Joseph Tony Pembroke

University of Limerick | UL · Department of Chemical Sciences

Integrative Conjugative Elements (ICEs) are a class of bacterial mobile elements that have the ability to mediate their own integration, excision and transfer from one host genome to another by a mechanism of site-specific recombination, self-circularisation and conjugative transfer. Members of the SXT/R391 ICE family of enterobacterial mobile gene...

SXT/R391 family of ICEs have been found to express an unusual function that enhances bacterial cell death post-UV irradiation. Previous analysis of ICE R391 found four core SXT/R391 ICE genes to be involved-orf96, orf90, orf91 and orf43. These genes functioned as part of a UV-inducible pathway, where upon exposure to UV, the levels of the Orf43 pro...

Many SXT/R391-like enterobacterial Integrative Conjugative Elements (ICEs) have been found to express an atypical, recA-dependent, UV-inducible, cell-sensitising phenotype observed as a reduction in post-irradiation cell survival rates in host cells. Characterisation of a complete deletion library of the prototype ICE R391 identified the involvemen...

ICE R391, a prototype member of the SXT/R391 family of site-specific integrative conjugative elements (ICEs), frequently isolated from enterobacterial pathogens, exhibits an unusual, recA-dependent, UV-inducible, cell-sensitising function. This significantly decreases postirradiation cell survival rates in Escherichia coli host cells, a trait that...

The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequentl...

A novel long period grating (LPG) inscribed balloon-shaped heterocore-structured plastic optical fibre (POF) sensor is described and experimentally demonstrated for real-time measurement of the ultra-low concentrations of ethanol in microalgal bioethanol production applications. The heterocore structure is established by coupling a 250 μm core diam...

Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the...

A carbapenem-resistant strain, UL-CPE-01, was isolated from a domestic wastewater treatment plant and subjected to antibiotic susceptibility testing showing resistance to a wide range of antibiotics. Complete genome and bioinformatic analysis of UL-CPE-01 was performed to investigate the nature of its resistance determinants and the strain identifi...

Human and animal pathogenic bacteria are constantly being released into the environment through human activity. Many of these organisms can harbour genes such as virulence genes, antibiotic resistance and heavy metal resistance genes that are inserted into plasmids, transposons and Integrating Conjugating elements (ICEs), leading to potential sprea...

Water resources are under continued pressure from anthropogenic sources, including acidic waste from abandoned mine sites and alkaline waste from a variety of industrial activities. Large quantities of mine and industrial wastes are typically stored in tailings facilities which can generate significant quantities of leachates due to weathering. If...

A range of optical fibre-based sensors for the measurement of ethanol, primarily in aqueous solution, have been developed and are reviewed here. The sensing approaches can be classified into four groups according to the measurement techniques used, namely absorption (or absorbance), external interferometric, internal fibre grating and plasmonic sen...

Autothermal thermophilic aerobic digestion (ATAD) is a microbial fermentation process characterized as a tertiary treatment of waste material carried out in jacketed reactors. Heat is generated which selects a thermoduric microbial population. The process results in a stabilised, pasteurised sludge suitable for land application as a fertiliser. The...

With escalating demand for metals, an increasing global population and rapid technology development, there is a worldwide challenge to secure a sustainable metal supply for industry. Current recycling rates for such metals are extremely low, mainly due to a lack of feasible recovery technologies. As a consequence, valuable metal resources are being...

A Light Talk on Industry 4.0 Prospects of Optical Fibre Sensing for Biofuel Processing Industry.

As the utilization and consumption of lignocellulosic biomass increases, so too will the need for an adequate supply of feedstock. To meet these needs, novel waste feedstock materials will need to be utilized. Exploitation of these novel feedstocks will require information both on the effects of solvent extraction on the succeeding analysis of pote...

BACKGROUND Chromium (Cr) is widely used in industrial processes and is considered a major source of pollution when released to the environment. Of particular concern, hexavalent chromium (Cr(VI)) is amongst the most toxic heavy metal affecting human health and living organisms when fugitive emissions contaminate aqueous environments. Consequently,...

Biofilm-related infections and contamination of biomaterials are major problems in the clinic. These contaminations are frequently caused by Staphylococcus aureus and are a pressing issue for implantable devices, catheters, contact lenses, prostheses, and wound dressings. Strategies to decrease contamination and biofilm related infections are vital...

A carbapenem-resistant strain, UL-CPE-01, was isolated from a domestic wastewater treatment plant and subjected to antibiotic susceptibility testing showing resistance to a wide range of antibiotics. Complete genome and bioinformatic analysis of UL-CPE-01 was performed to investigate the nature of its resistance determinants and the strain identifi...

Human and animal pathogenic bacteria are constantly being released into the environment through human activity. Many of these organisms can harbour genes such as virulence genes, antibiotic resistance and heavy metal resistance genes that are inserted into plasmids, transposons and Integrating Conjugating elements (ICEs), leading to potential sprea...

A U-bend POF Sensor is a potential solution for real-time monitoring of the production of biofuels, such as bioethanol even at the very low-level initial concentration of product which can occur during the initial production stage via recombinant Cyanobacteria strains such as Synechocystis PCC6803. The sensor demonstrates excellent repeatability an...

With escalating demand for metals, an increasing global population and rapid technology development, there is a worldwide challenge to secure a sustainable metal supply for industry. Current recycling rates for such metals are extremely low, mainly due to a lack of feasible recovery technologies. As a consequence, valuable metal resources are being...

The EraMin 2 project 'Biomimic' focusses on providing sustainable solutions to metal recovery within Europe. At the University of Limerick we have focused on the recovery of Vanadium from red mud leachate, which has a pH~12 by utilizing pH neutralization with CO 2 addition and fractionating the metal precipitate. Modified biomass in the form of bio...

Ochrobactrum species are non-enteric, Gram-negative organisms that are closely related to the genus Brucella. Since the designation of the genus in 1988, several distinct species have now been characterised and implicated as opportunistic pathogens in multiple outbreaks. Here, we examine the genus, its members, diagnostic tools used for identificat...

As the need to replace fossil fuels increases and global energy needs expand the drive to find alternative, sustainable sources of fuels have accelerated. Microbial sources are attractive because of the rapid growth rates of microorgan- isms and their potential techno-economic advantages. Cyanobacteria are prokary- otic photoautotrophs (utilise pho...

Vanadium exists as a mobile and toxic trace metal in many alkaline residue leachates. Its removal and recovery not only reduces a global environmental risk but is also critical to the emergence of innovative technologies and the circular economy. In parallel, the use of treated biomass feedstock is receiving increased attention as a low cost adsorb...

Integrative Conjugative Elements (ICE’s) of the SXT/R391 family have largely been detected in clinical or environmental isolates of Gammaproteobacteria, particularly Vibrio and Proteus species. As wastewater treatment plants accumulate a large and diverse number of such species, we examined raw water samples taken from a municipal wastewater treatm...

ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (...

To produce bioethanol from model cyanobacteria such as Synechocystis, a two gene cassette consisting of genes encoding pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are required to transform pyruvate first to acetaldehyde and then to ethanol. However the partition of pyruvate to ethanol comes at a cost, a reduction in biomass and pyr...

The European Commission has identified several metals as critical for a high-tech and green development but have a fluctuating availability caused by politically and economically driven factors. Ironically, metals of a high economic value are being landfilled or end up in hazardous waste, posing threat to the environment and health. The ERAMIN fun...

Autothermal thermophilic aerobic digestion (ATAD) is a microbial fermentation process characterized as a tertiary treatment of waste material carried out in jacketed reactors. The process can be carried out on a variety of waste sludge ranging from human, animal, food, or pharmaceutical waste where the addition of air initiates aerobic digestion of...

Pyruvate decarboxylase (PDC) from Zymobacter palmae (ZpPDC) has been reported to have a lower Km the Zymomonas mobilis PDC (ZmPDC). ZpPDC was combined with native slr1192 alcohol dehydrogenase (adh) in an attempt to increase ethanol production in the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803 over constructs created with Zmpdc. Nati...

The aim of this study was to analyse pMERPH, the first integrative and conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and to determine its relationship to other members of the SXT/R391 family of ICEs. Whole Genome Sequencing of Escherichia coli isolate KH802 (which contains the ICE pMERPH) was performed using Illumi...

An expanding global population not only increases the amounts of municipal solid waste and wastewater generated but also raises demand for a wide range of raw materials used to manufacture goods. Extraction of these raw materials and many subsequent manufacturing processes contribute significantly to the presence of a variety of metals in wastewate...

Photoautotrophic ethanol production using model cyanobacteria is an attractive technology that offers potential for sustainable ethanol production as a biofuel. Model strains of Synechocystis PCC6803 have been metabolically engineered to convert central metabolic intermediates such as pyruvate to acetaldehyde via cloned heterologous pyruvate decarb...

Enterobacterial Integrative Conjugative Elements (ICEs) are now detected regularly as carriers of drug resistance and adaptive functions in clinical, animal and environmental bacterial isolates. The elements, which appear as conjugative phage/ plasmid-like hybrids, have a core genetic structure comprising of integrative, regulatory and conjugative...

Innovative biotechnological absorption technologies are discussed in the context of the EraMin funded European Biomimic project for metal recovery from waste streams

Aldehyde dehydrogenases (ALDH) form a superfamily of dimeric or tetrameric enzymes that catalyze the oxidation of a broad range of aldehydes into their corresponding carboxylic acids with the concomitant reduction of the cofactor NAD(P) into NAD(P)H. Despite their varied polypeptide chain length and oligomerisation states, ALDHs possess a conserved...

We report a U-bend plastic optical fiber (POF) sensor for measuring ultralow concentration of ethanol corresponding to the initial bioethanol production rate by cyanobacteria, i.e., 0.1-0.5 gL⁻¹ day⁻¹. This production rate corresponds to 0.00499-0.0499 %wt of ethanol in total solution in terms of weight percent concentration. Refractive indices for...

production. Engineered strains of the photoautotrophic Cyanobacterium Synechocystis PCC6803 must balance the metabolic flux towards growth and biomass production against conversion of metabolic intermediates to ethanol. In addition ethanol has been shown to induce a stress response in this non-native producer such that decoupling may have significa...

Non-fermenting Gram-negative bacteria are problematic in clinical locations, being one of the most prevalent causes of nosocomial infections. Many of these non-fermenting Gram-negative bacteria are opportunistic pathogens that affect patients that are suffering with underlying medical conditions and diseases. Brevundimonas spp., in particular Brevu...

Flow cytometry was used to evaluate the effect of initial ethanol concentrations on cyanobacterial strains of Synechocystis PCC 6803 [wild-type (WT), and ethanol producing recombinants (UL 004 and UL 030)] in batch cultures. Ethanol recombinants, containing one or two metabolically engineered cassettes, were designed towards the development of an e...

Supplementary Data

The aim of this study was to analyse R997, the first integrative and conjugative element (ICE) isolated from the Indian Sub-Continent, and to determine its relationship to the SXT/R391 family of ICEs. WGS of Escherichia coli isolate AB1157 (which contains R997) was performed using Illumina sequencing technology. R997 context was assessed by de novo...

The integrative conjugative elements, ICE's SXT and R391 are the prototypes of a group of gram negative integrative elements known as the SXT/R391 group. R391 was identified in a clinical isolate of Providencia in the late 1960's in South Africa, while SXT was initially isolated in 1992 in a clinical isolate of Vibrio cholerae O139 and variants hav...

Biochar production, from pyrolysis of lignocellulosic feedstocks, agricultural residues, and animal and poultry manures are emerging globally as novel industrial and commercial products. It is important to develop and to validate a series of suitable protocols for the ecological monitoring of the qualities and properties of biochars. The highly sen...

Biofuel processing applications require concentration measurement of bio-ethanol during its evolution by algae in a proprietary chemical process to optimize the chemical parameters and the resulting yield of bio-ethanol. The production rate of bio-ethanol is initially very low with correspondingly minute concentration changes. This study presents a...

http://www.horizonpress.com/cyano3 Cyanobacteria are represented by a diverse group of microorganisms that, being a part of marine and freshwater phytoplankton, significantly contribute to the planetary fixation of atmospheric carbon and evolution of molecular oxygen via photosynthesis. Ancient cyanobacteria (~ 2.5 billion years of history) partici...

In this era of the 'Green Planet', cyanobacteria are ideally placed for exploitation as microbial cell factories, both for carbon capture and storage and for the sustainable production of secondary metabolites and biofuels. The application of omics technologies to cyanobacterial research has yielded a wealth of new information. However for today's...

SXT/R391-like ICEs are site-specific genome-integrating bacterial mobile elements, frequently isolated from human pathogens, most notably, pandemic Vibrio cholerae strains. They encode a range of known advantageous traits, including multiple antibiotic resistance determinants and DNA repair mechanisms. These ICEs have also been found to encode a nu...

Background: The use of photosynthetic autotrophs and in particular the model organism Synechocystis PCC6803 is receiving much attention for the production of sustainable biofuels and other economically useful products through metabolic engineering. Optimisation of metabolic-engineered organisms for high-level sustained production of product is a k...

Ultrasonication has recently received attention as a novel bioprocessing tool for process intensification in many areas of downstream processing. Ultrasonic intensification (periodic ultrasonic treatment during the fermentation process) can result in a more effective homogenization of biomass and faster energy and mass transfer to biomass over shor...

The photoautotrophic cyanobacterium Synechocystis PCC6803 has received much attention as a model photosynthetic cell factory for the production of a range of important biotech products. The biomass remaining from this activity may then have further utility in processes such as metal bioremediation. In addition Synechocystis being an inhabitant of m...

Ethanol production directly from CO2, utilizing genetically engineered photosynthetic cyanobacteria as a biocatalyst, offers significant potential as a renewable and sustainable source of biofuel. Despite the current absence of a commercially successful production system, significant resources have been deployed to realize this goal. Utilizing the...

The cation diffusion facilitator (CDF) family is ubiquitous across all three kingdoms of life with members found in bacteria, archaea and eukaryotes. These membrane bound integral secondary transporters facilitate the transport of heavy metals including iron, cobalt, cadmium, zinc and most likely nickel and copper ions. Bacterial CDFs are primarily...

Due to the rapid consumption of energy, climate change issues and the depletion of fossil fuels, attention has turned to renewable sources such as biofuels. Recently, cyanobacteria have been utilised for the production of biotechnological products like isoprene, ethylene and ethanol (1). These organisms, including the model cyanobacterium Synechocy...

Global energy demands are at an all-time high, and due to the depletion of fossil fuels, sustainable energy sources are being looked upon as a substitute. Cyanobacteria have been utilised for the production of biofuels, including the model microorganism Synechocystis sp. PCC 6803. These organisms have minimal requirements, needing only solar energy...

The rise in fuel costs as well as global warming and environmental pollution levels have driven the need for exploration of new renewable energy resources [1]. Amongst the many potential sources, bioethanol is of interest as it has a high potential to be a valuable low cost energy source, especially if it is produced photoautotrophically through cy...

Sourcing suitable substitutes for fossil fuels is becoming essential to meet current global energy demands. The utilisation of cyanobacteria for production of biofuels has received significant attention due to the phototrophic nature of the organism. In theory, cyanobacteria are an ideal production strain, having minimal requirements, needing only...

This project is concerned with the development of an optical fibre real-time sensor for accurate measurement of ethanol concentration during its evolution by algae in an Industrial Bio-Reactor. It is necessary to precisely determine the concentration in the proprietary chemical process for biofuel production so as to allow the end users to optimize...

The Cation Diffusion Facilitators (CDFs) form a family of membrane-bound proteins capable of transporting zinc and other heavy metal ions. Involved in metal tolerance/resistance by efflux of ions, CDF proteins share a two-modular architecture consisting of a transmembrane domain (TMD) and C-terminal domain (CTD) that protrudes into the cytoplasm. D...

The free availability of online software to undertake molecular evolutionary analysis coupled with the free availability of large amounts of sequence data has made the analysis of the spread of antibiotic resistance determinants amenable in an educational context. Software such as ACT (Artemis Comparison Tool) [1] can be utilised to extract useful...

First author: Noreen Layden. Optimising autothermal thermophilic aerobic digestion of sludge

Sustainable alternatives to fossil fuels are becoming critical to meet the growing global energy demand. Biofuel production via cyanobacteria show promise due to the high growth rates and minimal requirements of these photoautotrophic microorganisms which require only solar energy, carbon dioxide and minimal amounts of trace elements for growth. As...