Bacterial evolution by genomic island transfer occurs via DNA transformation in planta

Our understanding of the evolution of microbial pathogens has been advanced by the discovery of "islands" of DNA that differ from core genomes and contain determinants of virulence [1, 2]. The acquisition of genomic islands (GIs) by horizontal gene transfer (HGT) is thought to have played a major role in microbial evolution. There are, however, few practical demonstrations of the acquisition of genes that control virulence, and, significantly, all have been achieved outside the animal or plant host. Loss of a GI from the bean pathogen Pseudomonas syringae pv. phaseolicola (Pph) is driven by exposure to the stress imposed by the plant's resistance response [3]. Here, we show that the complete episomal island, which carries pathogenicity genes including the effector avrPphB, transfers between strains of Pph by transformation in planta and inserts at a specific att site in the genome of the recipient. Our results show that the evolution of bacterial pathogens by HGT may be achieved via transformation, the simplest mechanism of DNA exchange. This process is activated by exposure to plant defenses, when the pathogen is in greatest need of acquiring new genetic traits to alleviate the antimicrobial stress imposed by plant innate immunity [4].

Challenges of linking scientific knowledge to river basin management policy: AquaTerra as a case study

The EU Project AquaTerra generates knowledge about the river-soil-sediment-groundwater system and delivers scientific information of value for river basin management. In this article, the use and ignorance of scientific knowledge in decision making is explored by a theoretical review. We elaborate on the 'two-communities theory', which explains the problems of the policy-science interface by relating and comparing the different cultures, contexts, and languages of researchers and policy makers. Within AquaTerra, the EUPOL subproject examines the policy-science interface with the aim of achieving a good connection between the scientific output of the project and EU policies. We have found two major barriers, namely language and resources, as well as two types of relevant relationships: those between different research communities and those between researchers and policy makers. (c) 2007 Elsevier Ltd. All rights reserved.

Review: intellectual property aspects of plant transformation

One of the recurring themes of the debates concerning the application of genetic transformation technology has been the role of Intellectual Property Rights (IPR). This term covers both the content of patents and the confidential expertise usually related to methodology and referred to as 'Trade Secrets'. This review explains the concepts behind patent protection, and discusses the wide-ranging scope of existing patents that cover all aspects of transgenic technology, from selectable markers and novel promoters to methods of gene introduction. Although few of the patents in this area have any real commercial value, there are a small number of key patents that restrict the 'freedom to operate' of new companies seeking to exploit the methods. Over the last 20 years, these restrictions have forced extensive cross-licensing between ag-biotech companies and have been one of the driving forces behind the consolidation of these companies. Although such issues are often considered of little interest to the academic scientist working in the public sector, they are of great importance in any discussion of the role of 'public-good breeding' and of the relationship between the public and private sectors.

Solvent-induced dynamic single-crystal-to-single-crystal transformation of a synthetic peptide-based cyclic compound

Solvent induced single-crystal-to-single-crystal transformation has been demonstrated indicating the dynamic behavior of one dimensional arrays obtained from a self-assembled new synthetic cyclic peptide.

Unusual transformation of trialkylamines mediated by platinum

An interesting chemical transformation of trialkylamines has taken place during the reaction of 2-(2', 6'-dimethylphenylazo)- 4-methylphenol ( 1) with K-2[ PtCl4] in refluxing methanol in the presence of trialkylamines, leading to the formation of organoplatinum complexes ( 2 and 3), where ligand 1 is coordinated as a bidentate N, O donor and the transformed trialkylamines are coordinated as bidentate C, N donors.

Melt structure and its transformation by sequential crystallization of the two blocks within poly(L-lactide)-block-poly(epsilon-caprolactone) double crystalline diblock copolymers

Sequential crystallization of poly(L-lactide) (PLLA) followed by poly(epsilon-caprolactone) (PCL) in double crystalline PLLA-b-PCL diblock copolymers is studied by differential scanning calorimetry (DSC), polarized optical microscopy (POM), wide-angle X-ray scattering (WAXS) and small-angle X-ray scattering (SAXS). Three samples with different compositions are studied. The sample with the shortest PLLA block (32 wt.-% PLLA) crystallizes from a homogeneous melt, the other two (with 44 and 60% PLLA) from microphase separated structures. The microphase structure of the melt is changed as PLLA crystallizes at 122 degrees C (a temperature at which the PCL block is molten) forming spherulites regardless of composition, even with 32% PLLA. SAXS indicates that a lamellar structure with a different periodicity than that obtained in the melt forms (for melt segregated samples). Where PCL is the majority block, PCL crystallization at 42 degrees C following PLLA crystallization leads to rearrangement of the lamellar structure, as observed by SAXS, possibly due to local melting at the interphases between domains. POM results showed that PCL crystallizes within previously formed PLLA spherulites. WAXS data indicate that the PLLA unit cell is modified by crystallization of PCL, at least for the two majority PCL samples. The PCL minority sample did not crystallize at 42 degrees C (well below the PCL homopolymer crystallization temperature), pointing to the influence of pre-crystallization of PLLA on PCL crystallization, although it did crystallize at lower temperature. Crystallization kinetics were examined by DSC and WAXS, with good agreement in general. The crystallization rate of PLLA decreased with increase in PCL content in the copolymers. The crystallization rate of PCL decreased with increasing PLLA content. The Avrami exponents were in general depressed for both components in the block copolymers compared to the parent homopolymers. Polarized optical micrographs during isothermal crystalli zation of (a) homo-PLLA, (b) homo-PCL, (c) and (d) block copolymer after 30 min at 122 degrees C and after 15 min at 42 degrees C.

Literacy as a complex activity: deconstructing the simple view of reading

The Rose Review into the teaching of early reading recommended that the conceptual framework incorporated into the National Literacy Strategy Framework for Teaching – the Searchlights model of reading and its development – should be replaced by the Simple View of Reading. In this paper, we demonstrate how these two frameworks relate to each other, and show that nothing has been lost in this transformation from Searchlights to Simple View: on the contrary, much has been gained. That nothing has been lost is demonstrated by consideration of the underlying complexity inherent in each of the two dimensions delineated in the Simple View. That much has been gained is demonstrated by the increased understanding of each dimension that follows from careful scientific investigation of each. The better we understand what is involved in each dimension, the better placed we are to unravel and understand the essential, complex and continual interactions between each dimension which underlie skilled reading. This has clear implications for further improving the early teaching of reading.

Selected topics in probiotics and prebiotics: meeting report for the 2004 international scientific association for probiotics and prebiotics

On August 2931, 2004, 84 academic and industry scientists from 16 countries gathered in Copper Mountain, Colorado USA to discuss certain issues at the forefront of the science of probiotics and prebiotics. The format for this invitation only meeting included six featured lectures: engineering human vaginal lactobacilli to express HIV inhibitory molecules (Peter Lee, Stanford University), programming the gut for health (Thaddeus Stappenbeck, Washington University School of Medicine), immune modulation by intestinal helminthes (Joel Weinstock, University of Iowa Hospitals and Clinics), hygiene as a cause of autoimmune disorders (G. A. Rook, University College London), prebiotics and bone health (Connie Weaver, Purdue University) and prebiotics and colorectal cancer risk (Ian Rowland, Northern Ireland Centre for Food and Health). In addition, all participants were included in one of eight discussion groups on the topics of engineered probiotics, host-commensal bacteria communication, 'omics' technologies, hygiene and immune regulation, biomarkers for healthy people, prebiotic and probiotic applications to companion animals, development of a probiotic dossier, and physiological relevance of prebiotic activity. Brief conclusions from these discussion groups are summarized in this paper.

New scientific paradigms for probiotics and prebiotics

The inaugural meeting of the International Scientific Association for Probiotics and Prebiotics (ISAPP) was held May 3 to May 5 2002 in London, Ontario, Canada. A group of 63 academic and industrial scientists from around the world convened to discuss current issues in the science of probiotics and prebiotics. ISAPP is a non-profit organization comprised of international scientists whose intent is to strongly support and improve the levels of scientific integrity and due diligence associated with the study, use, and application of probiotics and prebiotics. In addition, ISAPP values its role in facilitating communication with the public and healthcare providers and among scientists in related fields on all topics pertinent to probiotics and prebiotics. It is anticipated that such efforts will lead to development of approaches and products that are optimally designed for the improvement of human and animal health and well being. This article is a summary of the discussions, conclusions, and recommendations made by 8 working groups convened during the first ISAPP workshop focusing on the topics of: definitions, intestinal flora, extra-intestinal sites, immune function, intestinal disease, cancer, genetics and genomics, and second generation prebiotics. Humans have evolved in symbiosis with an estimated 1014 resident microorganisms. However, as medicine has widely defined and explored the perpetrators of disease, including those of microbial origin, it has paid relatively little attention to the microbial cells that constitute the most abundant life forms associated with our body. Microbial metabolism in humans and animals constitutes an intense biochemical activity in the body, with profound repercussions for health and disease. As understanding of the human genome constantly expands, an important opportunity will arise to better determine the relationship between microbial populations within the body and host factors (including gender, genetic background, and nutrition) and the concomitant implications for health and improved quality of life. Combined human and microbial genetic studies will determine how such interactions can affect human health and longevity, which communication systems are used, and how they can be influenced to benefit the host. Probiotics are defined as live microorganisms which, when administered in adequate amounts confer a health benefit on the host.1 The probiotic concept dates back over 100 years, but only in recent times have the scientific knowledge and tools become available to properly evaluate their effects on normal health and well being, and their potential in preventing and treating disease. A similar situation exists for prebiotics, defined by this group as non-digestible substances that provide a beneficial physiological effect on the host by selectively stimulating the favorable growth or activity of a limited number of indigenous bacteria. Prebiotics function complementary to, and possibly synergistically with, probiotics. Numerous studies are providing insights into the growth and metabolic influence of these microbial nutrients on health. Today, the science behind the function of probiotics and prebiotics still requires more stringent deciphering both scientifically and mechanistically. The explosion of publications and interest in probiotics and prebiotics has resulted in a body of collective research that points toward great promise. However, this research is spread among such a diversity of organisms, delivery vehicles (foods, pills, and supplements), and potential health targets such that general conclusions cannot easily be made. Nevertheless, this situation is rapidly changing on a number of important fronts. With progress over the past decade on the genetics of lactic acid bacteria and the recent, 2,3 and pending, 4 release of complete genome sequences for major probiotic species, the field is now armed with detailed information and sophisticated microbiological and bioinformatic tools. Similarly, advances in biotechnology could yield new probiotics and prebiotics designed for enhanced or expanded functionality. The incorporation of genetic tools within a multidisciplinary scientific platform is expected to reveal the contributions of commensals, probiotics, and prebiotics to general health and well being and explicitly identify the mechanisms and corresponding host responses that provide the basis for their positive roles and associated claims. In terms of human suffering, the need for effective new approaches to prevent and treat disease is paramount. The need exists not only to alleviate the significant mortality and morbidity caused by intestinal diseases worldwide (especially diarrheal diseases in children), but also for infections at non-intestinal sites. This is especially worthy of pursuit in developing nations where mortality is too often the outcome of food and water borne infection. Inasmuch as probiotics and prebiotics are able to influence the populations or activities of commensal microflora, there is evidence that they can also play a role in mitigating some diseases. 5,6 Preliminary support that probiotics and prebiotics may be useful as intervention in conditions including inflammatory bowel disease, irritable bowel syndrome, allergy, cancer (especially colorectal cancer of which 75% are associated with diet), vaginal and urinary tract infections in women, kidney stone disease, mineral absorption, and infections caused by Helicobacter pylori is emerging. Some metabolites of microbes in the gut may also impact systemic conditions ranging from coronary heart disease to cognitive function, suggesting the possibility that exogenously applied microbes in the form of probiotics, or alteration of gut microecology with prebiotics, may be useful interventions even in these apparently disparate conditions. Beyond these direct intervention targets, probiotic cultures can also serve in expanded roles as live vehicles to deliver biologic agents (vaccines, enzymes, and proteins) to targeted locations within the body. The economic impact of these disease conditions in terms of diagnosis, treatment, doctor and hospital visits, and time off work exceeds several hundred billion dollars. The quality of life impact is also of major concern. Probiotics and prebiotics offer plausible opportunities to reduce the morbidity associated with these conditions. The following addresses issues that emerged from 8 workshops (Definitions, Intestinal Flora, Extra-Intestinal Sites, Immune Function, Intestinal Disease, Cancer, Genomics, and Second Generation Prebiotics), reflecting the current scientific state of probiotics and prebiotics. This is not a comprehensive review, however the study emphasizes pivotal knowledge gaps, and recommendations are made as to the underlying scientific and multidisciplinary studies that will be required to advance our understanding of the roles and impact of prebiotics, probiotics, and the commensal microflora upon health and disease management.

A catemer-to-dimer structural transformation in cyheptamide

A catemeric crystal structure of cyheptamide undergoes a transformation in the solid-state upon heating to produce a dimer-based form whose structure has been determined from laboratory X-ray powder diffraction ( XRPD) data, thereby providing the first conclusive evidence of a carbamazepine analogue crystallising in both hydrogen bonded motifs.

Towards a unifying framework for pattern transformation in swarm systems

This paper identifies the major challenges in the area of pattern formation. The work is also motivated by the need for development of a single framework to surmount these challenges. A framework based on the control of macroscopic parameters is proposed. The issue of transformation of patterns is specifically considered. A definition for transformation and four special cases, namely elementary and geometrical transformations by repositioning all or some robots in the pattern are provided. Two feasible tools for pattern transformation namely, a macroscopic parameter method and a mathematical tool - Moebius transformation also known as the linear fractional transformation are introduced. The realization of the unifying framework considering planning and communication is reported.