SNaPe: a versatile method to generate multiplexed protein fusions using synthetic linker peptides for in vitro applications

Understanding the structure and function of protein complexes and multi‐domain proteins is highly important in biology, although the in vitro characterization of these systems is often complicated by their size or the transient nature of protein/protein interactions. To assist in the characterization of such protein complexes, we have developed a modular approach to fusion protein generation that relies upon S ortase‐mediated and Na tive chemical ligation using synthetic Pe ptide linkers (SNaPe) to link two separately expressed proteins. In this approach, we utilize two separate linking steps – sortase‐mediated and native chemical ligation – together with a library of peptide linkers to generate libraries of fusion proteins. We have demonstrated the viability of SNaPe to generate libraries from fusion protein constructs taken from the biosynthetic enzymes responsible for late stage aglycone assembly during glycopeptide antibiotic biosynthesis. Crucially, SNaPe was able to generate fusion proteins that are inaccessible via direct expression of the fusion construct itself. This highlights the advantages of SNaPe to not only access fusion proteins that have been previously unavailable for biochemical and structural characterization but also to do so in a manner that enables the linker itself to be controlled as an experimental parameter of fusion protein generation. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Self-help materials for the prevention of smoking relapse: study protocol for a randomised controlled trial

ABSTRACT: BACKGROUND: Most people who stop smoking successfully for a few weeks will return to smoking again in the medium term. There are few effective interventions to prevent this relapse and none used routinely in clinical practice. A previous exploratory meta-analysis suggested that self-help booklets may be effective but requires confirmation. This trial aims to evaluate the effectiveness and cost-effectiveness of a set of self-help educational materials to prevent smoking relapse in the NHS Stop Smoking Service. METHODS: This is an open, randomised controlled trial. The target population is carbon monoxide (CO) verified quitters at 4 weeks in the NHS stop smoking clinic (total sample size N=1,400). The experimental intervention tested is a set of 8 revised Forever Free booklets, including an introduction booklet and more extensive information on all important issues for relapse prevention. The control intervention is a leaflet that has no evidence to suggest it is effective but is currently given to some patients using NHS stop smoking services. Two follow-up telephone interviews will be conducted at 3 and 12 months after quit date. The primary outcome will be prolonged abstinence from months 4-12 with no more than 5 lapses, confirmed by carbon monoxide test at 12 month assessment. The secondary outcomes will be 7-day self-report point prevalence abstinence at 3 months and 7-day biochemically confirmed point prevalence abstinence at 12 months. To assess cost-effectiveness, costs will be estimated from a health service perspective and the EQ-5D will be used to estimate the QALY (Quality Adjusted Life Year) gain associated with each intervention. The comparison of smoking abstinence rates (and any other binary outcomes) between the two trial arms will be carried out using odds ratio as the outcome statistic and other related statistical tests. Exploratory subgroup analyses, including logistic regression analyses with interaction terms, will be conducted to investigate possible effect modifying variables. DISCUSSION: The possible effect of self-help educational materials for the prevention of smoking relapse has important public health implications. Trial Registration: Current Controlled Trials ISRCTN36980856.     

Syn-Vivo Bioerosion of Nautilus by Endo- and Epilithic Foraminiferans (New Caledonia and Vanuatu)

A variety of syn-vivo bioerosion traces produced by foraminiferans is recorded in shells of Nautilus sampled near New Caledonia and Vanuatu. These are two types of attachment scars of epilithic foraminiferans and two forms of previously undescribed microborings, a spiral-shaped and a dendritic one, both most likely being the work of endolithic ''naked'' foraminiferans. Scanning electron microscopy of epoxy-resin casts of the latter revealed that these traces occur in clusters of up to many dozen individuals and potentially are substrate-specific. The foraminiferan traces are the sole signs of bioerosion in the studied Nautilus conchs, and neither traces of phototrophic nor other chemotrophic microendoliths were found. While the complete absence of photoautotrophic endoliths would be in good accordance with the life habit of Nautilus, which resides in aphotic deep marine environments and seeks shallower waters in the photic zone for feeding only during night-time, the absence of any microbial bioerosion may also be explained by an effective defence provided by the nautilid periostracum. Following this line of reasoning, the recorded foraminiferan bioerosion traces in turn would identify their trace makers as being specialized in their ability to penetrate the periostracum barrier and to bioerode the shell of modern Nautilus.     

Isothermal amplification and multimerization of DNA by Bst DNA polymerase

We have demonstrated the isothermal in vitro amplification and multimerization of several different linear DNA targets using only two primers and the strongly strand-displacing exonuclease-negative Bst DNA polymerase. This reaction has been termed linear target isothermal multimerization and amplification (LIMA). LIMA has been compared with cascade rolling-circle amplification and has been found to be less sensitive but to yield similar variable-length multimeric dsDNA molecules. Products from several different LIMA reactions were characterized by restriction analysis and partial sequence determination. They were found to be multimers of subsets of the target sequence and were not purely primer derived. The sensitivities with respect to target concentration of several different LIMA reactions were determined, and they varied from 0.01 amol to 1 fmol. The sensitivity and specificity of LIMA were further tested using E. coli genomic DNA, and the selective amplification of a transposon fragment was demonstrated. A successful strategy for reducing LIMA-dependent background DNA synthesis in rolling-circle amplification embodiments was devised. This entailed the affinity purification of circular DNA templates before amplification.     

Intrathecal Fas ligand infusion strengthens immunoprivilege of central nervous system and suppresses experimental autoimmune encephalomyelitis

Fas ligand (FasL) is an essential molecule strongly expressed in some immunoprivileged sites, but is expressed at very low levels in normal CNS. In this study, acute experimental autoimmune encephalomyelitis (EAE) was induced in Lewis rats with guinea pig myelin basic protein. Intrathecal infusion of recombinant FasL before EAE onset dose dependently suppressed acute EAE and alleviated pathological inflammation in lumbosacral spinal cord. This treatment greatly increased apoptosis in CNS inflammatory cells, but did not inhibit systemic immune response to myelin basic protein. Systemic administration of a similar dose of rFasL was ineffective. In vitro, encephalitogenic T cells were highly sensitive to rFasL-induced cell death, and activated macrophages were also susceptible. In addition, in vitro rFasL treatment potentiated the immunosuppressive property of rat cerebrospinal fluid. We conclude that intrathecal infusion of rFasL eliminated the initial wave of infiltrating T cells and macrophages, and therefore blocked the later recruitment of inflammatory cells into CNS. Although Fas receptor expression was observed on spinal cord neurons, astrocytes, and oligodendrocytes, no damage to these cells or to the myelin structure was detected after rFasL infusion.     

State of Brassica rapa photosynthetic membranes in microgravity

The structural characteristics of the photosynthetic apparatus of Brassica rapa plants grown on board the space shuttle Columbia (STS-87) for 15 days were examined using the methods of transmission electron microscopy and statistic programme STAT. Maintaining of the same growth conditions for control plants was realized with great accuracy using the Orbiter Environmental simulator in Kennedy Space Center. A grana number per a medial section 1.8 times decreased in microgravity. Considerable changes were also revealed in the grana structure in microgravity in comparison with th ground control, namely: 1/a greater diversity in the thylakoid length with granae and 2/ lateral shifting of the thylakoids lateral shifting of the thylakoids relative one to another. The previous mentioned pheomenon was found for 64% of the invested granae. Shifting of the thylakoids in the granae in microgravity led to increasing of the grana thylakoid surface exposed to a stroma. In addition, the volume of stromal thylakoids increased. The peculiarities in the photosynthetic apparatus structure in microgravity are supposed to be an evidence of decreasing in the light harvesting complex amount of photosystem II (PSII).     

Keimung verschieden alter Konidien von Aspergillus niger und Wachstum aus ihnen gezogener Mycelien.

Zusammenfassung 12–13 Jahre alte Konidien von 5 Aspergillus niger-Rassen keimten später als 12 Monate alte und junge, etwa 4 Tage alte, wobei die Versuchstemperatur grundsätzlich ohne Bedeutung war, falls sie Keimung gestattete.Verzögert war nach mikroskopischen Beobachtungen sowohl die der eigentlichen Keimung vorausgehende Quellung der Sporen, als auch die Keimung selbst.Die spätere Keimung der älteren Konidien beruhte zu einem geringen Teil auf stärkerer Austrocknung, die eine mechanische Wasseraufnahme erschwerte, in der Hauptsache jedoch war sie eine Folge des Alters, eine Alterserscheinung.Hatte Keimung stattgefundeu, so war kein Unterschied festzustellen in der Waschstumsstärke und der Konidienfruktifikation zwischen den Mycelien, die auf ungleichalterige Konidien zurückgingen; sie breiteten sich auf Nähragarplatten gleich schnell aus, bildeten auf Nährlösungen Decken von gleichem Gewicht und entwickelten Konidien von nor maler Form und Farbe.Die Untersuchungen wurden 1943/44 in der pharmakognostischen Abteilung der Botanischen Anstalten Breslau durchgeführt.     

Bioremediation of Polyaromatic Hydrocarbon-Contaminated Sediments in Aerated Bioslurry Reactors

Treatment of dredged sediments contaminated by polyaromatic hydrocarbons (PAHs) is a significant problem in the New York/New Jersey (NY/NJ) Harbor. 0.5 m³-scale slurry-phase bioreactors were used to determine whether bioaugmentation with a PAH-degradative bacterial consortium, or with the salt marsh grass S. alterniflora, could enhance the biodegradation of PAHs added to dredged estuarine sediments from the NY/NJ Harbor. The results were compared to biodegradation effected by the indigenous sediment microbial community. Sediments were diluted 1:1 in tap water and spiked to a final concentration of 20 mg/kg dry weight sediment of phenanthrene, anthracene, acenaphthene, fluorene, fluoranthene, and pyrene. The sediment slurry was then continuously sparged with air over 3 months. In all bioreactors a rapid reduction of greater than 95% of the initial phenanthrene, acenaphthene, and fluorene occurred within 14 days. Pyrene and fluoranthene reductions of 70 to 90% were achieved by day 77 of treatment. Anthracene was more recalcitrant and reductions ranged from 30 to 85%. Separate experiments showed that the sediment microbial communities mineralized ¹⁴C-pyrene and ¹⁴C-phenanthrene. PAH degradation, and the number of phenanthrene-degrading bacteria, were not enhanced by microbial or plant bioaugmentation. These data demonstrate that bioaugmentation is not required to effect efficient remediation of PAH-contaminated dredged sediments in slurry-phase bioreactors.