Nursing practice in stroke rehabilitation: systematic review and meta-ethnography

AIMS AND OBJECTIVES

To identify and synthesise the available research evidence in order to generate an explanatory framework for nursing practice in stroke rehabilitation.

BACKGROUND

Although nurses are the largest professional group working with stroke survivors, there is limited understanding of nursing practice in stroke units. In particular, there is currently very little evidence in respect of nurses' involvement in poststroke rehabilitation.

DESIGN

Meta-ethnography.

METHOD

A systematic review was undertaken. The review question was: 'What is the nature of nursing practice in the care and rehabilitation of inpatient stroke survivors?' Searches of 12 electronic databases identified 14,655 publications, and after screening, 778 remained; 137 papers were obtained and 54 retained for mapping. Sixteen qualitative studies were included in the meta-ethnography.

RESULTS

Nurses' involvement in poststroke rehabilitation was limited. Contextual factors impacted on nurses' perceptions and practice. Nurses' integration of rehabilitation skills was perceived to be contingent on adequate nurse staffing levels and management of demands on nurses' time. Team working practices and use of the built environment indicated separation of nursing and therapy work. Physical care and monitoring were prioritised. Stroke-specific education and training was evident, but not consistent in content or approach. Stroke survivors and families needed help to understand nurses' role in rehabilitation.

CONCLUSION

The review provides compelling evidence that there is an need to re-examine the role of nurses in contributing to poststroke rehabilitation, including clarifying when this process can safely begin and specifying the techniques that can be integrated in nurses' practice.

RELEVANCE TO CLINICAL PRACTICE

Integrating stroke-specific rehabilitation skills in nurses' practice could contribute substantially to improving outcomes for stroke survivors. The explanatory framework developed from the review findings identifies issues which will need to be addressed in order to maximise nurses' contribution to the rehabilitation of stroke survivors.

The chemical basis of serine palmitoyltransferase inhibition by myriocin

Sphingolipids (SLs) are essential components of cellular membranes formed from the condensation of L-serine and a long-chain acyl thioester. This first step is catalyzed by the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT) which is a promising therapeutic target. The fungal natural product myriocin is a potent inhibitor of SPT and is widely used to block SL biosynthesis despite a lack of a detailed understanding of its molecular mechanism. By combining spectroscopy, mass spectrometry, X-ray crystallography, and kinetics, we have characterized the molecular details of SPT inhibition by myriocin. Myriocin initially forms an external aldimine with PLP at the active site, and a structure of the resulting co-complex explains its nanomolar affinity for the enzyme. This co-complex then catalytically degrades via an unexpected 'retro-aldol-like' cleavage mechanism to a C18 aldehyde which in turn acts as a suicide inhibitor of SPT by covalent modification of the essential catalytic lysine. This surprising dual mechanism of inhibition rationalizes the extraordinary potency and longevity of myriocin inhibition.

Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats

The type II restriction endonuclease TseI recognizes the DNA target sequence 5′-G^CWGC-3′ (where W = A or T) and cleaves after the first G to produce fragments with three-base 5′-overhangs. We have determined that it is a dimeric protein capable of cleaving not only its target sequence but also one containing A:A or T:T mismatches at the central base pair in the target sequence. The cleavage of targets containing these mismatches is as efficient as cleavage of the correct target sequence containing a central A:T base pair. The cleavage mechanism does not apparently use a base flipping mechanism as found for some other type II restriction endonuclease recognizing similarly degenerate target sequences. The ability of TseI to cleave targets with mismatches means that it can cleave the unusual DNA hairpin structures containing A:A or T:T mismatches formed by the repetitive DNA sequences associated with Huntington’s disease (CAG repeats) and myotonic dystrophy type 1 (CTG repeats).

(E)-5-[3-Cyano-2-(dicyanomethylene)-1-oxaspiro[4.5]dec-3-en-4-yl]-3-(1-methyl-1,4-dihydropyridin-4-ylidene)pent-4-en-1-yl 3,5-bis(benzyloxy)benzoate

In the title compound, C₄₅H₄₀N₄O₅, the cyclo­hexane entity on the (3-cyano-2,5-dihydro­furan-2-yl­idene)propane­dinitrile group, which replaces the usual dimethyl substituents, has not perturbed the delocalization geometry significantly. Weak inter­molecular inter­actions, viz. C—H⋯N(cyano), C—H⋯O(ether), C—H⋯π and π–π [between the aromatic rings with the shortest centroid–centroid distance of 3.603 (3) Å], consolidate the crystal packing, which exhibits voids of 57 ų.

Cellular redox potential and the biomolecular electrochemical series: a systems hypothesis

The role of cellular redox potential in the regulation of protein activity is becoming increasingly appreciated and characterized. In this paper we put forward a new hypothesis relating to redox regulation of cellular physiology. We have exemplified our hypothesis using apoptosis since its redox phenomenology is well established, but believe that it is equally applicable to several other pathways. Our hypothesis is that since multiple proteins in the apoptosis pathway are thought to be regulated via oxidation/reduction reactions and since cellular redox potentials have been shown to become progressively more oxidative during apoptosis, that the proteins could be arranged in an electrochemical series where the protein's standard potential correlates with its position in the pathway. Since the most stable oxidation state of the protein is determined by its standard potential and the redox potential of its environment (in a way predictable by the Nernst equation), a quantitative model of the redox regulation of the pathway could be developed. We have outlined our hypothesis, illustrating it using a pathway map which assembles a selection of the literature on apoptosis into a readable graphical format. We have also outlined experimental approaches suitable for testing our hypothesis.

The development of evidence based guidelines for clinical practice portfolios

AIMS

Although the use of portfolios is widespread within healthcare education, agreement on their purpose, content, assessment and value is still debated. The objective of this study was to achieve consensus on quality criteria for clinical practice portfolios that would act as guidance for students and lecturers.

METHODS

A Delphi survey was undertaken to seek consensus on the opinions of 23 'expert participants' through a series of rounds of structured questionnaires. The Delphi tool was produced as an on-line survey questionnaire and panel experts were invited to score statements using a discrete 7 point visual analogue scale. The statements were written as quality criteria relating to portfolio development which had been identified from the literature and by the research team. The survey employed three rounds of feedback and consensus was measured as 80% agreement for each quality criteria scoring 5 and above.

RESULTS

Consensus was reached on 31 quality criteria which were categorised into 4 areas: structured collection of labelled evidence; nature of evidence; critical reflection; and assessment and judgement. Mean scores for the final wording of the quality criteria ranged from 5.3 to 6.8 with the standard deviation for all of the mean scores being below 1.5. There was consensus that these quality criteria were relevant to health and social care professionals involved in developing clinical practice portfolios.

CONCLUSIONS

The Delphi process facilitated exchange of ideas amongst panel 'experts' about the content and evaluation of clinical practice portfolios, with most debate relating to judgement of competence and rewarding originality and creativity. These issues illustrate the tensions between educational values and professional constraints. The Delphi process proved to be an effective method for achieving consensus on quality criteria for clinical practice portfolios and enabled the development of validated guidelines.

Pilot testing of guidelines to support good practice in the development of professional portfolios

AIMS

The aims of this study were to evaluate whether the introduction of new evidence based portfolio guidelines helped students and assessors to understand the expectations for completion of a clinical practice portfolio, and whether this understanding resulted in the submission of evidence consistent with the guidelines.

METHODS

New evidence based portfolio guidelines were introduced to an undergraduate BSc (Hons) Radiography (Diagnostic) programme. A total of 134 students completed 12 item questionnaires relating to using the portfolio guidelines. Semi-structured interviews were undertaken with 12 students and 5 lecturer practitioners. Documentary analysis was undertaken on 26 portfolios.

RESULTS

Survey data indicated that the new guidelines increased students' understanding of portfolio evidence requirements. Statistically significant increases in scores were evident for only two out of 12 questions; these related to understanding the need for critical reflection and which elements of the portfolio would be rewarded in assessment. Survey data also indicated some dissatisfaction with the role of lecturer practitioners and clinical assessors in relation to portfolio development. Interviews provided more mixed perceptions of the contribution of enhanced guidelines and identified some reasons for dissatisfaction with the lecturer practitioner and clinical assessor role. Documentary analysis indicated that whilst the guidelines improved students' and lecturers' understanding of evidence requirements, this did not translate into portfolio evidence which matched guideline expectations. Portfolio evidence was restricted to meeting the minimum profession specific task requirements and often indicated a mis-match between guideline expectations and assessor assessment judgements.

CONCLUSIONS

New evidence based guidelines improved understanding of evidence and presentation requirements for clinical practice portfolios. Consistent interpretation of portfolio guidelines however requires structured preparation and ongoing support of students, assessors and lecturers if the pedagogic aims for clinical portfolio use are to become an integral part of providing evidence of meeting professional competence requirements.

Mapping a noncovalent protein-peptide interface by top-down FTICR mass spectrometry using electron capture dissociation

Noncovalent protein-ligand and protein-protein complexes are readily detected using electrospray ionization mass spectrometry (ESI MS). Furthermore, recent reports have demonstrated that careful use of electron capture dissociation (ECD) fragmentation allows covalent backbone bonds of protein complexes to be dissociated without disruption of noncovalent protein-ligand interactions. In this way the site of protein-ligand interfaces can be identified. To date, protein-ligand complexes, which have proven tractable to this technique, have been mediated by ionic electrostatic interactions, i.e., ion pair interactions or salt bridging. Here we extend this methodology by applying ECD to study a protein-peptide complex that contains no electrostatics interactions. We analyzed the complex between the 21 kDa p53-inhibitor protein anterior gradient-2 and its hexapeptide binding ligand (PTTIYY). ECD fragmentation of the 1:1 complex occurs with retention of protein-peptide binding and analysis of the resulting fragments allows the binding interface to be localized to a C-terminal region between residues 109 and 175. These finding are supported by a solution-phase competition assay, which implicates the region between residues 108 and 122 within AGR2 as the PTTIYY binding interface. Our study expands previous findings by demonstrating that top-down ECD mass spectrometry can be used to determine directly the sites of peptide-protein interfaces. This highlights the growing potential of using ECD and related top-down fragmentation techniques for interrogation of protein-protein interfaces.

Effects on quality of life, anti-cancer responses, breast conserving surgery and survival with neoadjuvant docetaxel: a randomised study of sequential weekly versus three-weekly docetaxel following neoadjuvant doxorubicin and cyclophosphamide in women with primary breast cancer

Background

Weekly docetaxel has occasionally been used in the neoadjuvant to downstage breast cancer to reduce toxicity and possibly enhance quality of life. However, no studies have compared the standard three weekly regimen to the weekly regimen in terms of quality of life. The primary aim of our study was to compare the effects on QoL of weekly versus 3-weekly sequential neoadjuvant docetaxel. Secondary aims were to determine the clinical and pathological responses, incidence of Breast Conserving Surgery (BCS), Disease Free Survival (DFS) and Overall Survival (OS).

Methods

Eighty-nine patients receiving four cycles of doxorubicin and cyclophosphamide were randomised to receive twelve cycles of weekly docetaxel (33 mg/m²) or four cycles of 3-weekly docetaxel (100 mg/m²). The Functional Assessment of Cancer Therapy-Breast and psychosocial questionnaires were completed.

Results

At a median follow-up of 71.5 months, there was no difference in the Trial Outcome Index scores between treatment groups. During weekly docetaxel, patients experienced less constipation, nail problems, neuropathy, tiredness, distress, depressed mood, and unhappiness. There were no differences in overall clinical response (93% vs. 90%), pathological complete response (20% vs. 27%), and breast-conserving surgery (BCS) rates (49% vs. 42%). Disease-free survival and overall survival were similar between treatment groups.

Conclusions

Weekly docetaxel is well-tolerated and has less distressing side-effects, without compromising therapeutic responses, Breast Conserving Surgery (BCS) or survival outcomes in the neoadjuvant setting.

Trial registration

ISRCTN: ISRCTN09184069

Degradation of the extracellular matrix components by bacterial-derived metalloproteases: implications for inflammatory bowel diseases

BACKGROUND

Proteolytic degradation of the extracellular matrix, a feature of mucosal homeostasis and tissue renewal, also contributes to the complications of intestinal inflammation. Whether this proteolytic activity is entirely host-derived, or, in part, produced by the gut microbiota, is unknown.

METHODS

We screened the bacterial colonies for gelatinolytic activity from fecal samples of 20 healthy controls, 23 patients with ulcerative colitis, and 18 with Crohn's disease (CD). In addition, the genes encoding metalloproteases were detected by conventional or real-time polymerase chain reaction (PCR).

RESULTS

Gelatinolytic activity was found in approximately one-quarter of samples regardless of the presence of inflammation and without any attempt to enhance the sensitivity of the culture-based screen. This was associated with a diversity of bacteria, particularly in CD, but was predominantly linked with Clostridium perfringens. Culture supernatants from C. perfringens degraded gelatin, azocoll, type I collagen, and basement membrane type IV collagen, but different isolates varied in the degree of proteolytic activity. Results were confirmed by detection of the C. perfringens colA gene (encoding collagenase) in fecal DNA, again regardless of the presence or absence of inflammation. However, the biologic significance and potential implications of microbial-derived proteolytic activity were confirmed by reduced transepithelial resistance (TER) after exposure of rat distal colon to culture supernatants of C. perfringens in Ussing chambers.

CONCLUSIONS

The study shows that microbial-derived proteolytic activity has the capacity to contribute to mucosal homeostasis and may participate in the pathogenesis of inflammatory bowel disease.

Identification of two reactive cysteine residues in the tumor suppressor protein p53 using top-down FTICR mass spectrometry

The tumor suppressor p53 is a redox-regulated transcription factor involved in cell cycle arrest, apoptosis and senescence in response to multiple forms of stress, as well as many other cellular processes such as DNA repair, glycolysis, autophagy, oxidative stress and differentiation. The discovery of cysteine-targeting compounds that cause re-activation of mutant p53 and the death of tumor cells in vivo has emphasized the functional importance of p53 thiols. Using a combination of top-down and middle-down FTICR mass spectrometry, we show that of the 10 Cys residues in the core domain of wild-type p53, Cys182 and Cys277 exhibit a remarkable preference for modification by the alkylating reagent N-ethylmaleimide. The assignment of Cys182 and Cys277 as the two reactive Cys residues was confirmed by site-directed mutagenesis. Further alkylation of p53 beyond Cys182 and Cys277 was found to trigger co-operative modification of the remaining seven Cys residues and protein unfolding. This study highlights the power of top-down FTICR mass spectrometry for analysis of the cysteine reactivity and redox chemistry in multiple cysteine-containing proteins.

Dissecting the immune response to the entomopathogen Photorhabdus

Bacterial pathogens either hide from or modulate the host's immune response to ensure their survival. Photorhabdus is a potent insect pathogenic bacterium that uses entomopathogenic nematodes as vectors in a system that represents a useful tool for probing the molecular basis of immunity. During the course of infection, Photorhabdus multiplies rapidly within the insect, producing a range of toxins that inhibit phagocytosis of the invading bacteria and eventually kill the insect host. Photorhabdus bacteria have recently been established as a tool for investigating immune recognition and defense mechanisms in model hosts such as Manduca and Drosophila. Such studies pave the way for investigations of gene interactions between pathogen virulence factors and host immune genes, which ultimately could lead to an understanding of how some Photorhabdus species have made the leap to becoming human pathogens.

The serine palmitoyltransferase from Sphingomonas wittichii RW1: An interesting link to an unusual acyl carrier protein

Serine palmitoyltransferase (SPT) catalyses the first step in the de novo biosynthesis of sphingolipids (SLs). It uses a decarboxylative Claisen-like condensation reaction to couple L-serine with palmitoyl-CoA to generate a long-chain base product, 3-ketodihydrosphingosine. SLs are produced by mammals, plants, yeast, and some bacteria, and we have exploited the complete genome sequence of Sphingomonas wittichii to begin a complete analysis of bacterial sphingolipid biosynthesis. Here, we describe the enzymatic characterization of the SPT from this organism and present its high-resolution x-ray structure. Moreover, we identified an open reading frame with high sequence homology to acyl carrier proteins (ACPs) that are common to fatty acid biosynthetic pathways. This small protein was co-expressed with the SPT and we isolated and characterised the apo- and holo-forms of the ACP. Our studies suggest a link between fatty acid and sphingolipid metabolism.

Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation

Cycloserine (CS, 4-amino-3-isoxazolidone) is a cyclic amino acid mimic that is known to inhibit many essential pyridoxal 5'-phosphate (PLP)-dependent enzymes. Two CS enantiomers are known; D-cycloserine (DCS, also known as Seromycin) is a natural product that is used to treat resistant Mycobacterium tuberculosis infections as well as neurological disorders since it is a potent NMDA receptor agonist, and L-cycloserine (LCS) is a synthetic enantiomer whose usefulness as a drug has been hampered by its inherent toxicity arising through inhibition of sphingolipid metabolism. Previous studies on various PLP-dependent enzymes revealed a common mechanism of inhibition by both enantiomers of CS; the PLP cofactor is disabled by forming a stable 3-hydroxyisoxazole/pyridoxamine 5'-phosphate (PMP) adduct at the active site where the cycloserine ring remains intact. Here we describe a novel mechanism of CS inactivation of the PLP-dependent enzyme serine palmitoyltransferase (SPT) from Sphingomonas paucimobilis. SPT catalyses the condensation of l-serine and palmitoyl-CoA, the first step in the de novo sphingolipid biosynthetic pathway. We have used a range of kinetic, spectroscopic and structural techniques to postulate that both LCS and DCS inactivate SPT by transamination to form a free pyridoxamine 5'-phosphate (PMP) and beta-aminooxyacetaldehyde that remain bound at the active site. We suggest this occurs by ring opening of the cycloserine ring followed by decarboxylation. Enzyme kinetics show that inhibition is reversed by incubation with excess PLP and that LCS is a more effective SPT inhibitor than DCS. UV-visible spectroscopic data, combined with site-directed mutagenesis, suggest that a mobile Arg(378) residue is involved in cycloserine inactivation of SPT.

The Rcs phosphorelay: more than just a two-component pathway

The Rcs phosphorelay is a complex signaling pathway found in many, but not all, members of the Enterobacteriaceae. The complexity of this pathway is due to the direct involvement of three proteins (RcsC, RcsD and RcsB) in the phosphorelay and the presence of multiple accessory proteins with important roles in modulating the inputs and outputs associated with this signaling pathway. This article will discuss the various inputs and outputs associated with the Rcs phosphorelay and also present a model suggesting an important role for this signaling pathway in the temporal control of virulence in Salmonella enterica and biofilm formation in Escherichia coli.

Achieving teamwork in stroke units: the contribution of opportunistic dialogue

Collaborative interdisciplinary working is central to contemporary health policy. The specialized and co-ordinated multidisciplinary care provided in stroke units is considered to contribute to improved patient outcomes in such units. However, how stroke unit teams co-ordinate their work is not clearly understood. This paper reports on a grounded theory study which explains how health professionals in two stroke units in northern England achieved teamwork. Data were generated through 220 hours of participant observation and 34 semi-structured interviews. Interviews were undertaken during and following participant observations. A basic social process common to teamworking in both units was identified; this was termed "opportunistic dialogue". The division of labour in respect of rehabilitation activities was negotiated through this interactional process. Co-location of most team members led to repeated engagement in sharing patient information and in exploring different perspectives. Opportunistic dialoguing contributed to mutual learning and explained the shift in thinking and team culture as team members moved from concern with discrete disciplinary actions to dialogue and negotiations focused on meeting patients' needs. The findings indicate that routinely incorporating periods of joint working in which team members articulate the reasoning for their decisions and interventions, contributes to achieving interdisciplinary teamworking in rehabilitation settings.

The role of iron uptake in pathogenicity and symbiosis in Photorhabdus luminescens TT01

Background

Photorhabdus are Gram negative bacteria that are pathogenic to insect larvae whilst also having a mutualistic interaction with nematodes from the family Heterorhabditis. Iron is an essential nutrient and bacteria have different mechanisms for obtaining both the ferrous (Fe²⁺) and ferric (Fe³⁺) forms of this metal from their environments. In this study we were interested in analyzing the role of Fe³⁺ and Fe²⁺ iron uptake systems in the ability of Photorhabdus to interact with its invertebrate hosts.

Results

We constructed targeted deletion mutants of exbD, feoABC and yfeABCD in P. luminescens TT01. The exbD mutant was predicted to be crippled in its ability to obtain Fe³⁺ and we show that this mutant does not grow well in iron-limited media. We also show that this mutant was avirulent to the insect but was unaffected in its symbiotic interaction with Heterorhabditis. Furthermore we show that a mutation in feoABC (encoding a predicted Fe²⁺ permease) was unaffected in both virulence and symbiosis whilst the divalent cation transporter encoded by yfeABCD is required for virulence in the Tobacco Hornworm, Manduca sexta (Lepidoptera) but not in the Greater Wax Moth, Galleria mellonella (Lepidoptera). Moreover the Yfe transporter also appears to have a role during colonization of the IJ stage of the nematode.

Conclusion

In this study we show that iron uptake (via the TonB complex and the Yfe transporter) is important for the virulence of P. luminescens to insect larvae. Moreover this study also reveals that the Yfe transporter appears to be involved in Mn²⁺-uptake during growth in the gut lumen of the IJ nematode. Therefore, the Yfe transporter in P. luminescens TT01 is important during colonization of both the insect and nematode and, moreover, the metal ion transported by this pathway is host-dependent.

Online quench-flow electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for elucidating kinetic and chemical enzymatic reaction mechanisms

We have developed an automated quench-flow microreactor which interfaces directly to an electrospray ionization (ESI) mass spectrometer. We have used this device in conjunction with ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) to demonstrate the potential of this approach for studying the mechanistic details of enzyme reactions. For the model system chosen to test this device, namely, the pre-steady-state hydrolysis of p-nitrophenyl acetate by the enzyme chymotrypsin, the kinetic parameters obtained are in good agreement with those in the literature. To our knowledge, this is the first reported use of online quench-flow coupled with FTICR MS. Furthermore, we have exploited the power of FTICR MS to interrogate the quenched covalently bound enzyme intermediate using top-down fragmentation. The accurate mass capabilities of FTICR MS permitted the nature of the intermediate to be assigned with high confidence. Electron capture dissociation (ECD) fragmentation allowed us to locate the intermediate to a five amino acid section of the protein--which includes the known catalytic residue, Ser(195). This experimental approach, which uniquely can provide both kinetic and chemical details of enzyme mechanisms, is a potentially powerful tool for studies of enzyme catalysis.

Conformational preferences of linear beta-defensins are revealed by ion mobility-mass spectrometry

In recent times there has been an enormous rise in resistance to synthetic antibiotics as well as an increase in the virulence of bacteria, the so-called "superbugs". This problem has catalyzed a search for novel molecules to fight bacteria, which in turn relies on a better understanding of the molecular basis of the immune response. Beta-defensins are a class of small, cationic, cysteine-rich antimicrobial peptides expressed by humans and other animals to act against incoming pathogens. As well as their antimicrobial properties, beta-defensins also act as chemokines, recruiting cells to the sites of infection. Here the relationship between the tertiary structures of beta-defensin analogs and their chemotactic activities has been investigated using ion mobility-mass spectrometry (IM-MS) and biochemical assays. A panel of derivatives of the murine beta-defensin Defb14 has been formed and the ability of these peptides to chemoattract the receptor CCR6 has been assessed in vitro. The derivatives can be divided into two groups, those with chemotactic activity equal to that of the unmodified parent peptide, and those whose chemotactic activity has been lost upon modification. Analysis by ion mobility-mass spectrometry reveals the conformational preferences of these peptides upon ionization from different solvents. Under denaturing conditions, the chemotactic peptides adopt more compact conformations in the gas-phase at higher charge states than those which are inactive. While the conditions of these experiments are not akin to the environment around the receptor in vivo, this technique provides an in vacuo method for distinguishing between the different chemotactic activities of beta-defensin derivatives.

Implementing arbitrary phase gates with Ising anyons

Ising-type non-Abelian anyons are likely to occur in a number of physical systems, including quantum Hall systems, where recent experiments support their existence. In general, non-Abelian anyons may be utilized to provide a topologically error-protected medium for quantum information processing. However, the topologically protected operations that may be obtained by braiding and measuring topological charge of Ising anyons are precisely the Clifford gates, which are not computationally universal. The Clifford gate set can be made universal by supplementing it with single-qubit pi/8-phase gates. We propose a method of implementing arbitrary single-qubit phase gates for Ising anyons by running a current of anyons with interfering paths around computational anyons.

Subdivision of the bacterioferritin comigratory protein family of bacterial peroxiredoxins based on catalytic activity

Peroxiredoxins are ubiquitous proteins that catalyze the reduction of hydroperoxides, thus conferring resistance to oxidative stress. Using high-resolution mass spectrometry, we recently reclassified one such peroxiredoxin, bacterioferritin comigratory protein (BCP) of Escherichia coli, as an atypical 2-Cys peroxiredoxin that functions through the formation of an intramolecular disulfide bond between the active and resolving cysteine. An engineered E. coli BCP, which lacked the resolving cysteine, retained enzyme activity through a novel catalytic pathway. Unlike the active cysteine, the resolving cysteine of BCP peroxiredoxins is not conserved across all members of the family. To clarify the catalytic mechanism of native BCP enzymes that lack the resolving cysteine, we have investigated the BCP homologue of Burkholderia cenocepacia. We demonstrate that the B. cenocepacia BCP (BcBCP) homologue functions through a 1-Cys catalytic pathway. During catalysis, BcBCP can utilize thioredoxin as a reductant for the sulfenic acid intermediate. However, significantly higher peroxidase activity is observed utilizing glutathione as a resolving cysteine and glutaredoxin as a redox partner. Introduction of a resolving cysteine into BcBCP changes the activity from a 1-Cys pathway to an atypical 2-Cys pathway, analogous to the E. coli enzyme. In contrast to the native B. cenocepacia enzyme, thioredoxin is the preferred redox partner for this atypical 2-Cys variant. BCP-deficient B. cenocepacia exhibit a growth-phase-dependent hypersensitivity to oxidative killing. On the basis of sequence alignments, we believe that BcBCP described herein is representative of the major class of bacterial BCP peroxiredoxins. To our knowledge, this is the first detailed characterization of their catalytic activity. These studies support the subdivision of the BCP family of peroxiredoxins into two classes based on their catalytic activity.

Binding a heparin derived disaccharide to defensin inspired peptides: insights to antimicrobial inhibition from gas-phase measurements

Due to the ubiquitous presence of polysaccharide moieties on bacterial surfaces, it is hypothesised that a peptide-saccharide interaction plays a key role during the recognition of invading microorganisms by beta-defensins. We have employed different gas-phase methods to investigate these interactions. This manuscript describes: an MS-based titration assay measuring the gas-phase binding of ten beta-defensin related peptides to a sulfated disaccharide derived from heparin (HDD); ion mobility-mass spectrometry-determined collision cross sections of 3 peptides (both free and binding HDD); and results from molecular modelling with the aim of reconciling some of our experimental observations. We observe a clear qualitative correlation between the antimicrobial activity of several beta-defensins and related peptides and their gas-phase binding to a heparin-derived disaccharide (HDD). Four of the ten peptides show >100 micromolar K(d) values with HDD, and no bacteriocidal activity, illustrating that HDD binding correlates with peptide antimicrobial activity. For five of the remaining six peptides, bacteriocidal activity was re-measured with HDD present. For the peptides containing intramolecular disulfide bonds in two out of five, bacteriocidal activity was reduced approximately 10-fold; for the remaining three peptides, which lack intramolecular disulfide bonds, HDD addition had little effect on bacteriocidal activity. The latter results are suggested to arise from the greater degree of flexibility imparted by the removal of disulfide bonds giving the peptides the ability to envelope HDD and assume a "defensin-like" fold. Thus gas-phase analysis is put forward as a powerful tool for assessing the properties of antimicrobial peptides providing valuable insights in the mechanism of antimicrobial inhibition.

Identification of genes involved in the mutualistic colonization of the nematode Heterorhabditis bacteriophora by the bacterium Photorhabdus luminescens

Background

Photorhabdus are Gram negative entomopathogenic bacteria that also have a mutualistic association with nematodes from the family Heterorhabditis. An essential part of this symbiosis is the ability of the bacterium to colonize the gut of the freeliving form of the nematode called the infective juvenile (IJ). Although the colonization process (also called transmission) has been described phenomonologically very little is known about the underlying molecular mechanisms. Therefore, in this study, we were interested in identifying genes in Photorhabdus that are important for IJ colonization.

Results

In this work we genetically tagged P. luminescens TT01 with gfp and constructed a library containing over 3200 mutants using the suicide vector, pUT-Km2. Using a combination of in vitro symbiosis assays and fluorescent microscopy we screened this library for mutants that were affected in their ability to colonize the IJ i.e. with decreased transmission frequencies. In total 8 mutants were identified with transmission frequencies of ≤ 30% compared to wild-type. These mutants were mapped to 6 different genetic loci; the pbgPE operon, galE, galU, proQ, asmA and hdfR. The pbgPE, galE and galU mutants were all predicted to be involved in LPS biosynthesis and, in support of this, we have shown that these mutants are avirulent and sensitive to the cationic antimicriobial peptide, polymyxin B. On the other hand the proQ, asmA and hdfR mutants were not affected in virulence and were either as resistant (proQ) or slightly more sensitive (asmA, hdfR) to polymyxin B than the wild-type (WT).

Conclusions

This is the first report describing the outcome of a comprehensive screen looking for transmission mutants in Photorhabdus. In total 6 genetic loci were identified and we present evidence that all of these loci are involved in the assembly and/or maintenance of LPS and other factors associated with the cell surface. Interestingly several, but not all, of the transmission mutants identified were also avirulent suggesting that there is a significant, but not complete, genetic overlap between pathogenicity and mutualism. Therefore, this study highlights the importance of the cell surface in mediating the symbiotic and pathogenic interactions of Photorhabdus.

Efficient production of human beta-defensin 2 (HBD2) in Escherichia coli

Human beta-defensin 2 (HBD2) has been shown to interact with pathogenic bacteria and components of the mammalian innate and adaptive immune response. We describe a quick and reliable method for the production of HBD2 in Escherichia coli. HBD2 was expressed as an insoluble fusion, chemically cleaved and oxidised to give a single, folded HBD2 beta-isoform. The purified peptide was analysed by high resolution mass spectrometry, displayed a well-dispersed (1)H NMR spectrum, was a chemoattractant to HEK293 cells expressing CCR6 and acted as an antimicrobial agent against E. coli, P. aeruginosa, C. albicans and S. aureus.

Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification

The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modifying the negative charges on the Ocr surface. Our analysis reveals that removal of about 46% of the carboxylate groups per Ocr monomer results in an approximately 50-fold reduction in binding affinity for a methyltransferase from a model type I restriction/modification system. The reduced affinity between Ocr with this degree of modification and the methyltransferase is comparable with the affinity of DNA for the methyltransferase. Additional modification to remove approximately 86% of the carboxylate groups further reduces its binding affinity, although the modified Ocr still binds to the methyltransferase via a mechanism attributable to the shape mimicry of a bent DNA molecule. Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to approximately 800-fold.

Dying and necrotic neutrophils are anti-inflammatory secondary to the release of alpha-defensins

Neutrophils are recruited to sites of injury but their timely removal is thought to be vital to prevent exacerbating inflammation. In addition, the recognition of apoptotic cells by cells of the innate immune system provides potent anti-inflammatory and anti-immunogenic signals. In this article, we describe how human neutrophils dying by apoptosis or necrosis release anti-inflammatory peptides, the alpha-defensins. This family of small cationic peptides effectively inhibits the secretion of multiple proinflammatory cytokines and NO from macrophages, the main innate immune cell found at sites of chronic inflammation. In addition, the systemic administration of necrotic neutrophil supernatants and alpha-defensins protects mice from a murine model of peritonitis. Hence. their effects may be far-reaching and serve to kill microbes while regulating a potentially tissue-destructive inflammatory response.

Structural and functional studies of the biotin protein ligase from Aquifex aeolicus reveal a critical role for a conserved residue in target specificity

Biotin protein ligase (BPL; EC 6.3.4.15) catalyses the formation of biotinyl-5'-AMP from biotin and ATP, and the succeeding biotinylation of the biotin carboxyl carrier protein. We describe the crystal structures, at 2.4 A resolution, of the class I BPL from the hyperthermophilic bacteria Aquifex aeolicus (AaBPL) in its ligand-free form and in complex with biotin and ATP. The solvent-exposed beta- and gamma-phosphates of ATP are located in the inter-subunit cavity formed by the N- and C-terminal domains. The Arg40 residue from the conserved GXGRXG motif is shown to interact with the carboxyl group of biotin and to stabilise the alpha- and beta-phosphates of the nucleotide. The structure of the mutant AaBPL R40G in both the ligand-free and biotin-bound forms reveals that the mutated loop has collapsed, thus hindering ATP binding. Isothermal titration calorimetry indicated that the presence of biotin is not required for ATP binding to wild-type AaBPL in the absence of Mg(2+), and the binding of biotin and ATP has been determined to occur via a random but cooperative process. The affinity for biotin is relatively unaffected by the R40G mutation. In contrast, the thermodynamic data indicate that binding of ATP to AaBPL R40G is very weak in the absence or in the presence of biotin. The AaBPL R40G mutant remains catalytically active but shows poor substrate specificity; mass spectrometry and Western blot studies revealed that the mutant biotinylates both the target A. aeolicus BCCPDelta67 fragment and BSA, and is subject to self-biotinylation.

Preparation of isotopically labelled recombinant beta-defensin for NMR studies

beta-Defensins are a family of cationic peptides that contain six invariant cysteine residues that form characteristic disulfide bonds between Cys(1)-Cys(5), Cys(2)-Cys(4) and Cys(3)-Cys(6). They have been shown to act as potent antimicrobial agents and chemokines. Human beta-defensin 2 (HBD2) was first isolated from psoriatic skin lesions and the structure of this peptide has been solved by X-ray crystallography and NMR spectroscopy both of which are consistent with a fold that contains an N-terminal alpha-helix and three antiparallel beta-strands. Here, we report the expression and purification of the first isotopically labelled beta-defensin ((15)N HBD2) with 100% incorporation of (15)N using a recombinant Escherichia coli method. Multidimensional NMR spectroscopy experiments: 2D (1)H-(15)N HSQC, 3D HSQC-TOCSY and 3D HSQC-NOESY allows for the assignment of resonances with no overlapping or ambiguous peaks. This isotopically labelled peptide is highly suitable for studying the interactions between HBD2 and a range of components from both the mammalian immune system and bacterial pathogens.

Plant host and sugar alcohol induced exopolysaccharide biosynthesis in the Burkholderia cepacia complex

The species that presently constitute the Burkholderia cepacia complex (Bcc) have multiple roles; they include soil and water saprophytes, bioremediators, and plant, animal and human pathogens. Since the first description of pathogenicity in the Bcc was based on sour skin rot of onion bulbs, this study returned to this plant host to investigate the onion-associated phenotype of the Bcc. Many Bcc isolates, which were previously considered to be non-mucoid, produced copious amounts of exopolysaccharide (EPS) when onion tissue was provided as the sole nutrient. EPS production was not species-specific, was observed in isolates from both clinical and environmental sources, and did not correlate with the ability to cause maceration of onion tissue. Chemical analysis suggested that the onion components responsible for EPS induction were primarily the carbohydrates sucrose, fructose and fructans. Additional sugars were investigated, and all alcohol sugars tested were able to induce EPS production, in particular mannitol and glucitol. To investigate the molecular basis for EPS biosynthesis, we focused on the highly conserved bce gene cluster thought to be involved in cepacian biosynthesis. We demonstrated induction of the bce gene cluster by mannitol, and found a clear correlation between the inability of representatives of the Burkholderia cenocepacia ET12 lineage to produce EPS and the presence of an 11 bp deletion within the bceB gene, which encodes a glycosyltransferase. Insertional inactivation of bceB in Burkholderia ambifaria AMMD results in loss of EPS production on sugar alcohol media. These novel and surprising insights into EPS biosynthesis highlight the metabolic potential of the Bcc and show that a potential virulence factor may not be detected by routine laboratory culture. Our results also highlight a potential hazard in the use of inhaled mannitol as an osmolyte to improve mucociliary clearance in individuals with cystic fibrosis.

Motility is required for the competitive fitness of entomopathogenic Photorhabdus luminescens during insect infection

Background

Photorhabdus are motile members of the family Enterobactericeae that are pathogenic to insect larvae whilst also maintaining a mutualistic interaction with entomophagous nematodes of the family Heterorhabditiae. The interactions between Photorhabdus and its hosts are thought to be an obligate part of the bacteria's life-cycle in the environment. Motility often plays a key role in mediating bacteria-host interactions and, in this study, we were interested in characterising the role of motility in the Photorhabdus-nematode-insect tripartite association.

Results

We constructed deletion mutants of flgG (blocking flagella production) and motAB (blocking flagella rotation) in P. luminescens TT01. Using these mutants we show that both the ΔflgG and ΔmotAB mutants are equally as good as the wild-type (WT) bacteria in killing insects and supporting nematode growth and development suggesting that flagella production and motility are not required for pathogenicity or mutualism. However we show that the production of flagella is associated with a significant metabolic cost during growth on agar plates suggesting that, although not required for pathogenicity or mutualism, there must be a strong selective pressure to retain flagella production (and motility) during the interactions between Photorhabdus and its different hosts. To this end we show that both the ΔflgG and ΔmotAB mutants are out-competed by WT Photorhabdus during prolonged incubation in the insect revealing that motile bacteria do have a fitness advantage during colonisation of the insect larva.

Conclusion

This is the first report of a role for motility in Photorhabdus and we show that, although not required for either pathogenicity or mutualism, motility does contribute to the competitive fitness of Photorhabdus during infection of the insect (and, to a lesser extent, the nematode). This adaptive function is similar to the role ascribed to motility in mammalian pathogens such as uropathogenic Escherichia coli (UPEC). Therefore, in addition to describing a role for motility in Photorhabdus, this study reinforces the relevance and utility of this bacterium as a model for studying bacteria-host interactions.