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Site-specific covalent conjugation offers a powerful tool to identify and understand protein–protein interactions. In this study, we discover that sulfur fluoride exchange (SuFEx) warheads effectively crosslink the Escherichia coliacyl carrier protein (AcpP) with its partner BioF, a key pyridoxal 5′-phosphate (PLP)-dependent enzyme in the early steps of biotin biosynthesis by targeting a tyrosine residue proximal to the active site. We identify the site of crosslink by MS/MS analysis of the peptide originating from both partners. We further evaluate the BioF–AcpP interface through protein crystallography and mutational studies. Among the AcpP-interacting BioF surface residues, three critical arginine residues appear to be involved in AcpP recognition so that pimeloyl-AcpP can serve as the acyl donor for PLP-mediated catalysis. These findings validate an evolutionary gain-of-function for BioF, allowing the organism to build biotin directly from fatty acid biosynthesis through surface modifications selective for salt bridge formation with acidic AcpP residues.

The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.

3′-O-β-Glucosyl-4′,5′-didehydro-5′-deoxyadenosine 13is identified as a natural product of Streptomyces calvusand Streptomyces virens. It is also generated in vitroby direct β-glucosylation of 4′,5′-didehydro-5′-deoxyadenosine 12with the enzyme NucGT. The intact incorporation of oxygen-18 and deuterium isotopes from (±)[1-18O,1-2H2]-glycerol 14into C-5′ of nucleocidin 1and its related metabolites precludes 3′-O-β-glucosyl-4′,5′-didehydro-5′-deoxyadenosine 13as a biosynthetic precursor to nucleocidin 1.

Aggregation of alpha-synuclein (α-Syn) drives Parkinson’s disease (PD), although the initial stages of self-assembly and structural conversion have not been directly observed inside neurons. In this study, we tracked the intracellular conformational states of α-Syn using a single-molecule Förster resonance energy transfer (smFRET) biosensor, and we show here that α-Syn converts from a monomeric state into two distinct oligomeric states in neurons in a concentration-dependent and sequence-specific manner. Three-dimensional FRET-correlative light and electron microscopy (FRET-CLEM) revealed that intracellular seeding events occur preferentially on membrane surfaces, especially at mitochondrial membranes. The mitochondrial lipid cardiolipin triggers rapid oligomerization of A53T α-Syn, and cardiolipin is sequestered within aggregating lipid–protein complexes. Mitochondrial aggregates impair complex I activity and increase mitochondrial reactive oxygen species (ROS) generation, which accelerates the oligomerization of A53T α-Syn and causes permeabilization of mitochondrial membranes and cell death. These processes were also observed in induced pluripotent stem cell (iPSC)–derived neurons harboring A53T mutations from patients with PD. Our study highlights a mechanism of de novo α-Syn oligomerization at mitochondrial membranes and subsequent neuronal toxicity.

AbstractSequence-specific protein-basedribonucleases are not found in nature. Absolute sequence selectivity in RNA cleavage in vivonormally requires multi-component complexes that recruit a guide RNA or DNA for target recognition and a protein–RNA assembly for catalytic functioning (e.g. RNAi molecular machinery, RNase H). Recently discovered peptidyl-oligonucleotide synthetic ribonucleases selectively knock down pathogenic RNAs by irreversible cleavage to offer unprecedented opportunities for control of disease-relevant RNA. Understanding how to increase their potency, selectivity and catalytic turnover will open the translational pathway to successful therapeutics. Yet, very little is known about how these chemical ribonucleases bind, cleave and leave their target. Rational design awaits this understanding in order to control therapy, particularly how to overcome the trade-off between sequence specificity and potency through catalytic turnover. We illuminate this here by characterizing the interactions of these chemical RNases with both complementary and non-complementary RNAs using Tmprofiles, fluorescence, UV-visible and NMR spectroscopies. Crucially, the level of counter cations, which are tightly-controlled within cellular compartments, also controlled these interactions. The oligonucleotide component dominated interaction between conjugates and complementarytargets in the presence of physiological levels of counter cations (K+), sufficient to prevent repulsion between the complementary nucleic acid strands to allow Watson-Crick hydrogen bonding. In contrast, the positively-charged catalytic peptide interacted poorly with target RNA, when counter cations similarly screened the negatively-charged sugar-phosphate RNA backbones. The peptide only became the key player, when counter cations were insufficient for charge screening; moreover, only under such non-physiological conditions did conjugates form strong complexes with non-complementaryRNAs.Communicated by Ramaswamy H. Sarma

Herein we discuss recent developments in mass spectrometry (MS)-based approaches for exploring the challenging interfaces of transiently interacting protein–protein interactions (PPIs).This includes an overview of liquid chromatography (LC)-MS linked protein footprinting and protein painting as tools for inferring the interacting interface of PPIs.In addition, we describe the development of native MS as a tool for developing PPI modulators and identifying PPI mediating short linear motifs (SLiMs)This is placed in the context of the significant potential that PPI characterizing, and modulation has for developing novel chemotherapeutics to address unmet medical needs.

Multicellular tumor spheroids (MTS) are a well-established model system for drug development and are a valuable in vitro research tool for use prior to employing animal models. These 3D-cell cultures are thought to display chemical gradients of oxygen and nutrients throughout their structure, giving rise to distinct microenvironments in radial layers, thus, mimicking the pathophysiological environment of a tumor. Little is known about the localized distributions of metabolites within these microenvironments. To address this, here we utilize high spectral resolution Fourier-transform ion cyclotron resonance (FT-ICR), MALDI mass spectrometry imaging (MSI) to image the distribution of endogenous metabolites in breast cancer MCF-7 spheroids. We show that known specific metabolite markers (adenosine phosphates and glutathione) indicate that the central region of these cell culture models experiences increased hypoxic and oxidative stress. By using discriminatory analysis, we have identified which m/zvalues localize toward the outer proliferative or central hypoxic regions of an MTS. Elemental formulae were assigned with sub-ppm mass accuracy, allowing metabolite assignment. Using this information, we have mapped these metabolites back to distinct pathways to improve our understanding of the molecular environment and biochemistry of these tumor models.

DNA and RNA biomarkers have not progressed beyond the automated specialized clinic due to failure in the reproducibility necessary to standardize robust and rapid nucleic acid detection at the point of care, where health outcomes can be most improved by early-stage diagnosis and precise monitoring of therapy and disease prognosis. We demonstrate here a new analytical platform to meet this challenge using functional 3D hydrogels engineered from peptide and oligonucleotide building blocks to provide sequence-specific, PCR-free fluorescent detection of unlabeled nucleic acid sequences. We discriminated at picomolar detection limits (<7 pM) “perfect-match” from mismatched sequences, down to a single nucleotide mutation, buried within longer lengths of the target. Detailed characterization by NMR, TEM, mass spectrometry, and rheology provided the structural understanding to design these hybrid peptide–oligonucleotide biomaterials with the desired sequence sensitivity and detection limit. We discuss the generic design, which is based on a highly predictable secondary structure of the oligonucleotide components, as a platform to detect genetic abnormalities and to screen for pathogenic conditions at the level of both DNA (e.g., SNPs) and RNA (messenger, micro, and viral genomic RNA).

Isotope labels are frequently used tools to track metabolites through complex biochemical pathways and to discern the mechanisms of enzyme-catalyzed reactions. Isotopically labeled l-serine is often used to monitor the activity of the first enzyme in sphingolipid biosynthesis, serine palmitoyltransferase (SPT), as well as labeling downstream cellular metabolites. Intrigued by the effect that isotope labels may be having on SPT catalysis, we characterized the impact of different l-serine isotopologues on the catalytic activity of recombinant SPT isozymes from humans and the bacterium Sphingomonas paucimobilis. Our data show that S. paucimobilisSPT activity displays a clear isotope effect with [2,3,3-D]l-serine, whereas the human SPT isoform does not. This suggests that although both human and S. paucimobilisSPT catalyze the same chemical reaction, there may well be underlying subtle differences in their catalytic mechanisms. Our results suggest that it is the activating small subunits of human SPT that play a key role in these mechanistic variations. This study also highlights that it is important to consider the type and location of isotope labels on a substrate when they are to be used in in vitro and in vivo studies.

Fourier transform mass spectrometry (FTMS) is widely used to characterize the chemical complexity of mixtures, such as natural organic matter (NOM), petroleum, and agri-food products (including Scotch whisky). Although electrospray ionization (ESI) is by far the most widely used ionization source in these studies, other ionization techniques are available and may offer complementary information. In a recent study, we found matrix free laser desorption/ionization (LDI) to be effective for the analysis of Suwannee river fulvic acid (SRFA), and to provide complementary chemical insights. In this study, LDI along with atmospheric pressure photoionization (APPI) and atmospheric pressure chemical ionization (APCI) were compared to ESI for the analysis of Scotch whisky. High mass accuracy (54 ppb, mean) allowed for the assignment of 86% of peaks, with 3993 unique molecular formulas identified from four representative samples analyzed. All four ionization techniques, performed in negative mode, identified thousands of formulas. Many were unique to each ionization source, while 699 formulas were common to all techniques. Ions were identified in both deprotonated and radical anion forms. Our study highlights the importance of a multi-ionization source approach; we recommend that analysis of complex mixtures, especially novel ones, should not be limited solely to ESI.

Successful matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) relies on the selection of the most appropriate matrix and optimization of the matrix application parameters. In order to achieve reproducible high spatial-resolution imaging data, several commercially available automated matrix application platforms have become available. However, the high cost of these commercial matrix sprayers is restricting access into this emerging research field. Here, we report an automated platform for matrix deposition, employing a converted commercially available 3D printer ($300) and other parts commonly found in an analytical chemistry lab as a low-cost alternative to commercial sprayers. Using printed fluorescent rhodamine B microarrays and employing experimental design, the matrix deposition parameters were optimized to minimize surface analyte diffusion. Finally, the optimized matrix application method was applied to image three-dimensional MCF-7 cell culture spheroid sections (ca. 500 μm diameter tissue samples) and sections of mouse brain. Using this system, we demonstrate robust and reproducible observations of endogenous metabolite and steroid distributions with a high spatial resolution.

The reductions in the transmission of emission originating from a fluorophore dissolved in a polymer matrix due to light scattering were compared in two forms of planar waveguides used as luminescent solar concentrators: a thin film of poly(methylmethacrylate) (PMMA) spin-coated on a glass plate and a solid PMMA plate of the same dimensions. The losses attributable to light scattering encountered in the waveguide consisting of the thin film of polymer coated on a glass plate were not detectable within experimental uncertainty, whereas the losses in the solid polymer plate were significant. The losses in the solid plate are interpreted as arising from light-scattering centers comprising minute bubbles of vapor/gas, incomplete polymerization or water clusters that are introduced during or after the thermally induced polymerization process.

Sphingolipids (SLs) are ubiquitous elements in eukaryotic membranes and are also found in some bacterial and viral species. As well as playing an integral structural role, SLs also act as potent signaling molecules involved in numerous cellular pathways and have been linked to many human diseases. A central SL signaling molecule is sphingosine-1-phosphate (S1P), whose breakdown is catalyzed by S1P lyase (S1PL), a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the cleavage of S1P to (2E)-hexadecenal (2E-HEX) and phosphoethanolamine. Here, we show that the pathogenic bacterium, Burkholderia pseudomalleiK96243, encodes two homologous proteins (S1PL2021 and S1PL2025) that display moderate sequence identity to known eukaryotic and prokaryotic S1PLs. Using an established MS-based methodology, we show that recombinant S1PL2021 is catalytically active. We also used recombinant human fatty aldehyde dehydrogenase to develop a spectrophotometric enzyme-coupled assay to detect 2E-HEX formation and measure the kinetic constants of the two B. pseudomalleiS1PL isoforms. Furthermore, we determined the X-ray crystal structure of the PLP-bound form of S1PL2021 at 2.1 Å resolution revealing that the enzyme displays a conserved structural fold and active site architecture comparable with known S1PLs. The combined data suggest that B. pseudomalleihas the potential to degrade host SLs in a S1PL-dependent manner.

Atopic dermatitis (AD) is a common chronic inflammatory skin disease that results in significant morbidity. A hallmark of AD is disruption of the critical barrier function of upper epidermal layers, causatively linked to environmental stimuli, genetics, and infection, and a critical current target for the development of new therapeutic and prophylactic interventions. Staphylococcus aureusis an AD-associated pathogen producing virulence factors that induce skin barrier disruption in vivo and contribute to AD pathogenesis. We show, using immortalized and primary keratinocytes, that S. aureusprotease SspA/V8 is the dominant secreted factor (in laboratory and AD clinical strains of S. aureus) inducing barrier integrity impairment and tight junction damage. V8-induced integrity damage was inhibited by an IL-1β–mediated mechanism, independent of effects on claudin-1. Induction of keratinocyte expression of the antimicrobial/host defense peptide human β-defensin 2 (hBD2) was found to be the mechanism underpinning this protective effect. Endogenous hBD2 expression was required and sufficient for protection against V8 protease-mediated integrity damage, and exogenous application of hBD2 was protective. This modulatory property of hBD2, unrelated to antibacterial effects, gives new significance to the defective induction of hBD2 in the barrier-defective skin lesions of AD and indicates therapeutic potential.

Under the auspices of its ‘Education Revolution’, the Federal Labor Government is currently implementing a national curriculum for schools. Representing an important intervention into educational practice and governance, the Australian Curriculum offers a unique research opportunity, providing substantial scope for the examination of the changing systems and school-level practices entailed in large-scale curriculum reform. Research into the Australian Curriculum also presents a valuable opportunity to develop educational research methodologies that attend to the complex and multifaceted processes of curriculum reform, from systems to classrooms. Taking two of the disciplinary towers of modern curricula (English and mathematics) and Australia’s two largest jurisdictions (New South Wales and Victoria) as the focus, this article draws on a three-year Australian Research Council Linkage Project to outline an approach to researching major curriculum reform.

Human β-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 β-isoform. The purified peptide was analysed by high resolution mass spectrometry, displayed a well-dispersed 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.

Beta defensins comprise a family of cationic, cysteine-rich antimicrobial peptides, predominantly expressed at epithelial surfaces. Previously we identified a unique five-cysteine defensin-related peptide (Defr1) that, when synthesized, is a mixture of dimeric isoforms and exhibits potent antimicrobial activity against Escherichia coli and Pseudomonas aeruginosa. Here we report that Defr1 displays antimicrobial activity against an extended panel of multidrug-resistant nosocomial pathogens for which antimicrobial treatment is limited or nonexistent. Defr1 fractions were collected by high-pressure liquid chromatography and analyzed by gel electrophoresis and mass spectrometry. Antimicrobial activity was initially investigated with the type strain Pseudomonas aeruginosa PAO1. All fractions tested displayed equivalent, potent antimicrobial activity levels comparable with that of the unfractionated Defr1. However, use of an oxidized, monomeric six-cysteine analogue (Defr1 Y5C), or of reduced Defr1, gave diminished antimicrobial activity. These results suggest that the covalent dimer structure of Defr1 is crucial to antimicrobial activity; this hypothesis was confirmed by investigation of a synthetic one-cysteine variant (Defr1-1cys). This gave an activity profile similar to that of synthetic Defr1 but only in an oxidized, dimeric form. Thus, we have shown that covalent, dimeric molecules based on the Defr1 {szligbeta}-defensin sequence demonstrate antimicrobial activity even in the absence of the canonical cysteine motif.

ABSTRACTBeta defensins comprise a family of cationic, cysteine-rich antimicrobial peptides, predominantly expressed at epithelial surfaces. Previously we identified a unique five-cysteine defensin-related peptide (Defr1) that, when synthesized, is a mixture of dimeric isoforms and exhibits potent antimicrobial activity against Escherichia coliand Pseudomonas aeruginosa. Here we report that Defr1 displays antimicrobial activity against an extended panel of multidrug-resistant nosocomial pathogens for which antimicrobial treatment is limited or nonexistent. Defr1 fractions were collected by high-pressure liquid chromatography and analyzed by gel electrophoresis and mass spectrometry. Antimicrobial activity was initially investigated with the type strain Pseudomonas aeruginosaPAO1. All fractions tested displayed equivalent, potent antimicrobial activity levels comparable with that of the unfractionated Defr1. However, use of an oxidized, monomeric six-cysteine analogue (Defr1 Y5C), or of reduced Defr1, gave diminished antimicrobial activity. These results suggest that the covalent dimer structure of Defr1 is crucial to antimicrobial activity; this hypothesis was confirmed by investigation of a synthetic one-cysteine variant (Defr1-1cys). This gave an activity profile similar to that of synthetic Defr1 but only in an oxidized, dimeric form. Thus, we have shown that covalent, dimeric molecules based on the Defr1 β-defensin sequence demonstrate antimicrobial activity even in the absence of the canonical cysteine motif.

Potent cytolytic peptides with specific tethering and cloaking sites have been synthesised and used to release payload from liposomes in a quantitative manner. A functionally located cloaking site has been modified specifically by simple conjugation without adversely affecting the cytolytic properties of the peptide. The cytolytic activity of modified peptides was then efficiently (>98%) cloaked and uncloaked by ligand-protein or hapten-antibody interactions. The principle of a dual response peptide has been demonstrated using an avidin-cloaked pH-sensitive peptide. Biospecific cloaking/uncloaking provided a new sensitive (∼12 pmol) homogeneous diagnostic and also appears potentially suited to bioresponsively targeted release of antimicrobial, anticancer and other drugs now delivered using liposomes.

It has been suggested that philosophy is a bit like manure: pile it high and it rots and stinks, but spread it around and it becomes surprisingly useful. Philosophical enquiry, used sparingly, can provide a means to develop critical and analytical ability in nurses. A key principle of philosophical enquiry is the development of skills to rigorously examine and debate ideas or explanations about, for example, the nature of being human. In recent years nurses have been exhorted to critically examine or critically analyse nursing knowledge and nursing theory. It is contended that nurses have rarely been formally prepared during their education to develop the necessary critical thinking skills to examine some of the central questions about the nature of their role, and the knowledge needed to be effective in that role. This paper will discuss the development and experience of delivering a module called ‘Nursing: Art and Science’ within a post-registration degree programme. It is argued that philosophical enquiry offers one means of equipping nurses with the critical capacity to examine the issues which may shape the future of nursing practice.

Three female Asian migrants to the United Kingdom presented with vomiting which was not of organic origin. Cultural, dynamic and other factors influenced the adop tion of vomiting as a manifestation of distress. Non-organic vomiting should be evaluated in terms of its symbolism, gains, and communicatory function for the individual.

Virulence of Photorhabdussp. strain K122 was assessed by injecting whole cells, spent culture medium, and lysate fractions into the hemocoel of larvae of wax moth, Galleria mellonella. Virulence correlated with the growth rate of the cultures and all larvae died after the cultures entered the stationary phase. Maximal production of protease and lipase exoenzymes occurred at the stationary phase and the extracellular fraction (spent culture medium from stationary phase cells) was found to be toxic to the insects. Part, but not all, of that toxicity was attributed to secreted lipase. Total lysates of K122 were toxic to G. mellonella, though they took three times longer to kill the larvae than did the same number of viable cells. The toxicity of the lysates was located in the membrane fraction, but this was found to be a nonspecific effect because the membrane fractions of Escherichia coliand Bacillus subtiliswere toxic to the same extent, whereas viable whole cells of these species were nonpathogenic. It is proposed that the nonspecific toxicity of bacterial lysates to G. mellonelladerives from the nonlocalized activation of its humoral immune response by components of the membrane fraction followed by damage to its tissues by a product of its own immune response.

The use of psychotropic medication to treat emotional and behavioural disorders among people with learning disability has been a cause of concern for some time. It has also been the subject of numerous surveys and reviews in a number of countries.

1. Sporulation of Clostridium pasteurianum effects several changes in its proton-translocating cell-membrane H+-ATPase. Notable among these are the acquisition of susceptibility to activation by trypsin and a changed protein subunit composition. 2. A protein was isolated from the mother-cell membrane that inhibited the ATP phosphohydrolase activity of purified vegetative-cell-membrane H+-ATPase [BF0F1 complex, which consists of soluble ATPase (BF1) and the proton-channel component (BF0)] and rendered it susceptible to trypsin activation. 3. This trypsin-sensitive inhibitor protein had a molecular weight of 10000 and on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis was indistinguishable from the novel protein subunit e of the mother-cell-membrane ATPase 4. In bacteriorhodopsin-containing everted membrane vesicles, the specific ATP synthetase activity of the mother-cell-membrane ATPase was significantly greater than that of the vegetative-cell-membrane ATPase. 5. Treatment with trypsin-sensitive inhibitor protein of artificial proteoliposomes containing bacteriorhodopsin and vegetative-cell-membrane H+-ATPase (BF0F1) significantly increased the specific ATP synthetase activity of this enzyme. 6. The ATP synthetase activity of crude cell-membrane preparations from cultures of Clostridium pasteurianum increased during that period in the course of sporulation when the membrane ATP phosphohydrolase was both most rapidly decreasing in specific activity and acquiring its susceptibility to activation by trypsin.

A minority of people with mental retardation have sexual behaviour which is socially unacceptable or which brings them into conflict with the law. Such behaviour may be the result of ignorance about sexual matters, often best managed by counselling or by a behavioural approach. There are a small number of men with mental retardation and aberrant sexual behaviour who benefit from the prescription of an antilibidinal drug. Treatment with an antilibidinal drug alone reduces the intensity of sexual drive but does not alter its direction; concurrent sexual counselling or psychotherapy is often indicated. The various antilibidinal medications available are reviewed, with particular attention to reports which have described the treatment of people with mental retardation. Of the antilibidinals currently used, medroxyprogesterone acetate and cyproterone acetate are those for which there is most evidence of efficacy. Cyproterone acetate is preferable because it has a specific antiandrogenic action and fewer adverse effects.There is a need for controlled studies of antilibidinal drugs, with clearly defined inclusion criteria and adequate measures of both behavioural and attitudinal change.