title: Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase

authors: Buddrus, Lisa

subjects: Science & Technology

abstract: Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophos­phate- and Mg2+ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P3221, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were Rwork = 0.246 (0.3671 in the highest resolution bin) and Rfree = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.

text: Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophos­phate- and Mg2+ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P3221, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were Rwork = 0.246 (0.3671 in the highest resolution bin) and Rfree = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.

year: 2018

title: Evaluating research – peer review team assessment and journal based bibliographic measures: New Zealand PBRF research output scores in 2006

authors: Anderson, David L.

subjects: bibliometrics

abstract: This paper concerns the relationship between the assessment of the research of individual academics by peer or expert review teams with a variety of bibliometric schemes based on journal quality weights. Specifically, for a common group of economists from New Zealand departments of economics the relationship between Performance-Based Research Fund (PBRF) Research Output measures for those submitting new research portfolios in 2006 are compared with evaluations of journal-based research over the 2000–2005 assessment period. This comparison identifies the journal weighting schemes that appear most similar to PBRF peer evaluations. The paper provides an indication of the ‘power or aggressiveness’ of PBRF evaluations in terms of the weighting given to quality. The implied views of PBRF peer review teams are also useful in assessing common assumptions made in evaluating journal based research.

text: Evaluating research – peer review team assessment and journal based bibliographic measures: New Zealand PBRF research output scores in 2006 This paper concerns the relationship between the assessment of the research of individual academics by peer or expert review teams with a variety of bibliometric schemes based on journal quality weights. Specifically, for a common group of economists from New Zealand departments of economics the relationship between Performance-Based Research Fund (PBRF) Research Output measures for those submitting new research portfolios in 2006 are compared with evaluations of journal-based research over the 2000–2005 assessment period. This comparison identifies the journal weighting schemes that appear most similar to PBRF peer evaluations. The paper provides an indication of the ‘power or aggressiveness’ of PBRF evaluations in terms of the weighting given to quality. The implied views of PBRF peer review teams are also useful in assessing common assumptions made in evaluating journal based research.

year: 2013

title: Portfolio of Compositions: Systematic composition of cross-genre hybrid music

authors: Mayall, Jeremy Mark

subjects: cross-genre hybrid music

abstract: The research focus of this PhD thesis is the development of a new technique for composing original musical compositions in which elements from different musical genres are hybridised. The innovative aspect of achieving balanced hybridity is the development of a systematic approach to selecting and synthesising or hybridising key musical elements across a range of different genres. The major component of this submission is a portfolio of nine original works with attached CD/DVD recordings. 

1. Tracking Forward for viola, backing track and video 
2. The Long White Cloud for chamber band and electronics 
3. ‘Colorless green ideas sleep furiously’ for orchestra 
4. Push for Miles for electric bass and backing track 
5. Norse Suite for viola and cello 
6. The Foggy Field a studio construction 
7. Into the Nocturnal Sunshine for flute, viola, cello, drums and electronics 
8. One Night, New Breath for taonga puoro, viola, drums and electronics 
9. Sketches of an Intergalactic Earworm for piano trio and boombox

The accompanying documentation clarifies, and contextualises the creation and presentation of these works; and illuminates the aesthetic underpinnings and compositional techniques developed and utilised as a part of this hybrid-genre compositional approach. The structure of the supporting exegesis is in two parts: the methodology of practice-based research, and reflective investigation. Part One (Chapters 1 and 2) is an introductory overview; an observation of the existing literature and related work, relevant creative practice in the composer’s previous work; and the compositional methodology – including an explanation of the genre matrix. Part Two (Chapters 3 to 12) analyses the use of genre, the balance of hybridity, and relevant compositional techniques utilised in the development of each individual piece.

text: Portfolio of Compositions: Systematic composition of cross-genre hybrid music The research focus of this PhD thesis is the development of a new technique for composing original musical compositions in which elements from different musical genres are hybridised. The innovative aspect of achieving balanced hybridity is the development of a systematic approach to selecting and synthesising or hybridising key musical elements across a range of different genres. The major component of this submission is a portfolio of nine original works with attached CD/DVD recordings. 

1. Tracking Forward for viola, backing track and video 
2. The Long White Cloud for chamber band and electronics 
3. ‘Colorless green ideas sleep furiously’ for orchestra 
4. Push for Miles for electric bass and backing track 
5. Norse Suite for viola and cello 
6. The Foggy Field a studio construction 
7. Into the Nocturnal Sunshine for flute, viola, cello, drums and electronics 
8. One Night, New Breath for taonga puoro, viola, drums and electronics 
9. Sketches of an Intergalactic Earworm for piano trio and boombox

The accompanying documentation clarifies, and contextualises the creation and presentation of these works; and illuminates the aesthetic underpinnings and compositional techniques developed and utilised as a part of this hybrid-genre compositional approach. The structure of the supporting exegesis is in two parts: the methodology of practice-based research, and reflective investigation. Part One (Chapters 1 and 2) is an introductory overview; an observation of the existing literature and related work, relevant creative practice in the composer’s previous work; and the compositional methodology – including an explanation of the genre matrix. Part Two (Chapters 3 to 12) analyses the use of genre, the balance of hybridity, and relevant compositional techniques utilised in the development of each individual piece.

year: 2015