oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2020 ( 2 )

2019 ( 263 )

2018 ( 341 )

2017 ( 366 )

Custom range...

Search Results: 1 - 10 of 248682 matches for " Peter C. Fineran "
All listed articles are free for downloading (OA Articles)
Page 1 /248682
Display every page Item
Advances in Bacteriophage-Mediated Control of Plant Pathogens
Rebekah A. Frampton,Andrew R. Pitman,Peter C. Fineran
International Journal of Microbiology , 2012, DOI: 10.1155/2012/326452
Abstract: There is continuing pressure to maximise food production given a growing global human population. Bacterial pathogens that infect important agricultural plants (phytopathogens) can reduce plant growth and the subsequent crop yield. Currently, phytopathogens are controlled through management programmes, which can include the application of antibiotics and copper sprays. However, the emergence of resistant bacteria and the desire to reduce usage of toxic products that accumulate in the environment mean there is a need to develop alternative control agents. An attractive option is the use of specific bacteriophages (phages), viruses that specifically kill bacteria, providing a more targeted approach. Typically, phages that target the phytopathogen are isolated and characterised to determine that they have features required for biocontrol. In addition, suitable formulation and delivery to affected plants are necessary to ensure the phages survive in the environment and do not have a deleterious effect on the plant or target beneficial bacteria. Phages have been isolated for different phytopathogens and have been used successfully in a number of trials and commercially. In this paper, we address recent progress in phage-mediated control of plant pathogens and overcoming the challenges, including those posed by CRISPR/Cas and abortive infection resistance systems.
Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) / CRISPR Associated (Cas) Systems
Corinna Richter,James T. Chang,Peter C. Fineran
Viruses , 2012, DOI: 10.3390/v4102291
Abstract: Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous ‘innate’ mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific ‘adaptive’ immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas) proteins, into short interfering RNAs (crRNAs), which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s) of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.
In Vivo Protein Interactions and Complex Formation in the Pectobacterium atrosepticum Subtype I-F CRISPR/Cas System
Corinna Richter, Tamzin Gristwood, James S. Clulow, Peter C. Fineran
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049549
Abstract: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and their associated proteins (Cas; CRISPR associated) are a bacterial defense mechanism against extra-chromosomal elements. CRISPR/Cas systems are distinct from other known defense mechanisms insofar as they provide acquired and heritable immunity. Resistance is accomplished in multiple stages in which the Cas proteins provide the enzymatic machinery. Importantly, subtype-specific proteins have been shown to form complexes in combination with small RNAs, which enable sequence-specific targeting of foreign nucleic acids. We used Pectobacterium atrosepticum, a plant pathogen that causes soft-rot and blackleg disease in potato, to investigate protein-protein interactions and complex formation in the subtype I-F CRISPR/Cas system. The P. atrosepticum CRISPR/Cas system encodes six proteins: Cas1, Cas3, and the four subtype specific proteins Csy1, Csy2, Csy3 and Cas6f (Csy4). Using co-purification followed by mass spectrometry as well as directed co-immunoprecipitation we have demonstrated complex formation by the Csy1-3 and Cas6f proteins, and determined details about the architecture of that complex. Cas3 was also shown to co-purify all four subtype-specific proteins, consistent with its role in targeting. Furthermore, our results show that the subtype I-F Cas1 and Cas3 (a Cas2-Cas3 hybrid) proteins interact, suggesting a protein complex for adaptation and a role for subtype I-F Cas3 proteins in both the adaptation and interference steps of the CRISPR/Cas mechanism.
Advances in Bacteriophage-Mediated Control of Plant Pathogens
Rebekah A. Frampton,Andrew R. Pitman,Peter C. Fineran
International Journal of Microbiology , 2012, DOI: 10.1155/2012/326452
Abstract: There is continuing pressure to maximise food production given a growing global human population. Bacterial pathogens that infect important agricultural plants (phytopathogens) can reduce plant growth and the subsequent crop yield. Currently, phytopathogens are controlled through management programmes, which can include the application of antibiotics and copper sprays. However, the emergence of resistant bacteria and the desire to reduce usage of toxic products that accumulate in the environment mean there is a need to develop alternative control agents. An attractive option is the use of specific bacteriophages (phages), viruses that specifically kill bacteria, providing a more targeted approach. Typically, phages that target the phytopathogen are isolated and characterised to determine that they have features required for biocontrol. In addition, suitable formulation and delivery to affected plants are necessary to ensure the phages survive in the environment and do not have a deleterious effect on the plant or target beneficial bacteria. Phages have been isolated for different phytopathogens and have been used successfully in a number of trials and commercially. In this paper, we address recent progress in phage-mediated control of plant pathogens and overcoming the challenges, including those posed by CRISPR/Cas and abortive infection resistance systems. 1. Introduction In October 2011 the United Nations announced that the global human population had reached 7 billion. The world is facing not only this increase in population, but also a decrease in land availability for agriculture and a changing climate [1]. It is apparent that there is a requirement to increase food production to feed the growing population and a need to achieve this with diminished land and water resources [1]. A major threat to food production is plant diseases, which are influenced by changing agricultural practices and more global trade [2]. Recent topical examples include citrus greening of oranges caused by psyllids that transmit bacteria belonging to the genus Candidatus Liberibacter [3] and canker of kiwifruit caused by the bacterium Pseudomonas syringae pv. actinidiae [4]. Citrus greening has doubled the cost of orange production for growers in Florida, where the disease was first identified in 2005 [3]. In New Zealand, where Pseudomonas syringae pv. actinidiae was discovered in late 2010, 40% of orchards have been infected resulting in a significant economic cost to the industry [5]. A variety of approaches are required to minimise the impact of bacterial plant diseases
Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism
Tim R. Blower,Terry J. Evans,Rita Przybilski,Peter C. Fineran,George P. C. Salmond
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1003023
Abstract: Abortive infection, during which an infected bacterial cell commits altruistic suicide to destroy the replicating bacteriophage and protect the clonal population, can be mediated by toxin-antitoxin systems such as the Type III protein–RNA toxin-antitoxin system, ToxIN. A flagellum-dependent bacteriophage of the Myoviridae, ΦTE, evolved rare mutants that “escaped” ToxIN-mediated abortive infection within Pectobacterium atrosepticum. Wild-type ΦTE encoded a short sequence similar to the repetitive nucleotide sequence of the RNA antitoxin, ToxI, from ToxIN. The ΦTE escape mutants had expanded the number of these “pseudo-ToxI” genetic repeats and, in one case, an escape phage had “hijacked” ToxI from the plasmid-borne toxIN locus, through recombination. Expression of the pseudo-ToxI repeats during ΦTE infection allowed the phage to replicate, unaffected by ToxIN, through RNA–based molecular mimicry. This is the first example of a non-coding RNA encoded by a phage that evolves by selective expansion and recombination to enable viral suppression of a defensive bacterial suicide system. Furthermore, the ΦTE escape phages had evolved enhanced capacity to transduce replicons expressing ToxIN, demonstrating virus-mediated horizontal transfer of genetic altruism.
The PhoBR two-component system regulates antibiotic biosynthesis in Serratia in response to phosphate
Tamzin Gristwood, Peter C Fineran, Lee Everson, Neil R Williamson, George P Salmond
BMC Microbiology , 2009, DOI: 10.1186/1471-2180-9-112
Abstract: We demonstrate that a mutation in the high affinity phosphate transporter pstSCAB-phoU, believed to mimic low phosphate conditions, causes upregulation of secondary metabolism and QS in Serratia 39006, via the PhoBR two-component system. Phosphate limitation also activated secondary metabolism and QS in Serratia 39006. In addition, a pstS mutation resulted in upregulation of rap. Rap, a putative SlyA/MarR-family transcriptional regulator, shares similarity with the global regulator RovA (regulator of virulence) from Yersina spp. and is an activator of secondary metabolism in Serratia 39006. We demonstrate that expression of rap, pigA-O (encoding the prodigiosin biosynthetic operon) and smaI are controlled via PhoBR in Serratia 39006.Phosphate limitation regulates secondary metabolism in Serratia 39006 via multiple inter-linked pathways, incorporating transcriptional control mediated by three important global regulators, PhoB, SmaR and Rap.Phosphate is an essential component of numerous biomolecules. Therefore, the control of intracellular phosphate concentrations is vital for bacterial survival. At least two major systems are involved in managing intracellular concentrations of inorganic orthophosphate (Pi), the preferred primary source of phosphate [1]. When Pi is abundant, the low affinity Pit transporter appears to be primarily responsible for Pi uptake [2-4]. When Pi becomes limited, the high affinity Pst transport system (PstSCAB-PhoU) is activated, and takes over as the predominant Pi uptake system [5-8].In Escherichia coli and other Enterobacteriaceae, the cellular response to Pi availability is mediated via the PhoBR two-component system. Under conditions of Pi limitation, the sensor histidine kinase PhoR is autophosphorylated [9]. PhoR then activates its cognate response regulator, PhoB [9], which in turn activates expression of multiple genes, termed the Pho regulon, via direct binding to a conserved Pho box sequence found overlapping -35 regions in target
Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands
Reuben B. Vercoe,James T. Chang,Ron L. Dy,Corinda Taylor,Tamzin Gristwood,James S. Clulow,Corinna Richter,Rita Przybilski,Andrew R. Pitman,Peter C. Fineran
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003454
Abstract: In prokaryotes, clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (Cas) proteins constitute a defence system against bacteriophages and plasmids. CRISPR/Cas systems acquire short spacer sequences from foreign genetic elements and incorporate these into their CRISPR arrays, generating a memory of past invaders. Defence is provided by short non-coding RNAs that guide Cas proteins to cleave complementary nucleic acids. While most spacers are acquired from phages and plasmids, there are examples of spacers that match genes elsewhere in the host bacterial chromosome. In Pectobacterium atrosepticum the type I-F CRISPR/Cas system has acquired a self-complementary spacer that perfectly matches a protospacer target in a horizontally acquired island (HAI2) involved in plant pathogenicity. Given the paucity of experimental data about CRISPR/Cas–mediated chromosomal targeting, we examined this process by developing a tightly controlled system. Chromosomal targeting was highly toxic via targeting of DNA and resulted in growth inhibition and cellular filamentation. The toxic phenotype was avoided by mutations in the cas operon, the CRISPR repeats, the protospacer target, and protospacer-adjacent motif (PAM) beside the target. Indeed, the natural self-targeting spacer was non-toxic due to a single nucleotide mutation adjacent to the target in the PAM sequence. Furthermore, we show that chromosomal targeting can result in large-scale genomic alterations, including the remodelling or deletion of entire pre-existing pathogenicity islands. These features can be engineered for the targeted deletion of large regions of bacterial chromosomes. In conclusion, in DNA–targeting CRISPR/Cas systems, chromosomal interference is deleterious by causing DNA damage and providing a strong selective pressure for genome alterations, which may have consequences for bacterial evolution and pathogenicity.
A New Recombination Tree Algorithm for Mean-Reverting Interest-Rate Dynamics  [PDF]
Peter C. L. Lin
American Journal of Computational Mathematics (AJCM) , 2013, DOI: 10.4236/ajcm.2013.34038
Abstract:

In light of the fact that no existing tree algorithms can guarantee the recombination property for general Ornstein-Uhlenbeck processes with time-dependent parameters, a new trinomial recombination-tree algorithm is designed in this research. The proposed algorithm enhances the existing mechanisms in interest-rate modelings with the comparisons to [1,2] methodologies, and the proposed framework provides a more efficient way in discrete-time mean-reverting simulations.

Interest-Rate Modeling Conundrums  [PDF]
Peter C. L. Lin
Journal of Mathematical Finance (JMF) , 2014, DOI: 10.4236/jmf.2014.45030
Abstract: The mainstream research in interest-rate modeling has been focusing on a collection of risk tools and pricing formulas which are developed based on the simplified market assumptions and hypotheses. Despite the elegance of the structure, it is noticed that a crucial yet natural factor is missing: the relationship between curve-fitting algorithms and no-arbitrage restrictions on a bond portfolio. Also, the discrepancy between risk-free and default-free bonds is often ignored. This study discusses the modeling conundrums and proposes a framework based on the preferred-habitat hypothesis for advanced term-structure construction that overcomes these limitations in current models. This article serves as an introduction for future work.
Alternative Alphas from Hedge Fund ETF Speculation  [PDF]
Peter C. L. Lin
Journal of Mathematical Finance (JMF) , 2016, DOI: 10.4236/jmf.2016.61004
Abstract:

Alternative alpha represents risk-adjust absolute return of an alternative investing instrument regressed on alternative risk factors. Over the years, the definition is extended to the absolute return generated from alternative asset speculation-long-only or long-short strategy on alternative assets to generate additional return on top of existence alpha. In this article, we examine and propose a model with state-dependent stochastic differential equations based on Gaussian mixture model and multi-class Gaussian-kernel support vector machine to analyze hedge fund ETF alpha. We provide a new type of long-short speculation which trades on hedge fund strategies. This long-short alternative portfolio is build based on a Sharpe-ratio-like alpha ratio optimization program, and the historical performance from the portfolio shows statistically significant improvement adding to existing alphas. For passive investors, the portfolio also yields a simple portable alpha strategy which outperforms the S&P 500 benchmark return by 7.8% since 2012.

Page 1 /248682
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.