ORCID Profile
0000-0001-8268-583X
Current Organisation
The University of Newcastle
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Enzymes | Microbial Genetics | Microbiology | Bacteriology | Genome Structure and Regulation | Biochemistry and Cell Biology | Condensed Matter Physics | Biochemistry and Cell Biology not elsewhere classified | Analytical Biochemistry | Condensed Matter Imaging | Biological Physics
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Preventive Medicine | Expanding Knowledge in the Chemical Sciences | Scientific Instruments | Expanding Knowledge in the Medical and Health Sciences |
Related Links
Publications
Gut microbes modulate bioaccessibility of lead in soil
Publisher: Elsevier BV
Date: 05-2021
The Unlikeability of a Cuddly Toy Interface: An Experimental Study of Preschoolers’ Likeability and Usability of a 3D Game Played with a Cuddly Toy Versus a Keyboard
Publisher: Springer Berlin Heidelberg
Date: 2008
Exploring challenging group dynamics in participatory design with children
Publisher: ACM
Date: 17-06-2014
DNA recombination and RNA cleavage activities of the Flp protein: roles of two histidine residues in the orientation and activation of the nucleophile for strand cleavage 1 1Edited by M. Gottesman
Publisher: Elsevier BV
Date: 12-2001
Challenging group dynamics in participatory design with children
Publisher: ACM
Date: 21-06-2015
Measuring product liking in preschool children: An evaluation of the Smileyometer and This or That methods
Publisher: Elsevier BV
Date: 05-2013
Complete Genome Sequences of Bacteriophages Kaya, Guyu, Kopi, and TehO, Which Target Clinical Strains of Pseudomonas aeruginosa
Publisher: American Society for Microbiology
Date: 02-12-2021
DOI: 10.1128/MRA.01043-21
Abstract: Pseudomonas aeruginosa is a major public health concern, as drug-resistant strains increase mortality in hospital-acquired infections. We report the isolation and complete genome sequences of four lytic bacteriophages that target clinical multidrug-resistant P. aeruginosa strains.
Applications of Fungal Site-specific Recombination as a Tool in Biotechnology and Basic Biology
Publisher: Elsevier
Date: 2005
Geometry of site alignment during Int family recombination: antiparallel synapsis by the Flp recombinase
Publisher: Elsevier BV
Date: 05-2000
A Mini-ISY100 Transposon Delivery System Effective in γ Proteobacteria
Publisher: Frontiers Media SA
Date: 27-02-2019
Stability of blocked replication forksin vivo
Publisher: Oxford University Press (OUP)
Date: 20-10-2015
DOI: 10.1093/NAR/GKV1079
Replication fork collapse at a protein‐DNA roadblock leads to fork reversal, promoted by the RecQ helicase
Publisher: Wiley
Date: 09-12-2019
DOI: 10.1111/MMI.14166
Abstract: Proteins that bind DNA are the cause of the majority of impediments to replication fork progression and can lead to subsequent collapse of the replication fork. Failure to deal with fork collapse efficiently leads to mutation or cell death. Several models have been proposed for how a cell processes a stalled or collapsed replication fork eukaryotes and bacteria are not dissimilar in terms of the general pathways undertaken to deal with these events. This study shows that replication fork regression, the combination of replication fork reversal leading to formation of a Holliday Junction along with exonuclease digestion, is the preferred pathway for dealing with a collapsed fork in Escherichia coli. Direct endo-nuclease activity at the replication fork was not observed. The protein that had the greatest effect on these fork processing events was the RecQ helicase, while RecG and RuvABC, which have previously been implicated in this process, were found to play a lesser role. Eukaryotic RecQ homologues, BLM and WRN, have also been implicated in processing events following replication fork collapse and may reflect a conserved mechanism. Finally, the SOS response was not induced by the protein-DNA roadblock under these conditions, so did not affect fork processing.
Fingerprinting Plastic-Associated Inorganic and Organic Matter on Plastic Aged in the Marine Environment for a Decade
Publisher: American Chemical Society (ACS)
Date: 19-05-2021
Mobilization of pdif modules in Acinetobacter: A novel mechanism for antibiotic resistance gene shuffling?
Publisher: Wiley
Date: 21-07-2020
DOI: 10.1111/MMI.14563
Biological Nanomotors with Linear, Rotation, or Revolution Motion Mechanism
Publisher: CRC Press
Date: 12-07-2023
Conformational Changes Induced by Nucleotide Binding in Cdc6/ORC From Aeropyrum pernix
Publisher: Elsevier BV
Date: 10-2004
DOI: 10.1016/J.JMB.2004.08.044
Abstract: Archaea contain one or more proteins with homology to eukaryotic ORC/Cdc6 proteins. Sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature ORC1 and ORC2. We have determined crystal structures of the ORC2 protein from the archaeon Aeropyrum pernix in complexes with ADP or a non-hydrolysable ATP analogue, ADPNP. Between two crystal forms, there are three crystallographically independent views of the ADP complex and two of the ADPNP complex. The protein molecules in the three complexes with ADP adopt very different conformations, while the two complexes with ADPNP are the same. These structures indicate that there is considerable conformational flexibility in ORC2 but that ATP binding stabilises a single conformation. We show that the ORC2 protein can bind DNA, and that this activity is associated with the C-terminal domain of the protein. We present a model for the interaction of the winged helix (WH) domain of ORC2 with DNA that differs from that proposed previously for Pyrobaculum aerophilum ORC/Cdc6.
Editorial: the evolving field of tangible interaction for children: the challenge of empirical validation
Publisher: Springer Science and Business Media LLC
Date: 12-06-2011
Biochemical Characterization of the Minichromosome Maintenance (MCM) Protein of the Crenarchaeote Aeropyrum pernix and Its Interactions with the Origin Recognition Complex (ORC) Proteins
Publisher: American Chemical Society (ACS)
Date: 17-11-2008
DOI: 10.1021/BI801479S
Abstract: Replication in archaea is carried out by proteins that are homologues of eukaryotic counterparts. However, the archaeal systems tend to be much simpler with fewer different genes encoding the core functions than in eukaryotic counterparts. In many archaea, there is a single minichromosome maintenance (MCM) homologue, presumed to be the replicative helicase and between one and three origin recognition complex (ORC) homologues involved in binding to the replication origins. Here we describe the cloning and characterization of the MCM protein from the crenarchaeote Aeropyrum pernix. Like other eukaryotic and archaeal MCM proteins, it is found to be an ATP-dependent DNA helicase, and the putative active site residues involved in ATP binding and hydrolysis are confirmed by mutation. Deletion of the N-terminal 256 amino acids yielded a protein with higher ATPase activity in the absence of DNA and retained robust helicase activity. Interactions with the ORC proteins of A. pernix were examined, and it was found that both ORC homologues could inhibit the helicase activity of MCM. Further it was found that ORC2 could autophosphorylate in the presence of ATP and more remarkably could phosphorylate MCM in a species-specific manner.
Wild-type Flp recombinase cleaves DNA in trans
Publisher: Wiley
Date: 02-1999
FtsK DNA Translocase: The Fast Motor That Knows Where It's Going
Publisher: Wiley
Date: 04-10-2010
Abstract: FtsK is a double-stranded DNA translocase, a motor that converts the chemical energy of binding and hydrolysing ATP into movement of a DNA substrate. It moves DNA at an amazing rate->5000 bp per second-and is powerful enough to remove other proteins from the DNA. In bacteria it is localised to the site of cell ision, the septum, where it functions as a DNA pump at the late stages of the cell cycle, to expedite cytokinesis and chromosome segregation. The N terminus of the protein is involved in the cell-cycle-specific localisation and assembly of the cell- ision machinery, whereas the C terminus forms the motor. The motor portion of FtsK has been studied by a combination of biochemistry, genetics, X-ray crystallography and single-molecule mechanical assays, and these will be the focus here. The motor can be ided into three subdomains: α, β and γ. The α and β domains multimerise to produce a hexameric ring with a central channel for dsDNA, and contain a RecA-like nucleotide-binding/hydrolysis fold. The motor is given directionality by the regulatory γ domain, which binds to polarised chromosomal sequences-5'-GGGNAGGG-3', known as KOPS-to ensure that the motor is loaded onto DNA in a specific orientation such that subsequent translocation is always towards the region of the chromosome where replication usually terminates (the terminus), and specifically to the 28 bp dif site, located in this region. Once the FtsK translocase has located the dif site it then interacts with the XerCD site-specific recombinases to activate recombination.
Motivation profiles of online Poker players and the role of interface preferences: A laddering study among amateur and (semi-) professionals
Publisher: Elsevier BV
Date: 10-2014
FtsK-dependent XerCD- dif recombination unlinks replication catenanes in a stepwise manner
Publisher: Proceedings of the National Academy of Sciences
Date: 11-11-2013
Abstract: Newly replicated circular chromosomes are topologically linked. XerC/XerD- dif (XerCD- dif )–FtsK recombination acts in the replication termination region of the Escherichia coli chromosome to remove links introduced during homologous recombination and replication, whereas Topoisomerase IV removes replication links only. Based on gel mobility patterns of the products of recombination, a stepwise unlinking pathway has been proposed. Here, we present a rigorous mathematical validation of this model, a significant advance over prior biological approaches. We show definitively that there is a unique shortest pathway of unlinking by XerCD- dif –FtsK that strictly reduces the complexity of the links at every step. We delineate the mechanism of action of the enzymes at each step along this pathway and provide a 3D interpretation of the results.
The Escherichia coli DNA translocase FtsK
Publisher: Portland Press Ltd.
Date: 22-03-2010
DOI: 10.1042/BST0380395
Abstract: Escherichia coli FtsK is a septum-located DNA translocase that co-ordinates the late stages of cytokinesis and chromosome segregation. Relatives of FtsK are present in most bacteria in Bacillus subtilis, the FtsK orthologue, SpoIIIE, transfers the majority of a chromosome into the forespore during sporulation. DNA translocase activity is contained within a ~ 512-amino-acid C-terminal domain, which is ided into three subdomains: α, β and γ. α and β comprise the translocation motor, and γ is a regulatory domain that interacts with DNA and with the XerD recombinase. In vitro rates of translocation of ~ 5 kb·s−1 have been measured for both FtsK and SpoIIIE, whereas, in vivo, SpoIIIE has a comparable rate of translocation. Translocation by both of these proteins is not only rapid, but also directed by DNA sequence. This directionality requires interaction of the γ subdomain with specific 8 bp DNA asymmetric sequences that are oriented co-directionally with replication direction of the bacterial chromosome. The γ subdomain also interacts with the XerCD site-specific recombinase to activate chromosome unlinking by recombination at the chromosomal dif site. In the present paper, the properties in vivo and in vitro of FtsK and its relatives are discussed in relation to the biological functions of these remarkable enzymes.
Separating speed and ability to displace roadblocks during DNA translocation by FtsK
Publisher: Wiley
Date: 08-04-2010
Tracking of controlled Escherichia coli replication fork stalling and restart at repressor-bound DNA in vivo
Publisher: Wiley
Date: 25-05-2006
miniPXI: Development and Validation of an Eleven-Item Measure of the Player Experience Inventory
Publisher: Association for Computing Machinery (ACM)
Date: 25-10-2022
DOI: 10.1145/3549507
Abstract: Questionnaires are vital in games user research (GUR) to assess player experience (PX). However, having too many questions in surveys prevents wider uptake among GUR professionals because of games' rapid production cycles. To address this issue, we present the miniPXI---an eleven-item measure of the popular Player Experience Inventory (PXI)---providing single items for each of its eleven constructs. To develop the scale and examine its reliability and validity, we present three studies, conducted with 15 experts and 628 digital game players across continents. In the first survey study (n=366, 15 experts), single items were selected. In a second survey study (n=232), we explored reliability and validity of the single-item scale. Participants completed both full and single-item (SI) variants in three days. In the last study (n=30), we established the validity and sensitivity via an experimental evaluation of two games. The results are nuanced SI reliability estimates for PXI constructs range from .51 to .83 with an average of .68, we could confirm the validity for nine constructs. We conclude that the miniPXI can be a valuable tool for PX evaluations where a longer measure is not feasible, and provide practical considerations for its use.
Activation of Xer-recombination at dif: structural basis of the FtsKγ–XerD interaction
Publisher: Springer Science and Business Media LLC
Date: 06-10-2016
DOI: 10.1038/SREP33357
Abstract: Bacterial chromosomes are most often circular DNA molecules. This can produce a topological problem a genetic crossover from homologous recombination results in dimerization of the chromosome. A chromosome dimer is lethal unless resolved. A site-specific recombination system catalyses this dimer-resolution reaction at the chromosomal site dif . In Escherichia coli , two tyrosine-family recombinases, XerC and XerD, bind to dif and carry out two pairs of sequential strand exchange reactions. However, what makes the reaction unique among site-specific recombination reactions is that the first step, XerD-mediated strand exchange, relies on interaction with the very C-terminus of the FtsK DNA translocase. FtsK is a powerful molecular motor that functions in cell ision, co-ordinating ision with clearing chromosomal DNA from the site of septation and also acts to position the dif sites for recombination. This is a model system for unlinking, separating and segregating large DNA molecules. Here we describe the molecular detail of the interaction between XerD and FtsK that leads to activation of recombination as deduced from a co-crystal structure, biochemical and in vivo experiments. FtsKγ interacts with the C-terminal domain of XerD, above a cleft where XerC is thought to bind. We present a model for activation of recombination based on structural data.
Bioavailability of arsenic, cadmium, lead and mercury as measured by intestinal permeability
Publisher: Springer Science and Business Media LLC
Date: 19-07-2021
DOI: 10.1038/S41598-021-94174-9
Abstract: In this study, the intestinal permeability of metal(loid)s (MLs) such as arsenic (As), cadmium (Cd), lead (Pb) and mercury (Hg) was examined, as influenced by gut microbes and chelating agents using an in vitro gastrointestinal/Caco-2 cell intestinal epithelium model. The results showed that in the presence of gut microbes or chelating agents, there was a significant decrease in the permeability of MLs (As-7.5%, Cd-6.3%, Pb-7.9% and Hg-8.2%) as measured by apparent permeability coefficient value ( P app ), with differences in ML retention and complexation amongst the chelants and the gut microbes. The decrease in ML permeability varied amongst the MLs. Chelating agents reduce intestinal absorption of MLs by forming complexes thereby making them less permeable. In the case of gut bacteria, the decrease in the intestinal permeability of MLs may be associated to a direct protection of the intestinal barrier against the MLs or indirect intestinal ML sequestration by the gut bacteria through adsorption on bacterial surface. Thus, both gut microbes and chelating agents can be used to decrease the intestinal permeability of MLs, thereby mitigating their toxicity.
Sporulation: SpoIIIE Is the Key to Cell Differentiation
Publisher: Elsevier BV
Date: 09-2008
DOI: 10.1016/J.CUB.2008.07.047
Abstract: Sporulation in Bacillus subtilis requires asymmetric cell ision, chromosome transfer into the spore and establishment of differential gene expression patterns. Several recent studies highlight the key roles of the SpoIIIE motor in this process.
Differential toxicity of potentially toxic elements to human gut microbes
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.CHEMOSPHERE.2022.134958
Abstract: Specific microorganisms in the human gut (i.e., gut microbes) provide mutually beneficial outcomes such as microbial balance by inhibiting the growth of pathogenic organisms, immune system modulation, fermentation of ingested products, and vitamin production. The intake of contaminants including potenially toxic elements (PTEs) can occur through food, air, water and some medicines. The gut microbes not only can be affected by environmental contaminants but they themselves can alter the speciation and bioavailability of these contaminants. This research work was designed to demonstrate the relationship between increasing level of selected PTEs including As, Cd, Pb and Hg on the growth of selected gut microbes. The toxicity of above mentioned PTEs to three gut bacteria (Lactobacillus rhamnosus, Lactobacillus acidophilus and Escherichia coli) was examined. While the toxicity of all the cationic PTEs including Cd, Pb and Hg towards gut bacteria decreased with increasing pH, the anionic As species exhibited an opposite effect. The order of toxicity was Hg > Cd > Pb > As(III)>As(V) for E. coli and Hg > Cd > As(III)>Pb > As(V) for the two Lactobacillus sp. Arsenite (AsIII) showed higher toxicity than arsenate (AsV) to gut bacteria. While As is an anion, Cd, Pb and Hg are cations and hence their binding capacity to the bacterial cell wall varied based on the charge dependent functional groups. However, the toxic effects of PTEs for a bacteria are controlled by their speciation and bioavailability.
Design and Preliminary Validation of The Player Experience Inventory
Publisher: ACM
Date: 15-10-2016
Simple topology: FtsK-directed recombination at the dif site
Publisher: Portland Press Ltd.
Date: 21-03-2013
DOI: 10.1042/BST20120299
Abstract: FtsK is a multifunctional protein, which, in Escherichia coli, co-ordinates the essential functions of cell ision, DNA unlinking and chromosome segregation. Its C-terminus is a DNA translocase, the fastest yet characterized, which acts as a septum-localized DNA pump. FtsK's C-terminus also interacts with the XerCD site-specific recombinases which act at the dif site, located in the terminus region. The motor domain of FtsK is an active translocase in vitro, and, when incubated with XerCD and a supercoiled plasmid containing two dif sites, recombination occurs to give unlinked circular products. Despite years of research the mechanism for this novel form of topological filter remains unknown.
Symmetric DNA Sites are Functionally Asymmetric Within Flp and Cre Site-specific DNA Recombination Synapses
Publisher: Elsevier BV
Date: 07-2002
DOI: 10.1016/S0022-2836(02)00517-X
Abstract: Flp and Cre-mediated recombination on symmetrized FRT and loxP sites, respectively, in circular plasmid substrates yield both DNA inversion and deletion. However, upon sequestering three negative supercoils outside the recombination complex using the resII-resIII synapse formed by Tn3 resolvase and the LER synapse formed by phage Mu transposase in the case of Flp and Cre, respectively, the reactions are channeled towards inversion at the expense of deletion. The inversion product is a trefoil, its unique topology being conferred by the external resolvase or LER synapse. Thus, Flp and Cre assign their symmetrized substrates a strictly antiparallel orientation with respect to strand cleavage and exchange. These conclusions are supported by the product profiles from tethered parallel and antiparallel native FRT sites in dilution and competition assays. Furthermore, the observed recombination bias favoring deletion over inversion in a nicked circular substrate containing two symmetrized FRT sites is consistent with the predictions from Monte Carlo simulations based on antiparallel synapsis of the DNA partners.
Understanding the Fundamental Basis for Biofilm Formation on Plastic Surfaces: Role of Conditioning Films
Publisher: Frontiers Media SA
Date: 25-06-2021
DOI: 10.3389/FMICB.2021.687118
Abstract: The formation and composition of conditioning films.
Two classes of nucleic acid translocation motors: rotation and revolution without rotation
Publisher: Springer Science and Business Media LLC
Date: 2014
Increasing the reliability and validity of quantitative laddering data with LadderUX
Publisher: ACM
Date: 05-05-2012
Activation of XerCD-dif recombination by the FtsK DNA translocase
Publisher: Oxford University Press (OUP)
Date: 02-03-2011
DOI: 10.1093/NAR/GKR078
Inhibition of Flp Recombinase by the Topoisomerase I-targeting Drugs, Camptothecin and NSC-314622
Publisher: Elsevier BV
Date: 03-2001
Neutral–Neutral 2-Dimensional Agarose Gel Electrophoresis for Visualization of E. coli DNA Replication Structures
Publisher: Springer US
Date: 2020
DOI: 10.1007/978-1-0716-0323-9_5
Abstract: Neutral-neutral 2-dimensional agarose gel electrophoresis enables the detection of replication intermediate structures in DNA. Here we describe how DNA from Escherichia coli cells can be purified to retain replication intermediates and then be separated by size and shape using two consecutive agarose gel electrophoresis protocols. The DNA structures present within a localized region can be visualized by a Southern blotting/radioactive hybridisation protocol.
Site-specific recombination
Publisher: Springer Berlin Heidelberg
Date: 2007
Laddering with young children in User eXperience evaluations
Publisher: ACM
Date: 09-06-2010
FtsK and SpoIIIE, coordinators of chromosome segregation and envelope remodeling in bacteria
Publisher: Elsevier BV
Date: 05-2022
DOI: 10.1016/J.TIM.2021.10.002
Abstract: The translocation of DNA during bacterial cytokinesis is mediated by the SpoIIIE/FtsK family of proteins. These proteins ensure efficient chromosome segregation into sister cells by ATP-driven translocation of DNA and they control chromosome dimer resolution. How FtsK/SpoIIIE mediate chromosome translocation during cytokinesis in Gram-positive and Gram-negative organisms has been the subject of debate. Studies on FtsK in Escherichia coli, and recent work on SpoIIIE in Bacillus subtilis, have identified interactions between each translocase and the ision machinery, supporting the idea that SpoIIIE and FtsK coordinate the final steps of cytokinesis with completion of chromosome segregation. Here we summarize and discuss the view that SpoIIIE and FtsK play similar roles in coordinating cytokinesis with chromosome segregation, during growth and differentiation.
Xer Site-specific Recombination
Publisher: Elsevier BV
Date: 03-1999
Biochemical and Kinetic Analysis of the RNase Active Sites of the Integrase/Tyrosine Family Site-specific DNA Recombinases
Publisher: Elsevier BV
Date: 12-2001
The Extended Likeability Framework: A Theoretical Framework for and a Practical Case of Designing Likeable Media Applications for Preschoolers
Publisher: Hindawi Limited
Date: 2008
DOI: 10.1155/2008/719291
Abstract: A theoretical framework and practical case for designing likeable interactive media applications for preschoolers in the home environment are introduced. First, we elaborate on the theoretical framework. We introduce the uses and gratifications paradigm (U& G). We argue that U& G is a good approach to researching likeability of media applications. Next, we complete the U& G framework with expectancy-value (EV) theory. EV theory helps us move from theoretical insights to concrete design guidelines. Together, the U& G framework and the EV model form the foundation of our extended likeability framework for the design and evaluation of interactive media applications, for preschoolers in the home environment. Finally, we demonstrate a practical case of our extended likeability framework via the research project CuTI. The CuTI project aims at revealing those particular user gratifications and design attributes that are important to support playful behaviour and fun activities of preschoolers in the home environment.
Imaging fluorescent protein fusions in live bacteria
Publisher: Elsevier
Date: 2012
FtsK – a bacterial cell division checkpoint?
Publisher: Wiley
Date: 15-10-2010
DOI: 10.1111/J.1365-2958.2010.07411.X
Abstract: FtsK is a multifunctional, multidomain protein that acts to co-ordinate chromosome unlinking, segregation and cell ision. In this issue of Molecular Microbiology, the report by Dubarry et al. reveals new insight into the surprisingly complex relationship between the different activities of FtsK. The new study makes extensive use of fusion proteins to highlight the role of the FtsK 'linker' domain in helping to co-ordinate these processes. This, taken together with previous studies, suggests that FtsK is intimately involved in septum constriction, physically contacting several other isome proteins. Further, it is attractive to speculate that FtsK can regulate the late stages of septation to act as a checkpoint to ensure DNA is fully cleared from the septum before it is allowed to close, as well as being the driving force to unlink the chromosomes and segregate the DNA away from the septum.
User eXperience Laddering with preschoolers: unveiling attributes and benefits of cuddly toy interfaces
Publisher: Springer Science and Business Media LLC
Date: 14-06-2011
Editorial: Learning from failures in game design for children
Publisher: Elsevier BV
Date: 05-2014
Towards a likeability framework that meets child-computer interaction & communication sciences
Publisher: ACM
Date: 06-06-2007
The integrase family of recombinases: organization and function of the active site
Publisher: Wiley
Date: 08-1999
DOI: 10.1046/J.1365-2958.1999.01493.X
Abstract: The integrase family of site-specific recombinases (also called the tyrosine recombinases) mediate a wide range of biological outcomes by the sequential exchange of two pairs of DNA strands at defined phosphodiester positions. The reaction produces a recombinant arrangement of the DNA sequences flanking the cross-over region. The crystal structures of four integrase family members have revealed very similar three-dimensional protein folds that belie the large ersity in amino acid sequences among them. The active sites are similar in organization to those seen in structures of eukaryotic type IB topoisomerases, and conservation of catalytic mechanism is expected. The crystal structures, combined with previous biochemical knowledge, allow the refinement of models for recombination and the assignment of catalytic function to the active site residues. However, each system has its own peculiarities, and the exact sequence of events that allows the reaction to proceed from the first exchange reaction to the second is still unclear for at least some family members.
Biochemical analysis of components of the pre-replication complex of Archaeoglobus fulgidus
Publisher: Oxford University Press (OUP)
Date: 15-08-2003
DOI: 10.1093/NAR/GKG662
Abstract: The eukaryotic pre-replication complex is assembled at replication origins in a reaction called licensing. Licensing involves the interactions of a variety of proteins including the origin recognition complex (ORC), Cdc6 and the Mcm2-7 helicase, homologues of which are also found in archaea. The euryarchaeote Archaeoglobus fulgidus encodes two genes with homology to Orc/Cdc6 and a single Mcm homologue. The A.fulgidus Mcm protein and one Orc/Cdc6 homologue have been purified and investigated in vitro. The Mcm protein is an ATP-dependent, hexameric helicase that can unwind between 200 and 400 bp of duplex DNA. Deletion of 112 amino acids from the N-terminus of A.f Mcm produced a protein, which was still capable of forming a hexamer, was competent in DNA binding and was able to unwind at least 1 kb of duplex DNA. The purified Orc/Cdc6 homologue was also able to bind DNA. Both Mcm and Orc/Cdc6 show a preference for specific DNA structures, namely molecules containing a single stranded bubble that mimics early replication intermediates. Nuclease protection showed that the binding sites for Mcm and Orc/Cdc6 overlap. The Orc/Cdc6 protein bound more tightly to these substrates and was able to displace pre-bound Mcm hexamer.
Action of site-specific recombinases XerC and XerD on tethered Holliday junctions
Publisher: Wiley
Date: 15-06-1997
Molecular Mechanism of Sequence-Directed DNA Loading and Translocation by FtsK
Publisher: Elsevier BV
Date: 08-2008
Development and validation of the player experience inventory: A scale to measure player experiences at the level of functional and psychosocial consequences
Publisher: Elsevier BV
Date: 03-2020
Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism
Publisher: American Society for Microbiology
Date: 03-2016
Abstract: The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation ( ovie.html ), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including F o F 1 ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell ision. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels ( nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt revolution motors use larger channels ( nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for ex le, helicase unwinding of DNA or translocase directional movement of DNA.
Biochemical Analysis of a DNA Replication Origin in the Archaeon Aeropyrum pernix
Publisher: Elsevier BV
Date: 10-2006
DOI: 10.1016/J.JMB.2006.07.076
Abstract: We have characterised the interaction of the Aeropyrum pernix origin recognition complex proteins (ORC1 and ORC2) with DNA using DNase I footprinting. Each protein binds upstream of its respective gene. However, ORC1 protein alone interacts more tightly with an additional region containing multiple origin recognition box (ORB) sites that we show to be a replication origin. At this origin, there are four ORB elements disposed either side of an A+T-rich region. An ORC1 protein dimer binds at each of these ORB sites. Once all four ORB sites have bound ORC1 protein, there is a transition to a higher-order assembly with a defined alteration in topology and superhelicity. Furthermore, after this transition, the A+T-rich region becomes sensitive to digestion by DNase I and P1 nuclease, revealing that the transition promotes distortion of the DNA in this region, presumably as a prelude to loading of MCM helicase.
Unlinking chromosome catenanes in vivo by site-specific recombination
Publisher: Wiley
Date: 06-09-2007
Biofilms Enhance the Adsorption of Toxic Contaminants on Plastic Microfibers under Environmentally Relevant Conditions
Publisher: American Chemical Society (ACS)
Date: 21-06-2021
Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing.
Publisher: American Chemical Society (ACS)
Date: 09-03-2021
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View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE160100127
Start Date: 2016
End Date: 12-2016
Amount: $355,000.00
Funder: Australian Research Council
View Funded Activity