that does not provide the higher capital expense of this infrastructure. However, the formula can be expanded beyond capital investment and regular operation and maintenance to include costs associated with human health. The installation of both decentralized and centralized systems were quoted and compared for an example community of 100 homes (500 people). The approximate capital cost of a centralized system and decentralized system were found to be $3,512,000 and$ 1,365,000, respectively. However, the extra costs associated with the decentralized system were $ 570,000 per year, which covers the greater capital investment for a centralized system in under 5 years. The provision of safe drinking water for human health justifies a greater capital investment on its own, but the inclusion of other variables in the funding formula suggests that it is economically feasible as well

Palatalization in Romanian — Acoustic properties and perception

This paper presents the results of an acoustic study of fricatives from four places of articulation produced by 31 native speakers of Romanian, as well as those of a perceptual study using the stimuli from the acoustic experiment, allowing for a direct comparison between acoustic properties and perception. It was found that there are greater acoustic differences between plain and palatalized labials and dorsals as compared to coronals. The acoustic results were paralleled by the perceptual findings. This pattern departs from cross-linguistic generalizations made with respect to the properties of secondary palatalization. A likely source of the differences is the fact that previous studies of secondary palatalization typically involved stops which tend to exhibit various enhancement phenomena at the coronal place of articulation. Since the enhancement generally involves additional frication, this is not a useful strategy for fricatives at the coronal, or any other place of articulation. These findings form the basis of a discussion highlighting the differences between enhanced and non-enhanced secondary palatalization

Effects of electron acceptors and donors on transformation of tetrachloromethane by Shewanella putrefaciens MR-1

Transformation of chlorinated aliphatic compounds was examined in Shewanella putrefaciens strain MR-1, an obligately respiring facultative anaerobe. Under anaerobic conditions, MR-1 has been shown to transform tetrachloromethane to trichloromethane (24%), CO 2 (7%), cell-bound material (50%) and unidentified nonvolatile products (4%). The highest rate and extent of transformation were observed with MR-1 cells grown under iron(III)-respiring conditions. Lactate, formate and hydrogen were the most effective electron donors. Tetrachloromethane was not degraded in the presence of oxygen. Transformation of other chlorinated methanes and ethenes was not observed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73742/1/j.1574-6968.1994.tb07126.x.pd

Human Pathogens Abundant in the Bacterial Metagenome of Cigarettes

International audienceBACKGROUND: Many studies have evaluated chemical, heavy metal, and other abiotic substances present in cigarettes and their roles in the development of lung cancer and other diseases, yet no studies have comprehensively evaluated bacterial diversity of cigarettes and the possible impacts of these microbes on respiratory illnesses in smokers and exposed nonsmokers. OBJECTIVES: The goal of this study was to explore the bacterial metagenomes of commercially available cigarettes. METHODS: A 16S rRNA-based taxonomic microarray and cloning and sequencing were used to evaluate total bacterial diversity of four brands of cigarettes. Normalized microarray data were compared using principal component analysis and hierarchical cluster analysis to evaluate potential differences in microbial diversity across cigarette brands. RESULTS: Fifteen different classes of bacteria and a broad range of potentially pathogenic organisms were detected in all cigarette samples. Most notably, we detected Acinetobacter, Bacillus, Burkholderia, Clostridium, Klebsiella, Pseudomonas aeruginosa, and Serratia in >= 90% of all cigarette samples. Other pathogenic bacteria detected included Campylobacter, Enterococcus, Proteus, and Staphylococcus. No significant variability in bacterial diversity was observed across the four different cigarette brands. CONCLUSIONS: Previous studies have shown that smoking is associated with colonization by pathogenic bacteria and an increased risk of lung infections. However, this is the first study to show that cigarettes themselves could be the direct source of exposure to a wide array of potentially pathogenic microbes among smokers and other people exposed to secondhand smoke. The overall public health implications of these findings are unclear at this time, and future studies arc necessary to determine whether bacteria in cigarettes could play important roles in the development of both infectious and chronic respiratory diseases

Assessment of a Pharmacist-Led Antibiotic Time-out for Transition of IV Vancomycin to Oral Linezolid

Introduction: Intravenous (IV) vancomycin requires therapeutic drug monitoring and line placement and may prolong hospital stay. Linezolid requires less monitoring, is orally bioavailable, and may expedite transitions of care. This study assessed the impact of a pharmacist-led antibiotic timeout for the transition from IV vancomycin to oral linezolid. Methods: This single-center, quasi-experimental study included admitted adult patients receiving IV vancomycin for over 48 hours. Patients receiving vasopressors, of immunocompromised status, or with specific antibiotic indications were excluded. The primary outcome was the pharmacist intervention acceptance rate. Secondary outcomes included median hospital length of stay, median antibiotic treatment days, and incidence of adverse effects. Results: Of the 317 screened patients, 94 were eligible for the antibiotic time-out assessment, of which 66 met the criteria for oral linezolid. Of those meeting the criteria, 27 interventions were made, of which 20 (74%) were accepted. The median length of antibiotic treatment days was six days between both groups (p = .352). No differences in safety outcomes were observed. Discussion: A pharmacist-led antibiotic timeout for IV vancomycin to oral linezolid resulted in a high intervention acceptance rate and increased oral linezolid use without impacting safety outcomes. These results support the use of this strategy for antimicrobial stewardship. Conclusion: This study illustrates the impact of a pharmacist-led antibiotic timeout for the transition from IV vancomycin to oral linezolid therapy as an antimicrobial stewardship tool

Dechlorination of 2,3,5,6-tetrachlorobiphenyl by a phototrophic enrichment culture

A phototrophic enrichment culture, using acetate as carbon source, reductively dechlorinated 2,3,5,6-tetrachlorobiphenyl. ortho chlorines were removed preferentially over meta chlorines. Tri- and dichlorobiphenyls were the major products. During 14 months incubation, chlorine was removed from 58% of the target molecules; 19% of the total chlorines were removed. Dechlorination did not occur in a control culture incubated in the dark.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29945/1/0000303.pd

Tailoring community-based wellness initiatives with latent class analysis--Massachusetts Community Transformation Grant projects

INTRODUCTION: Community-based approaches to preventing chronic diseases are attractive because of their broad reach and low costs, and as such, are integral components of health care reform efforts. Implementing community-based initiatives across Massachusetts\u27 municipalities presents both programmatic and evaluation challenges. For effective delivery and evaluation of the interventions, establishing a community typology that groups similar municipalities provides a balanced and cost-effective approach. METHODS: Through a series of key informant interviews and exploratory data analysis, we identified 55 municipal-level indicators of 6 domains for the typology analysis. The domains were health behaviors and health outcomes, housing and land use, transportation, retail environment, socioeconomics, and demographic composition. A latent class analysis was used to identify 10 groups of municipalities based on similar patterns of municipal-level indicators across the domains. RESULTS: Our model with 10 latent classes yielded excellent classification certainty (relative entropy = .995, minimum class probability for any class = .871), and differentiated distinct groups of municipalities based on health-relevant needs and resources. The classes differentiated healthy and racially and ethnically diverse urban areas from cities with similar population densities and diversity but worse health outcomes, affluent communities from lower-income rural communities, and mature suburban areas from rapidly suburbanizing communities with different healthy-living challenges. CONCLUSION: Latent class analysis is a tool that may aid in the planning, communication, and evaluation of community-based wellness initiatives such as Community Transformation Grants projects administrated by the Centers for Disease Control and Prevention

Encapsulation kinetics and dynamics of carbon monoxide in clathrate hydrate.

Carbon monoxide clathrate hydrate is a potentially important constituent in the solar system. In contrast to the well-established relation between the size of gaseous molecule and hydrate structure, previous work showed that carbon monoxide molecules preferentially form structure-I rather than structure-II gas hydrate. Resolving this discrepancy is fundamentally important to understanding clathrate formation, structure stabilization and the role the dipole moment/molecular polarizability plays in these processes. Here we report the synthesis of structure-II carbon monoxide hydrate under moderate high-pressure/low-temperature conditions. We demonstrate that the relative stability between structure-I and structure-II hydrates is primarily determined by kinetically controlled cage filling and associated binding energies. Within hexakaidecahedral cage, molecular dynamic simulations of density distributions reveal eight low-energy wells forming a cubic geometry in favour of the occupancy of carbon monoxide molecules, suggesting that the carbon monoxide-water and carbon monoxide-carbon monoxide interactions with adjacent cages provide a significant source of stability for the structure-II clathrate framework

Recent improvements in the CMU large-scale Chinese-English SMT system

In this paper we describe recent improvements to components and methods used in our statistical machine translation system for Chinese-English used in the January 2008 GALE evaluation. Main improvements are results of consistent data processing, larger statistical models and a POS-based word reordering approach