Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

The 15-minute family interview: a family health strategy tool

The 15-minute family interview is a condensed form of the Calgary Family Assessment and Intervention Models (CFAM and CFIM) that aims to contribute to the establishment of a therapeutic relationship between nurses and family and to implement interventions to promote health and suffering relief, even during brief interactions. This study investigated the experience of nurses from the Family Health Strategy (FHS) who used the 15-minute interview on postpartum home. The qualitative research was conducted in three stages: participants' training program, utilization of the 15-minute family interview by participants, and interviews with nurses. The data were collected through semi-structured interviews with eight nurses. The thematic analysis revealed two main themes: dealing with the challenge of a new practice and evaluating the assignment. This work shows that this tool can be used to deepen relationships between nurses and families in the Family Health Strategy.

Inactivation of the regulatory gene algU or gacA can affect the ability of biocontrol Pseudomonas fluorescens CHA0 to persist as culturable cells in nonsterile soil.

Rifampin-resistant Pseudomonas fluorescens CHA0-Rif and mutants in which the regulatory gene algU (encoding sigma factor sigma(E)) or gacA (encoding a global regulator of secondary metabolism) was inactivated were compared for persistence in three nonsterile soils. Functional algU and (particularly) gacA were needed for CHA0-Rif to maintain cell culturability in soil.

Development of a specific control banding tool for nanomaterials : report

[Table des matières] 1. Introduction to the control banding method : Nanomaterials and occupational risk assessment; Alternative method known as control banding; Scope and limits of control banding. - 2. Control banding process applied to manufactured nanomaterials: General points; Operating principle. - 3. Implementation of control banding: Gathering of information; Hazard bands; Exposure bands; Allocation of risk control bands. - 4. Bibliography: Publications; Books, reports, opinions, bulletins; Standards and references; Legislation and regulations; Websites. - Annexes

Soil Survey of Black Hawk County, Iowa, 2005

The general soil map, which is a color map, shows the survey area divided into groups of associated soils called general soil map units. This map is useful in planning the use and management of large areas. To find information about your area of interest, locate that area on the map, identify the name of the map unit in the area on the color-coded map legend, then refer to the section General Soil Map Units for a general description of the soils in your area.

Soil Survey of Clay County, Iowa, 2005

The general soil map, which is a color map, shows the survey area divided into groups of associated soils called general soil map units. This map is useful in planning the use and management of large areas. To find information about your area of interest, locate that area on the map, identify the name of the map unit in the area on the color-coded map legend, then refer to the section General Soil Map Units for a general description of the soils in your area.

Precision of a new tool to measure visceral adipose tissue (VAT) using dual-energy X-Ray absorptiometry (DXA).

OBJECTIVE: A new tool to quantify visceral adipose tissue (VAT) over the android region of a total body dual-energy x-ray absorptiometry (DXA) scan has recently been reported. The measurement, CoreScan, is currently available on Lunar iDXA densitometers. The purpose of the study was to determine the precision of the CoreScan VAT measurement, which is critical for understanding the utility of this measure in longitudinal trials. DESIGN AND METHODS: VAT precision was characterized in both an anthropomorphic imaging phantom (measured on 10 Lunar iDXA systems) and a clinical population consisting of obese women (n = 32). RESULTS: The intrascanner precision for the VAT phantom across 9 quantities of VAT mass (0-1,800 g) ranged from 28.4 to 38.0 g. The interscanner precision ranged from 24.7 to 38.4 g. There was no statistical dependence on the quantity of VAT for either the inter- or intrascanner precision result (p = 0.670). Combining inter- and intrascanner precision yielded a total phantom precision estimate of 47.6 g for VAT mass, which corresponds to a 4.8% coefficient of variance (CV) for a 1 kg VAT mass. Our clinical population, who completed replicate total body scans with repositioning between scans, showed a precision of 56.8 g on an average VAT mass of 1110.4 g. This corresponds to a 5.1% CV. Hence, the in vivo precision result was similar to the phantom precision result. CONCLUSIONS: The study suggests that CoreScan has a relatively low precision error in both phantoms and obese women and therefore may be a useful addition to clinical trials where interventions are targeted towards changes in visceral adiposity.

Report to Government Oversight Committee Regrading Soil and Water Conservation Districts Competition with Small Business, 2006

At the request of the Government Oversight Committee, the Ombudsman gathered information regarding competition by county Soil and Water Conservation Districts (SWCD) with small business through the sale of products and services. The goal of the Ombudsman’s review was to assist the Government Oversight Committee (Committee) in gaining an objective understanding of the issues so the Committee can ascertain whether there is a problem that requires legislation this legislative session. The Ombudsman focused on gathering specific information from four SWCD offices in central Iowa; Dallas, Greene, Guthrie and Jasper. These offices were specifically identified in documentation presented to the Government Oversight Committee by affected small business owners (contractors), Jon Judson of Diversity Farms and Dan Brouse of Iowa Restorations. However, with 100 SWCDs in Iowa,1 each with their own elected commissioners and each with different practices, priorities and fundraising activities, what the Ombudsman learned about these four counties may not be applicable to all the SWCDs in Iowa. The Ombudsman assigned the case to the Assistant Citizens’ Aide/Ombudsman for Small Business, Kristie Hirschman. For reference purposes in this report, actions taken by Ms. Hirschman will be ascribed to the Ombudsman.

DNR Interactive Mapping: A tool for Iowa Agriculture, 2006

The planning tools you need to improve both your farming operation and Iowa’s streams and lakes are right at your fingertips. With DNR interactive mapping online, you can access a large amount of information for free and without special software.

Synthetic RGD-containing alpha-helical coiled coil peptides promote integrin-dependent cell adhesion.

Integrin receptors are the main mediators of cell adhesion to the extracellular matrix. They bind to their ligands by interacting with short amino acid sequences, such as the RGD sequence. Soluble, small RGD-based peptides have been used to block integrin-binding to ligands, thereby interfering with cell adhesion, migration and survival, while substrate-immobilized RGD sequences have been used to enhance cell binding to artificial surfaces. This approach has several important medical applications, e.g. in suppression of tumor angiogenesis or stimulation of bone formation around implants. However, the relatively weak affinity of short RGD-containing peptides often results in incomplete integrin inhibition or ineffective ligation. In this work, we designed and synthesized several new multivalent RGD-containing molecules and tested their ability to inhibit or to promote integrin-dependent cell adhesion when used in solution or immobilized on substrates, respectively. These molecules consist of an oligomeric structure formed by alpha-helical coiled coil peptides fused at their amino-terminal ends with an RGD-containing fragment. When immobilized on a substrate, these peptides specifically promoted integrin alphaVbeta3-dependent cell adhesion, but when used in solution, they blocked alphaVbeta3-dependent cell adhesion to the natural substrates fibronectin and vitronectin. One of the peptides was nearly 10-fold more efficient than fibronectin or vitronectin in promoting cell adhesion, and almost 100-fold more efficient than a linear RGD tripeptide in blocking adhesion. These results indicate that alpha-helical coiled coil peptides carrying an amino-terminal RGD motif can be used as soluble antagonists or surface-immobilized agonists to efficiently inhibit or promote integrin alphaVbeta3-mediated cell adhesion, respectively.

Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism.

Abstract The plasmid pME6863, carrying the aiiA gene from the soil bacterium Bacillus sp. A24 that encodes a lactonase enzyme able to degrade N-acyl-homoserine lactones (AHLs), was introduced into the rhizosphere isolate Pseudomonas fluorescens P3. This strain is not an effective biological control agent against plant pathogens. The transformant P. fluorescens P3/pME6863 acquired the ability to degrade AHLs. In planta, P. fluorescens P3/pME6863 significantly reduced potato soft rot caused by Erwinia carotovora and crown gall of tomato caused by Agrobacterium tumefaciens to a similar level as Bacillus sp. A24. Little or no disease reduction was observed for the wild-type strain P3 carrying the vector plasmid without aiiA. Suppression of potato soft rot was observed even when the AHL-degrading P. fluorescens P3/pME6863 was applied to tubers 2 days after the pathogen, indicating that biocontrol was not only preventive but also curative. When antagonists were applied individually with the bacterial plant pathogens, biocontrol activity of the AHL degraders was greater than that observed with several Pseudomonas 2,4-diacetylphloroglucinol-producing strains and with Pseudomonas chlororaphis PCL1391, which relies on production of phenazine antibiotic for disease suppression. Phenazine production by this well characterized biological control strain P. chlororaphis PCL1391 is regulated by AHL-mediated quorum sensing. When P. chlororaphis PCL1391 was co-inoculated with P. fluorescens P3/pME6863 in a strain mixture, the AHL degrader interfered with the normally excellent ability of the antibiotic producer to suppress tomato vascular wilt caused by Fusarium oxysporum f. sp. lycopersici. Our results demonstrate AHL degradation as a novel biocontrol mechanism, but also demonstrate the potential for non-target interactions that can interfere with the biocontrol efficacy of other strains.

Soil and water conservation strategies and impact on sustainable livelihood in Cape Verde – Case study of Ribeira Seca watershed

Cape Verde, located off the coast of Senegal in western Africa, is a volcanic archipelago where a combination of human, climatic, geomorphologic and pedologic factors has led to extensive degradation of the soils. Like other Sahelian countries, Cape Verde has suffered the effects of desertification through the years, threatening the livelihood of the islands population and its fragile environment. In fact, the steep slopes in the ore agricultural islands, together with semi-arid and arid environments, characterized by an irregular and poorly distributed rainy season, with high intensity rainfall events, make dryland production a challenge. To survive in these fragile conditions, the stabilization of the farming systems and the maintenance of sustainable yields have become absolute priorities, making the islands an erosion control laboratory. Soil and water conservation strategies have been a centerpiece of the government0s agricultural policies for the last half century. Aiming to maintain the soil in place and the water inside the soil, the successive governments of Cape Verde have implemented a number of soil and water conservation techniques, the most common ones being terraces, half moons, live barriers, contour rock walls, contour furrows and microcatchments, check dams and reforestation with drought resistant species. The soil and water conservation techniques implemented have contributed to the improvement of the economical and environmental conditions of the treated landscape, making crop production possible, consequently, improving the livelihood of the people living on the islands. In this paper, we survey the existing soil and water conservation techniques, analyze their impact on the livelihood condition of the population through a thorough literature review and field monitoring using a semi-quantitative methodology and evaluate their effectiveness and impact on crop yield in the Ribeira Seca watershed. A brief discussion is given on the cost and effectiveness of the techniques to reduce soil erosion and to promote rainfall infiltration. Finally, we discuss the critical governance factors that lead to the successful implementation of such strategy in a country with scarce natural resources.