The expression of stlA in Photorhabdus luminescens is controlled by nutrient limitation

Photorhabdus is a genus of Gram-negative entomopathogenic bacteria that also maintain a mutualistic association with nematodes from the family Heterorhabditis. Photorhabdus has an extensive secondary metabolism that is required for the interaction between the bacteria and the nematode. A major component of this secondary metabolism is a stilbene molecule, called ST. The first step in ST biosynthesis is the non-oxidative deamination of phenylalanine resulting in the production of cinnamic acid. This reaction is catalyzed by phenylalanine-ammonium lyase, an enzyme encoded by the stlA gene. In this study we show, using a stlA-gfp transcriptional fusion, that the expression of stlA is regulated by nutrient limitation through a regulatory network that involves at least 3 regulators. We show that TyrR, a LysR-type transcriptional regulator that regulates gene expression in response to aromatic amino acids in E. coli, is absolutely required for stlA expression. We also show that stlA expression is modulated by σ^S and Lrp, regulators that are implicated in the regulation of the response to nutrient limitation in other bacteria. This work is the first that describes pathway-specific regulation of secondary metabolism in Photorhabdus and, therefore, our study provides an initial insight into the complex regulatory network that controls secondary metabolism, and therefore mutualism, in this model organism.

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.