CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery.

Nucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development.

Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation.

Whole-genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at a high resolution, thereby helping to characterize outbreaks. However, for Staphylococcus aureus, the accumulation of within-host diversity during carriage might limit the interpretation of sequencing data. In this study, we hypothesized the converse, namely, that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analyzed WGS data from 20 historical outbreaks and applied phylogenetic methods to assess genetic relatedness and to estimate the time to most recent common ancestor (TMRCA). The findings were compared with the routine investigation results and epidemiological evidence. Outbreaks with epidemiological evidence for an LTC source had a mean estimated TMRCA (adjusted for outbreak duration) of 243 days (95% highest posterior density interval [HPD], 143 to 343 days) compared with 55 days (95% HPD, 28 to 81 days) for outbreaks lacking epidemiological evidence for an LTC (P = 0.004). A threshold of 156 days predicted LTC involvement with a sensitivity of 0.875 and a specificity of 1. We also found 6/20 outbreaks included isolates with differing antimicrobial susceptibility profiles; however, these had only modestly increased pairwise diversity (mean 17.5 single nucleotide variants [SNVs] [95% confidence interval {CI}, 17.3 to 17.8]) compared with isolates with identical antibiograms (12.7 SNVs [95% CI, 12.5 to 12.8]) (P < 0.0001). Additionally, for 2 outbreaks, WGS identified 1 or more isolates that were genetically distinct despite having the outbreak pulsed-field gel electrophoresis (PFGE) pulsotype. The duration-adjusted TMRCA allowed the involvement of LTCs in outbreaks to be identified and could be used to decide whether screening for long-term carriage (e.g., in health care workers) is warranted. Requiring identical antibiograms to trigger investigation could miss important contributors to outbreaks.

Surgical resection of a rare cutaneous manifestation of Scedosporium apiospermum in a patient who underwent renal transplant.

A man aged 47 years who was immunosuppressed following renal transplantation for focal segmental glomerulosclerosis was referred to the Plastic Surgery team for management of a painful, chronic, granulomatous lesion of the right forearm. Serial ultrasound scans and MRI scans were not diagnostic, but microbiological specimens tested positive for the fungus Scedosporium apiospermum The renal transplant graft-which was failing-was removed, allowing him to cease immunosuppression. He then underwent a resection of the lesion and reconstruction with a split thickness skin graft. Analysis of the specimen revealed fibrosis, granulomatosis and a collection of S. apiospermum He was started on voriconazole which, in conjunction with his surgical resection, appears to have kept the disease at bay. With increasing numbers of solid organ transplants and improved survival, this case highlights the growing burden of rare, opportunistic infections, the difficulty in diagnosis and the need for specialist intervention.

Epidemiology and clinical presentation of canine distemper disease in dogs and ferrets in Australia, 2006-2014.

OBJECTIVE: To determine the status and distribution of distemper in Australian dogs and ferrets. DESIGN: Retrospective case series. METHODS: Cases were identified via a national voluntary disease reporting system, veterinarian groups and a national laboratory database. The geographic distribution, seasonal distribution, signalment and clinical presentation of cases were described using maps and frequency distributions. RESULTS: A total of 48 individually affected dogs and ferrets in 27 case groups were identified, including eight confirmed case groups (> one individual). Confirmed cases were more common in summer and on the central coast of New South Wales and southern Victoria, and occurred exclusively in young, unvaccinated dogs. For dogs there was no obvious sex predilection. A mortality rate of 100% in ferrets and up to 77% in dogs was estimated. Neurological, gastrointestinal and respiratory were the most commonly reported systems affected in dogs and ferrets. There was no evidence that any large, unreported outbreaks occurred during the study period. CONCLUSIONS: Continuation of vaccination against canine distemper virus is justified within Australia, particularly for younger dogs. Veterinarians should continue to consider distemper in their differential diagnosis of cases with neurological, gastrointestinal and respiratory presentation.

The NAE inhibitor pevonedistat (MLN4924) synergizes with TNF-α to activate apoptosis.

Predicting and understanding the mechanism of drug-induced toxicity is one of the primary goals of drug development. It has been hypothesized that inflammation may have a synergistic role in this process. Cell-based models provide an easily manipulated system to investigate this type of drug toxicity. Several groups have attempted to reproduce in vivo toxicity with combination treatment of pharmacological agents and inflammatory cytokines. Through this approach, synergistic cytotoxicity between the investigational agent pevonedistat (MLN4924) and TNF-α was identified. Pevonedistat is an inhibitor of the NEDD8-activating enzyme (NAE). Inhibition of NAE prevents activation of cullin-RING ligases, which are critical for proteasome-mediated protein degradation. TNF-α is a cytokine that is involved in inflammatory responses and cell death, among other biological functions. Treatment of cultured cells with the combination of pevonedistat and TNF-α, but not as single agents, resulted in rapid cell death. This cell death was determined to be mediated by caspase-8. Interestingly, the combination treatment of pevonedistat and TNF-α also caused an accumulation of the p10 protease subunit of caspase-8 that was not observed with cytotoxic doses of TNF-α. Under conditions where apoptosis was blocked, the mechanism of death switched to necroptosis. Trimerized MLKL was verified as a biomarker of necroptotic cell death. The synergistic toxicity of pevonedistat and elevated TNF-α was also demonstrated by in vivo rat studies. Only the combination treatment resulted in elevated serum markers of liver damage and single-cell hepatocyte necrosis. Taken together, the results of this work have characterized a novel synergistic toxicity driven by pevonedistat and TNF-α.

Oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA), a hidden resistant mechanism among clinically significant isolates in the Wessex region/UK.

PURPOSE: Methicillin-resistant Staphylococcus aureus (MRSA) is defined as S. aureus genetically having the mecA or mecC genes or phenotypically showing minimum inhibitory concentration (MIC) of oxacillin higher than 2 mg/L. However, recently, cefoxitin/oxacillin-susceptible mecA-positive S. aureus (OS-MRSA) has been reported worldwide. Little is known about the prevalence and virulence of these strains among clinically significant isolates in the UK. The aims were to (1) investigate the prevalence of OS-MRSA in seven major hospitals in the Wessex region/UK from a cohort of 500 clinically significant phenotypically identified MSSA isolates, (2) genetically characterise OS-MRSA strains by pulsed-field gel electrophoresis (PFGE) and compare these to common UK epidemic strains; and (3) to determine Panton-Valentine leukocidin (PVL; lukFS) gene carriage rates among these isolates. RESULTS: OS-MRSA was found in six isolates (1.2 %) of phenotypically identified and reported MSSA isolates by conventional methods. PFGE showed OS-MRSA strains to be genetically diverse and distinct from the common UK epidemic strains EMRSA-15 and EMRSA-16. None of these OS-MRSA stains carried the genes encoding PVL; however, overall positivity rate for PVL was 4.4 %, much higher than the nationally reported rates of 2 % in the UK. CONCLUSION: There are still many unknowns regarding phenotypic and/or genetic characterization of the emerging OS-MRSA isolates in the UK and worldwide. Data regarding their epidemiology and optimal therapy for infection are limited and need further investigation not only in the UK, but also worldwide, as it is likely to have an impact on the empirical treatment of S. aureus infections.

Increased levels of thiols protect antimony unresponsive Leishmania donovani field isolates against reactive oxygen species generated by trivalent antimony.

The current trend of antimony (Sb) unresponsiveness in the Indian subcontinent is a major impediment to effective chemotherapy of visceral leishmaniasis (VL). Although contributory mechanisms studied in laboratory-raised Sb-R parasites include an up-regulation of drug efflux pumps and increased thiols, their role in clinical isolates is not yet substantiated. Accordingly, our objectives were to study the contributory role of thiols in the generation of Sb unresponsiveness in clinical isolates. Promastigotes were isolated from VL patients who were either Sb responsive (n=2) or unresponsive (n=3). Levels of thiols as measured by HPLC and flow cytometry showed higher basal levels of thiols and a faster rate of thiol regeneration in Sb unresponsive strains as compared with sensitive strains. The effects of antimony on generation of reactive oxygen species (ROS) in normal and thiol-depleted conditions as also their H2O2 scavenging activity indicated that in unresponsive parasites, Sb-mediated ROS generation was curtailed, which could be reversed by depletion of thiols and was accompanied by a higher H2O2 scavenging activity. Higher levels of thiols in Sb-unresponsive field isolates from patients with VL protect parasites from Sb-mediated oxidative stress, thereby contributing to the antimony resistance phenotype.

Slc11a1 (formerly Nramp1) polymorphisms and susceptibility to post-transplant lymphoproliferative disease following pediatric liver transplantation.

BACKGROUND: Polymorphisms of the solute carrier family 11 member 1 (Slc11a1) gene have previously been associated with susceptibility to infectious disease, anti-tumor defenses, and autoimmune diseases. We postulated that polymorphisms of the gene may also be associated with susceptibility to post-transplant lymphoproliferative disease (PTLD), a disease thought to be related to an impaired immune response to Epstein-Barr virus (EBV) in immunosuppressed patients. METHODS: Whole blood samples were obtained from 45 pediatric patients who underwent liver transplantation. Polymerase chain reaction (PCR) was used to amplify a 3' region of the gene that includes an exon 15 single-nucleotide substitution (referred to as D543N) and a 4-bp deletion polymorphism (referred to as 3'-UTR). PCR products were digested using AvaII and FokI restriction enzymes for the D543N and 3'-UTR polymorphisms, respectively. PTLD disease status and EBV virus serum titers of all patients were obtained from hospital records. RESULTS: Six of the 45 pediatric transplant recipients developed PTLD. An association was found between 3'-UTR polymorphisms of Slc11a1 and incidence of PTLD after liver transplantation (P = 0.005). In addition, post-transplant serum EBV titers were higher (P = 0.009) for recipients with certain Slc11a1 polymorphisms. No association was found between the D543N polymorphism and incidence of PTLD. CONCLUSION: 3'-UTR polymorphisms of the Slc11a1 gene appear to be associated with susceptibility to PTLD and the immune response to EBV in pediatric liver transplant recipients. Genotyping of pediatric patients undergoing liver transplantation may enable early identification of patients at high risk for developing high EBV titers and/or PTLD.

Isolation and partial characterisation of a putative monoterpene synthase from Melaleuca alternifolia.

Melaleuca alternifolia (Cheel) is an Australia native tree harvested for its monoterpene-rich, essential oil. Monoterpene synthases (E.C. 4.2.3.20) were partially purified from the flush growth of the commercially important, high terpinen-4-ol chemotype of M. alternifolia. The purified fractions produced an acyclic monoterpene, linalool that is not present in the essential oil. To further characterise the monoterpene synthase, a cDNA library was constructed and 500 expressed sequence tags (ESTs) were sequenced to isolate putative terpene synthases. A single clone with similarity to the TspB gene sub-family of angiosperm monoterpene and isoprene synthases was isolated but was truncated at the 5' end. This single clone was used to design a probe for a cDNA library and was applied to isolate a full-length clone. This gene encoded a polypeptide 583 amino acids in length (67 kDa) including a putative transit peptide. Heterologous expression of the gene in Escherichia coli and subsequent assay of the recombinant enzyme did not result in the production of terpinen-4-ol, the major constituent of tea tree oil, or of its precursor sabinene hydrate. Significant quantities of linalool were observed in these assays, and in the assays of monoterpene synthase activity of a native enzyme in vitro, but the racemic nature of the linalool means that it may have a non-enzymatic origin.

To fix or not to fix: the role of 2-phenoxyethanol in rabbit, Oryctolagus cuniculus, chin gland secretion.

The European rabbit (Oryctolagus cuniculus) uses the secretion of the chin gland to maintain dominance hierarchies in the wild. Recent work has investigated changes in the secretion when social status is manipulated in the rabbit. When a rabbit becomes dominant, a new compound appears in his secretion, 2-phenoxyethanol. This compound is used as a fixative in the perfume industry. This study investigates whether the compound performs a similar function in the secretion of the rabbit. 2-Phenoxyethanol is not detected olfactorially by rabbits, and slows the release rate of some of the compounds that occur naturally in rabbit chin gland secretion. We suggest that when a rabbit becomes dominant, he adds a fixative to his secretion so that his scent will persist in the environment and not dissipate. He will thus come to dominate the olfactory environment, in much the same way as he does the physical environment.

Investigations of aroma volatile biosynthesis under anoxic conditions and in different tissues of "Redchief Delicious" apple fruit (Malus domestica Borkh.).

Disks from different tissues were obtained from "Redchief Delicious" apple fruit (Malus domestica Borkh.) and analyzed for the ability to metabolize 1-pentanol as well as synthesize constitutive esters and alcohols under anoxic and aerobic conditions. The skin tissue displayed a greater capacity to synthesize pentanal, pentyl acetate, pentyl propionate, pentyl butyrate, and pentyl hexanoate than the hypanthial and carpellary tissues during incubation with 1-pentanol. With the exception of pentyl acetate and pentyl propionate biosynthesis, the hypanthial tissue synthesized these compounds at a higher rate than the carpellary tissue. Anoxia inhibited both constituent and 1-pentanol-derived ester biosynthesis. While anoxia inhibited ester biosynthesis, ethanol biosynthesis increased at a greater rate in tissue disks held under these conditions. Biosynthesis of 1-butanol, 2-methyl-1-butanol, and 1-hexanol was greater in tissue disks held in air during the first part of the measurement period and dropped off more rapidly than those transpiring in tissue disks held under anoxic conditions. The biosynthetic rates of all esters, both constituent and 1-pentanol-derived, increased as a result of air exposure. While hypoxic or anoxic conditions may promote ethanol synthesis, these conditions also appear to inhibit the formation of the ethanol-derived esters partially responsible for the off-flavor in apples attributed to ultralow O(2) controlled atmosphere storage.

Semiochemicals and social signaling in the wild European rabbit in Australia: I. Scent profiles of chin gland secretion from the field.

The European rabbit (Oryctolagus cuniculus) uses the secretion of the chin gland in the maintenance of social status. Previous work has concentrated on secretion collected directly from the animal. In this study, the analysis was conducted by collecting scent marks made by free-ranging animals. Scent marks were found to be concentrated at the center of the area controlled by a social group, and at the boundaries between two adjacent social groups. Only the mark from dominant animals could be identified. Marks were also collected from the skin of rabbits, where they had been placed by the dominant individual. The mark found on the head of a subordinate animal may, in the future, be used to identify the dominant animal of the social group, who placed the mark.

Semiochemicals and social signaling in the wild European rabbit in Australia: II. Variations in chemical composition of chin gland secretion across sampling sites.

The volatile components of the chin gland secretion of the wild European rabbit, Oryctolagus cuniculus (L.), were investigated with the use of gas chromatography. Studies of the chemical nature of this secretion by previous workers demonstrated that it was important in the maintenance of social structure in this species. This study identified 34 different volatile components that consist primarily of aromatic and aliphatic hydrocarbons. Especially common are a series of alkyl-substituted benzene derivatives that provide most of the compound diversity in the secretion. Samples of chin gland secretion collected from animals at three different geographical locations, separated by more than 100 km, showed significant differences in composition. This work suggests that variation among populations needs to be considered when undertaking semiochemical research. Alternate nonparametric methods are also used for the analysis of chromatographic data.

Identifying regulators of transcription in an obligate intracellular pathogen: a metal-dependent repressor in Chlamydia trachomatis.

A prominent feature exhibited by Chlamydia trachomatis growing in an iron-limiting environment is a differential pattern of protein expression. In many bacteria, iron-responsive proteins are regulated at the level of transcription by a family of repressors resembling the Escherichia coli ferric uptake regulator (Fur) protein. Although the chlamydial genome sequencing project did not unveil an obvious Fur homologue, a detailed examination indicated five unassigned open reading frames (ORFs) that would encode products with limited sequence homology to Fur. In this report, each chlamydial ORF was engineered in E. coli, and recombinant proteins were examined for functional characteristics resembling Fur. A Fur-specific polyclonal antiserum revealed that the protein encoded by ORF CT296 shares antigenic cross-recognition. Moreover, this protein forms dimers in solution in a fashion analogous to E. coli Fur. Further studies confirmed that the product of ORF CT296 is able to (i) complement Fur activity in a mutant strain of E. coli; and (ii) specifically bind to a 19 bp consensus sequence found in promoters of iron-regulated genes in E. coli. We propose a designation of dcrA (divalent cation-dependent regulator A) for ORF CT296, which encodes a protein distantly related to E. coli Fur. DcrA represents the first repressor described for this obligate intracellular bacterium.

The bacterial multiple antibiotic resistant (Mar) phenotype leads to increased tolerance to tea tree oil.

Mutants of Escherichia coil strain AG100 exhibiting the multiple antibiotic resistance (Mar) phenotype demonstrated a greater level of tolerance to tea tree oil (TTO) compared with the parent strain. The ability of TTO to kill all E. coil strains studied was greater at 37 than at 30 degrees C. Growth of parent strain AG100 in the presence of salicylate, which induces the mar operon leading to the Mar phenotype, also increased tolerance to TTO. Escherichia coli Mar mutant YL1 demonstrated greater tolerance to antimicrobial terpenes found in TTO and did not leak K+ as rapidly in the presence of TTO when compared with its parent strain AG100. Attempts to isolate Mar mutants of Staphylococcus aureus using tetracycline gradients proved unsuccessful. However, when grown in the presence of salicylate, S. aureus strain BB255 demonstrated greater tolerance to TTO and did not leak K+ as rapidly in the presence of TTO compared with this strain grown without additions. This evidence demonstrates that bacterial Mar phenotypes increase tolerance to the killing action of TTO. This work also adds indirect evidence that the target of TTO is the cell membrane.

Improved method for the rapid determination of terpenoid aldehydes in cotton.

A simple, rapid method for the extraction of cotton terpenoid aldehydes from green tissues and seed is described. Samples were treated by ultrasonification with acidified acetonitrile/water followed by centrifugation. The resulting extract was injected directly onto a C(18) HPLC column and no sample concentration or further cleanup steps were required. The level of gossypol, the most labile of the target analytes, decreased by only 2% after 12 h of storage at room temperature, thus enabling automated analysis of individual terpenoid aldehydes by HPLC. The method gives excellent reproducibility and enables large numbers of samples to be screened quickly and accurately.

Fate of apple peel phenolics during cool storage.

Consumption of certain phenolics in the diet is considered beneficial to human health. In this study, individual phenolics were measured by diode-array HPLC at monthly intervals in the peel of Granny Smith, Lady Williams, and Crofton apple cultivars stored in air at 0 degrees C for 9 months. The concentrations of total phenolics significantly differed among the cultivars examined, with Lady Williams peel having significantly more phenolics (over 4000 microg x g(-1) peel fresh weight) than Crofton (2668 microg x g(-1) peel fresh weight) and Granny Smith, which had the lowest concentration of total phenolics (1275 microg x g(-1) peel fresh weight). There were also significant differences in individual phenolics among cultivars and during storage. Quercetin glycosides were the only flavonols identified, with quercetin rhamnoglucoside being the most abundant phenolic in the peel. Chlorogenic acid was the major cinnamic acid derivative, with high concentrations, up to 412 microg x g(-1)) peel fresh weight, in Crofton peel. A pre-storage diphenylamine (DPA) treatment had few significant effects on peel phenolic metabolism. Where differences did occur, fruit treated with DPA retained higher concentrations of total peel phenolics during storage than fruit not treated with DPA. Storage of all cultivars for up to 9 months in air at 0 degrees C induced few significant changes in the peel phenolic concentrations. This indicates that phenolic metabolism in apple peel is relatively stable, and the health benefits of phenolics in apple peel should be maintained during long-term storage.

Xanthine oxidase inhibitory activity of selected Australian native plants.

Twenty-eight extracts from 17 species of Australian native plants traditionally used as general anti-inflammatory medicines by Australian Aboriginal people were examined for inhibition of the enzyme xanthine oxidase (XO). The extracts from nine species were found to have more than 25% inhibition at a concentration of 100 microg/ml in the assay mixture. Extracts from three species Clerodendrum floribundum R. Br. (Verbenaceae), Eremophila maculata (Ker Gawler) (Myoporaceae) and Stemodia grossa Benth. (Scrophulariaceae) showed the greatest activity with inhibitions of 84, 61 and 57%, respectively, at 50 microg/ml, with four other species having more than 40% inhibitory activity at this concentration.