Active Human and Porcine Serum Induce Competence for Genetic Transformation in the Emerging Zoonotic Pathogen Streptococcus suis.

The acquisition of novel genetic traits through natural competence is a strategy used by bacteria in microbe-rich environments where microbial competition, antibiotics, and host immune defenses threaten their survival. Here, we show that virulent strains of Streptococcus suis, an important zoonotic agent and porcine pathogen, become competent for genetic transformation with plasmid or linear DNA when cultured in active porcine and human serum. Competence was not induced in active fetal bovine serum, which contains less complement factors and immunoglobulins than adult serum and was strongly reduced in heat-treated or low-molecular weight fractions of active porcine serum. Late competence genes, encoding the uptake machinery for environmental DNA, were upregulated in the active serum. Competence development was independent of the early competence regulatory switch involving XIP and ComR, as well as sigma factor ComX, suggesting the presence of an alternative stress-induced pathway for regulation of the late competence genes required for DNA uptake

Broadening the antibacterial spectrum of histidine kinase autophosphorylation inhibitors via the use of epsilon-poly-L-lysine capped mesoporous silica-based nanoparticles

[EN] Two-component systems (TCS) regulate diverse processes such as virulence, stress responses, metabolism and antibiotic resistance in bacteria but are absent in humans, making them promising targets for novel antibacterials. By incorporating recently described TCS histidine kinase autophosphorylation inhibitors (HKAIs) into epsilon-poly-L-lysine capped nanoparticles (NPs) we could overcome the Gram negative (Gr(-)) permeability barrier for the HKAIs. The observed bactericidal activity against Gr(-) bacteria was shown to be due to the enhanced delivery and internalization of the HKAIs and not an inhibitory or synergistic effect of the NPs. The NPs had no adverse effects on mammalian cell viability or the immune function of macrophages in vitro and showed no signs of toxicity to zebrafish larvae in vivo. These results show that HKAIs are promising antibacterials for both Gr(-) and Gr + pathogens and that NPs are a safe drug delivery technology that can enhance the selectivity and efficacy of HKAIs against bacteria. (C) 2016 Elsevier Inc. All rights reserved.This work was funded by FP7 ITN STARS-Scientific Training in Antimicrobial Research Strategies (Contract No. PITN-GA-2009-238490, J.M.W., A.M.), H2020 MSCA IF (AND-659121, N.V.), grant BIO2013-42619-P from the Ministerio de Economia y Competitividad (A.M.), grant from the Spanish Government (Project MAT2015-64139-C4-1-R,N. M., J.R.M, R.M.M.), and a grant from Generalitat Valenciana (Project PROMETEOII/2014/047, N.M.). and Prometeo II/2014/029, A.M.).Velikova, N.; Mas Font, N.; Miguel-Romero, L.; Polo, L.; Stolte, E.; Zaccaria, E.; Cao, R.... (2017). Broadening the antibacterial spectrum of histidine kinase autophosphorylation inhibitors via the use of epsilon-poly-L-lysine capped mesoporous silica-based nanoparticles. Nanomedicine Nanotechnology Biology and Medicine. 13(2):569-581. https://doi.org/10.1016/j.nano.2016.09.011S56958113

Minimum error correction-based haplotype assembly: considerations for long read data

The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the genome-phenotype association. Haplotype assembly is a well-known approach for reconstructing haplotypes, exploiting reads generated by DNA sequencing devices. The Minimum Error Correction (MEC) metric is often used for reconstruction of haplotypes from reads. However, problems with the MEC metric have been reported. Here, we investigate the MEC approach to demonstrate that it may result in incorrectly reconstructed haplotypes for devices that produce error-prone long reads. Specifically, we evaluate this approach for devices developed by Illumina, Pacific BioSciences and Oxford Nanopore Technologies. We show that imprecise haplotypes may be reconstructed with a lower MEC than that of the exact haplotype. The performance of MEC is explored for different coverage levels and error rates of data. Our simulation results reveal that in order to avoid incorrect MEC-based haplotypes, a coverage of 25 is needed for reads generated by Pacific BioSciences RS systems.Comment: 17 pages, 6 figure

Reliability criteria for re-engineering of large-scale pressurized irrigation systems

Presented during the Third international conference on irrigation and drainage held March 30 - April 2, 2005 in San Diego, California. The theme of the conference was "Water district management and governance."Includes bibliographical references.A study was conducted in a pressurized irrigation district in southern Italy to analyze current delivery performance and determine improvements needed to meet current and future delivery needs. Such an analysis is required due to changes that have occurred, since the system was first put into service, in cropping patterns, farming practices and irrigation techniques. The Combined Optimization and Performance Analysis Model (COPAM) was used to evaluate the irrigation system present performance under different operating conditions, to identify the areas within the irrigation district where rehabilitation and modernization are more urgently needed, and to suggest the most effective engineering and operational improvements. Post-intervention operating scenarios were simulated and analyzed to refine and validate the re-engineering process. Results show the usefulness of simulation models when analyzing modernization alternatives for irrigation schemes.Sponsored by USCID; co-sponsored by Association of California Water Agencies and International Network for Participatory Irrigation Management

Assessment of Constraints and Opportunities of Small- Scale Irrigation Practices in South Tigray, Ethiopia

Improper irrigation management practices play a vital role in decreament of agricultural productivity. The findings of this paper were focused on technical performane assessment of small scale irrigation systems. The technical performance of the small scale irrigation schemes in relation to the water harvesting structures and delivery canals of all schemes were assessed technically in order to check whether they meet their objective and to distinguish their problems. Survey were undertaken to investigate the technical performance of the water harvesting structures and challenges on irrigation water utilization and management. Farmers, professional experts and other stakeholders were participated on the investigation of the technical performance of small scale irrigation schemes. Sedimentation, structural failure, untreated upper watershed, poor irrigation water management, lack of knowledge, lack of technical training, free grazing, lack of market access and transport problems are the bottlenack problems to the small scale irrigation schemes.  57.4 % of the small scale irrigation scheme beneficiaries are practicing both full and supplementary irrigation systems. The irrigation rounds per year are 24.6%, 55.7 % and 19.7% for three, tw and one times respectively. The irrigation intervals for cabbage, onion and maize are 12, 15 and 24 days respectively. Problems related to crop productions are shortage of technical training on irrigation water management, recurrent drought, free grazing, lack of market access, transport problems, flood hazard and disease and pest. These problems are getting beyond the beneficiaries capacity and they cannot able to maintain. Any concerned governmental and non-governmental body has to support the farmers by making maintenance and provision of neccessary trainings and accesses. Keywords: irrigation, irrigation structure, performance indicators schemes, water managemen

Environmental sustainability

Presented at Ground water and surface water under stress: competition, interaction, solutions: a USCID water management conference on October 25-28, 2006 in Boise, Idaho.Includes bibliographical references.A study was conducted on a large-scale irrigated area located in southern Italy to analyze the cumulative effects of long-term water management practices on soils and aquifers. Assessing the environmental sustainability of irrigation systems operations was the main goal of the present research. This included envisaging feasible changes to "business-as-usual" in the study area with the aim of reducing pressures and of meeting current and future management objectives. The Determinants-Pressure-State-Impact-Response methodology suggested by the European Environmental Agency was applied to the case study to analyze cause-effect relationships between driving forces, pressures and potential impacts. Simulations of alternatives in water management and evaluation of resulting consequences were conducted by developing a spatial Decision Support System (DSS) on the study area. This basically involved development and ranking of alternatives by using a commercial software package (DEFINITE DSS). Evaluation of the most likely resulting consequences was conducted by creating maps of environmental risk by means of two commercial GIS software packages (ArcGIS and IDRISI). The used approach showed its usefulness for achieving better understanding of relevant aspects related to management of irrigation water at regional scale, for designing strategic monitoring programs to be implemented and for envisaging feasible management alternatives on large-scale irrigation systems

Activation, regulation and physiology of natural competence in Lactococcus lactis

Lactococcus lactis is a Gram-positive bacterium that is mainly used in dairy products and safe for consumption. Within species, strains might harbour different traits which makes one strain suitable for milk fermentation whereas the other strain is not. However, natural improvement of strain performance important point within the dairy industry. Many bacteria can perform horizontal gene transfer which encompasses natural mechanisms to take up DNA. These mechanisms include phage transduction, nanotubes, conjugation and natural competence. In this study, we examined whether L. lactis can develop natural competence. Strains that appear to have a complete set of competence genes were selected following comparative genomic analysis. A construct, comprising the gene comX encoding the master regulator of competence under control of the nisin promotor, was introduced into the L. lactis strain KF147 which produces ComX upon addition of nisin to the growth medium of L. lactis. Indeed, moderate expression of ComX allowed DNA-uptake from the environment but also efficient integration of homologous fragments into the genome. In addition, the pleiotropic stringent response regulator CodY appears to be involved in the natural competence state and high expression of ComX leads to stagnation of growth, overall stress/ stringent response, however, these cells remain metabolically active. The natural trigger for natural competence could not be established. However, our research shows that there is strong evidence that environmental factors leading to starvation or stringent response in L. lactis might possibly trigger natural competence

Control of Competence for DNA Transformation in Streptococcus suis by Genetically Transferable Pherotypes

Here we show that S. suis, a major bacterial pathogen of pigs and emerging pathogen in humans responds to a peptide pheromone by developing competence for DNA transformation. This species does not fall within any of the phylogenetic clusters of streptococci previously shown to regulate competence via peptide pheromones suggesting that more species of streptococci may be naturally competent. Induction of competence was dependent on ComX, a sigma factor that controls the streptococcal late competence regulon, extracellular addition of a comX-inducing peptide (XIP), and ComR, a regulator of comX. XIP was identified as an N-terminally truncated variant of ComS. Different comS alleles are present among strains of S. suis. These comS alleles are not functionally equivalent and appear to operate in conjuction with a cognate ComR to regulate comX through a conserved comR-box promoter. We demonstrate that these ‘pherotypes’ can be genetically transferred between strains, suggesting that similar approaches might be used to control competence induction in other lactic acid bacteria that lack ComR/ComS homologues but possess comX and the late competence regulon. The approaches described in this paper to identify and optimize peptide-induced competence may also assist other researchers wishing to identify natural competence in other bacteria. Harnessing natural competence is expected to accelerate genetic research on this and other important streptococcal pathogens and to allow high-throughput mutation approaches to be implemented, opening up new avenues for research