Proteogenomic analysis of bacteria and archaea: a 46 organism case study

Experimental evidence is increasingly being used to reassess the quality and accuracy of genome annotation. Proteomics data used for this purpose, called proteogenomics, can alleviate many of the problematic areas of genome annotation, e.g. short protein validation and start site assignment. We performed a proteogenomic analysis of 46 genomes spanning eight bacterial and archaeal phyla across the tree of life. These diverse datasets facilitated the development of a robust approach for proteogenomics that is functional across genomes varying in %GC, gene content, proteomic sampling depth, phylogeny, and genome size. In addition to finding evidence for 682 novel proteins, 1336 new start sites, and numerous dubious genes, we discovered sites of post-translational maturation in the form of proteolytic cleavage of 1175 signal peptides. The number of novel proteins per genome is highly variable (median 7, mean 15, stdev 20). Moreover, comparison of novel genes with the current genes did not reveal any consistent abnormalities. Thus, we conclude that proteogenomics fulfills a yet to be understood deficiency in gene prediction. With the adoption of new sequencing technologies which have higher error rates than Sanger-based methods and the advances in proteomics, proteogenomics may become even more important in the future.     

Self-assembly in tetrameric 1:1 silver(I) halide:tri-p-tolylphosphine complexes: An in-depth structural investigation

The reaction of silver(I) bromide with tri(p-tolyl)phosphine in MeCN solution in 1:1 molar ratios resulted in a complexes of the formula [AgBr{P(4-MeC₆H₄)₃}]₄. This compound has a tetrameric structure with a concave coordination polyhedron, in between a cube and a stella quadrangula. Weak silver-silver interactions were observed. The current compound is compared to the Cl and I analogs using distance-distance plots. The silver-silver interactions seem to dominate the geometry of these tetrameric type of complexes.     

Production,purification, and properties of β-glucosidase from Candida wickerhamii

Summary Candida wickerhamii growing on cellobiose produced -glucosidase with high activity against -nitrophenyl glucoside (PNPG) but low activity against cellobiose. -glucosidase production was constitutive, and was repressed by -glucosides and glucose. -glucosides containing an aromatic moiety in the aglycon were the best substrates for -glucosidase indicating that the enzyme is an aryl--glucosidase. A -glucosidase from C. wickerhamii cells was purified by (NH₄)₂SO₄ precipitation, dialysis, ion-exchange chromatography and gel filtration. The purified enzyme was homogeneous as shown by sodium-dodecyl-sulphate polyacrylamide gel electrophoresis and discontinuous gel electrophoresis. The purified enzyme hydrolysed PNPG but not cellobiose. The K_m of the enzyme was 0.185 mM. Glucose inhibited the enzyme competitively and the K_i was 7.5 mM. The apparent molecular mass was 97,000. The optimum pH and temperature for enzyme activity were between pH 7 and 7.4 and 40°C respectively. At temperatures of 45°C and greater the enzyme was inactivated. The activation energy of the enzyme was 29.4 kJ · mol^-1.     

A review of <Emphasis Type="Italic">Solanum mauritianum</Emphasis> biocontrol: prospects,promise and problems: a way forward for South Africa and globally

The invasive tree Solanum mauritianum Scopoli remains one of the world’s most widespread environmental weeds. Despite biocontrol providing one of the few viable long-term solutions to tackling S. mauritianum invasions globally, only South Africa and, more recently, New Zealand, have programmes in place. Ongoing biocontrol efforts against S. mauritianum are reviewed here with particular reference to South Africa. The South African programme has suffered a troubled history, with considerable research efforts culminating in the eventual release and establishment of only two insect agents, Gargaphia decoris Drake and Anthonomus santacruzi Hustache. The difficulties experienced have hindered research into new agents, causing apprehension in using biocontrol internationally. However, recent studies have demonstrated that biocontrol may be deserving of renewed investment, particularly within an integrated management context. In this review, we advocate for the revival of the S. mauritianum biocontrol programme in South Africa, and discuss possible avenues for future research internationally.     

Comparing glycaemic benefits of Active Versus passive lifestyle Intervention in kidney Allograft Recipients (CAVIAR): study protocol for a randomised controlled trial

BackgroundLifestyle modification is widely recommended to kidney allograft recipients post transplantation due to the cardiometabolic risks associated with immunosuppression including new-onset diabetes, weight gain and cardiovascular events. However, we have no actual evidence that undertaking lifestyle modification protects from any adverse outcomes post transplantation. The aim of this study is to compare whether a more proactive versus passive interventional approach to modify lifestyle is associated with superior outcomes post kidney transplantation.Methods/designWe designed this prospective, single-centre, open-label, randomised controlled study to compare the efficacy of active versus passive lifestyle intervention for kidney allograft recipients early post transplantation. A total of 130 eligible patients, who are stable, nondiabetic and between 3 and 24 months post kidney transplantation, will be recruited. Randomisation is being undertaken by random block permutations into passive (n = 65, leaflet guidance only) versus active lifestyle modification (n = 65, supervised intervention) over a 6-month period. Supervised intervention is being facilitated by two dietitians during the 6-month intervention period to provide continuous lifestyle intervention guidance, support and encouragement. Both dietitians are accredited with behavioural intervention skills and will utilise motivational aids to support study recruits randomised to active intervention. The primary outcome is change in abnormal glucose metabolism parameters after 6 months of comparing active versus passive lifestyle intervention. Secondary outcomes include changes in a wide array of cardiometabolic parameters, kidney allograft function and patient-reported outcome measures. Long-term tracking of patients via data linkage to electronic patient records and national registries will facilitate long-term comparison of outcomes after active versus passive lifestyle intervention beyond the 6-month intervention period.DiscussionThis is the first randomised controlled study to investigate the benefits of active versus passive lifestyle intervention in kidney allograft recipients for the prevention of abnormal cardiometabolic outcomes. In addition, this is the first example of utilising behaviour therapy intervention post kidney transplantation to achieve clinically beneficial outcomes, which has potential implications on many spheres of post-transplant care.

Trial registration

This study was registered with the Clinical Trials Registry on 27 August 2014 (ClinicalTrials.org Identifier: {"type":"clinical-trial","attrs":{"text":"NCT02233491","term_id":"NCT02233491"}}NCT02233491).     

Autoantibodies and monoclonal antibodies in the purification and molecular characterization of neurotransmitter receptors

The combination of immunological advances with membrane receptor research has promoted rapid progress in the molecular characterization of neurotransmitter receptor molecules. We have to date produced monoclonal antibodies to β₁-, β₂-, and β₁-adrenergic, D₂-dopaminergic, and muscarinic receptors. In addition we have discovered that some allergic respiratory disease patients possess circulating autoantibodies to β₂-adrenergic receptors. These antireceptor antibodies in conjunction with specific receptor affinity reagents have allowed us to isolate, purify, and begin to characterize α- and β-adrenergic, dopaminergic, and muscarinic receptors. For example, immunoprecipitation of turkey erythrocyte β₁ receptors with monoclonal antibodies yields a single polypeptide M_r 65–70 K. In contrast, purification of β₂-adrenergic receptors using either autoantibodies or monoclonal antibodies yields a receptor species with a subunit of M_r 55–59 K. Autoantibodies to β₂ receptors demonstrate a 50–100% homology among β₂ receptors from humans to rats, whereas monoclonal antibody FV-104 recognizes a determinant in the ligand binding site of all β₁ and β₂ receptors tested to date. These data suggest that β₁- and β₂-adrenergic receptors may have evolved from a common ancestor, perhaps by gene duplication.     

Cell cycle-specific changes in β-adrenergic receptor concentrations in C6 glioma cells

The concentration of β-adrenergic receptors in synchronized C6 cells is lowest during mitosis and G₁ (1000–2000 receptors/cell). A rapid increase in β-receptor concentration occurs in early S phase to 9000 receptors/cell, followed by a decrease during G₂ to the low concentration found at mitosis. In non-synchronized C6 cell populations, mitotic cells have one-half of the average β-receptor concentration of the population as a whole, confirming the observations made with synchronized cells.     

Effect of iron compounds on nodulation and growth ofTrifolium pratense L. In water culture

Summary Different iron compounds were compared for use in nutrient solutions for nodulation studies withTrifolium pratense L. (Montgomery Red). Iron(III)-EDTA was found to be the best source of iron when taking both nodulation and yield into account. The possibility of toxic effects under certain experimental conditions can, however, not be excluded.