Characterization of the bifunctional cytochrome c reductase-processing peptidase complex from potato mitochondria

In potato, cytochrome c reductase, a protein complex of the respiratory chain, exhibits processing activity toward mitochondrial precursor proteins. One of the two cooperating components of the processing peptidase was shown to be identical with subunit III of the complex. Here we report that two additional proteins of the complex (subunit I and II) share 40-50% sequence identity with the processing enhancing protein, the other component of the processing enzyme from fungi and mammals. Thus the composition and structure of the complex integrated processing peptidase seems to be different from its fungal and mammalian counterparts. Cytochrome c reductase from potato is extraordinarily stable, and separation of subunit III from the complex leads to aggregation of the remaining subcomplex and irreversible loss of processing activity. Expression of the three high molecular weight subunits of the complex allowed purification of each individual protein. Neither the individual subunits nor their combinations are active in in vitro processing assays suggesting that they may need the structural support of the complex for activity. In contrast to mitochondrial processing peptidases from other organisms, the purified potato enzyme is active in the presence of high salt (above 1 M NaCl) and works efficiently without addition of metal ions. These data indicate that potato cytochrome c reductase is a bifunctional protein complex with unique features. Possibly, there is a more general evolutionary relationship between cytochrome c reductases and mitochondrial processing peptidases than hitherto assumed

Average nucleotide identity of genome sequences supports the description of Rhizobium lentis sp. nov., Rhizobium bangladeshense sp. nov. and Rhizobium binae sp. nov. from lentil (Lens culinaris) nodules

Rhizobial strains isolated from effective root nodules of field-grown lentil (Lens culinaris) from different parts of Bangladesh were previously analysed using sequences of the 16S rRNA gene, three housekeeping genes (recA, atpD and glnll) and three nodulation genes (nodA, nodC and nodD), DNA fingerprinting and phenotypic characterization. Analysis of housekeeping gene sequences and DNA fingerprints indicated that the strains belonged to three novel clades in the genus Rhizobium. In present study, a representative strain from each clade was further characterized by determination of cellular fatty acid compositions, carbon substrate utilization patterns and DNA DNA hybridization and average nucleotide identity (ANI) analyses from whole-genome sequences. DNA DNA hybridization showed 50-62 % relatedness to their closest relatives (the type strains of Rhizobium etli and Rhizobium phaseoh) and 50-60 % relatedness to each other. These results were further supported by ANI values, based on genome sequencing, which were 87-92 % with their close relatives and 88-89 % with each other. On the basis of these results, three novel species, Rhizobium lentis sp. nov. (type strain BLR27(T)=LMG 28441(T)=DSM 29286(T)), Rhizobium bangladeshense sp. nov. (type strain BLR175(T)=LMG 28442(T)=DSM 29287(T)) and Rhizobium binae sp. nov. (type strain BLR195(T)=LMG 28443(T)=DSM 29288(T)), are proposed. These species share common nodulation genes (nodA, nodC and nodD) that are similar to those of the symbiovar viciae

Using a multi-level tailored design process to develop a customer satisfaction survey for university evaluation

A multi-level procedure is described in order to develop a total quality management survey tool in the field of engineering academia. As a first step a review of available evaluation tools for universities is conducted, resulting in over 150 items used for evaluation purposes. Secondly all dimensions of educational evaluation used in previous research are summarized, resulting in 15 dimensions. In a third step, items are assigned to the dimensions, overlapping items were combined or removed, and item content and dimensions were adjusted to the specific conditions of the target faculty. Fourthly, the resulting twelve dimensions were used in first, investigative interviews in the target population. Results indicate that eleven dimensions sufficiently mapped all aspects of evaluation. After revising the items to improve understanding in a fifth step cognitive pretests were conducted. The final revision resulted in 83 items assigned to eleven dimensions

Presentations of Wess-Zumino-Witten Fusion Rings

The fusion rings of Wess-Zumino-Witten models are re-examined. Attention is drawn to the difference between fusion rings over Z (which are often of greater importance in applications) and fusion algebras over C. Complete proofs are given characterising the fusion algebras (over C) of the SU(r+1) and Sp(2r) models in terms of the fusion potentials, and it is shown that the analagous potentials cannot describe the fusion algebras of the other models. This explains why no other representation-theoretic fusion potentials have been found. Instead, explicit generators are then constructed for general WZW fusion rings (over Z). The Jacobi-Trudy identity and its Sp(2r) analogue are used to derive the known fusion potentials. This formalism is then extended to the WZW models over the spin groups of odd rank, and explicit presentations of the corresponding fusion rings are given. The analogues of the Jacobi-Trudy identity for the spinor representations (for all ranks) are derived for this purpose, and may be of independent interest.Comment: 32 pages, 3 figures, added references, minor additions to text. To be published in Rev. Math. Phy

Simultaneously Optimizing Dose and Schedule of a New Cytotoxic Agent

Traditionally, phase I clinical trial designs determine a maximum tolerated dose of an experimental cytotoxic agent based on a fixed schedule, usually one course consisting of multiple administrations, while varying the dose per administration between patients. However, in actual medical practice patients often receive several courses of treatment, and some patients may receive one or more dose reductions due to low-grade (non-dose limiting) toxicity in previous courses. As a result, the overall risk of toxicity for each patient is a function of both the schedule and the dose used at each adminstration. We propose a new paradigm for Phase I clinical trials that allows both the dose per administration and the schedule to vary, making treatment two-dimensional. We provide an outcome-adaptive Bayesian design that simultaneously optimizes both dose and schedule in terms of the overall risk of toxicity, based on time-to-toxicity outcomes. The method is illustrated with a trial of an agent hypothesized to prolong cancer remission after allogeneic bone marrow transplantation, and a simulation study in the context of this trial is presented

Energy and Charged Particle Flow in 10.8 A GeV/c Au+Au Collisions

Experimental results and a detailed analysis are presented of the transverse energy and charged particle azimuthal distributions measured by the E877 collaboration for different centralities of Au+Au collisions at a beam momentum of 10.8 A GeV/c. The anisotropy of these distributions is studied with respect to the reaction plane reconstructed on an event-by-event basis using the transverse energy distribution measured by calorimeters. Results are corrected for the reaction plane resolution. For semicentral events we observe directed flow signals of up to ten percent. We observe a stronger anisotropy for slow charged particles. For both the charged particle and transverse energy distributions we observe a small but non zero elliptic anisotropy with the major axis pointing into the reaction plane. Combining the information on transverse energy and charged particle flow we obtain information on the flow of nucleons and pions. The data are compared to event generators and the need to introduce a mean field or nucleon-nucleon potential is discussed.Comment: RevTex, 25 pages, 13 figures included as one Postscript file, submitted to Phys. Rev.

Surfaces, depths and hypercubes: Meyerholdian scenography and the fourth dimension

An appreciation of Meyerhold’s engagement with theatrical space is fundamental to understanding his directorial and pedagogic practice. This article begins by establishing Meyerhold’s theoretical and practical engagement with theatre as a fundamentally scenographic process, arguing for a reconceptualisation of the director as ‘director-scenographer’. Focusing on the construction of depth and surface in Meyerholdian theatre, the article goes on to identify trends in the director’s approach to space, with an emphasis on the de-naturalisation of depth on stage. This denaturalisation is seen as taking three forms: the rejection of depth as a prerequisite in theatrical space, the acknowledgement of the two-dimensional surface as surface, and the restructuring of depth space into a series of restricted planes. The combination of these trends indicates a consistent and systematic process of experimentation in Meyerhold’s work. In addition, this emphasis on depth and surface, and the interaction between the two, also highlights the contextualisation of Meyerhold’s practice within the visual, philosophical and scientific culture of the early twentieth century, echoing the innovations in n-dimensional geometry and particularly, the model of the fourth spatial dimension seen in the work of Russian philosopher P. D. Ouspensky

Using Joint Utilities of the Times to Response and Toxicity to Adaptively Optimize Schedule–Dose Regimes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/101836/1/biom12065-sm-0001-SuppData.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/101836/2/biom12065.pd

Two-dimensional blue native/blue native polyacrylamide gel electrophoresis for the characterization of mitochondrial protein complexes and supercomplexes.

Blue native polyacrylamide gel electrophoresis (BN-PAGE) employs the dye Coomassie for the labeling of proteins and protein complexes under native conditions. Electrophoresis under native conditions subsequently allows resolution of proteins and protein complexes according to their molecular mass. BN-PAGE can be combined with second gel dimensions. Best known is the two-dimensional (2D)-BN/sodium dodecyl sulfate (SDS)-PAGE system, which allows resolution of subunits of protein complexes. A 2D-BN/BN-PAGE system was developed that proved useful for investigating the substructure of protein complexes and protein supercomplexes. The basis of this 2D system is a variation of the conditions used for the two BN gel dimensions. Here, we present a basic protocol for the analysis of mitochondrial fractions by 2D-BN/BN-PAGE. Because both el dimensions are carried out under native conditions, the 2D-BN/BN system is compatible with in-gel enzyme activity staining

Comprehensive characterization of molecular interactions based on nanomechanics

Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6) Da) adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da) to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions