DOCSLIB.ORG

1Bbi Lichtarge Lab 2006

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1Bbi Lichtarge Lab 2006 Pages 1–5 1bbi Evolutionary trace report by report maker September 26, 2008 4.3.3 DSSP 4 4.3.4 HSSP 4 4.3.5 LaTex 4 4.3.6 Muscle 4 4.3.7 Pymol 4 4.4 Note about ET Viewer 4 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 5 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1bbi): Title: Three-dimensional structure of soybean trypsin(slash) chy- motrypsin bowman-birk inhibitor in solution Compound: Mol id: 1; molecule: trypsin/chymotrypsin bowman- birk inhibitor; chain: a; engineered: yes Organism, scientific name: Glycine Max CONTENTS 1bbi contains a single unique chain 1bbiA (71 residues long). This 1 Introduction 1 is an NMR-determined structure – in this report the first model in the file was used. 2 Chain 1bbiA 1 2.1 Q84LF5 overview 1 2.2 Multiple sequence alignment for 1bbiA 1 2.3 Residue ranking in 1bbiA 1 2.4 Top ranking residues in 1bbiA and their position on 2 CHAIN 1BBIA the structure 1 2.1 Q84LF5 overview 2.4.1 Clustering of residues at 25% coverage. 1 2.4.2 Possible novel functional surfaces at 25% From SwissProt, id Q84LF5, 100% identical to 1bbiA: coverage. 2 Description: Bowman-Birk protease inhibitor. Organism, scientific name: Glycine microphylla. 3 Notes on using trace results 3 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 3.1 Coverage 3 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3.2 Known substitutions 3 eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoi- 3.3 Surface 3 deae; Phaseoleae; Glycine. 3.4 Number of contacts 3 3.5 Annotation 3 3.6 Mutation suggestions 3 2.2 Multiple sequence alignment for 1bbiA 4 Appendix 4 For the chain 1bbiA, the alignment 1bbiA.msf (attached) with 27 4.1 File formats 4 sequences was used. The alignment was assembled through combi- 4.2 Color schemes used 4 nation of BLAST searching on the UniProt database and alignment 4.3 Credits 4 using Muscle program. It can be found in the attachment to this 4.3.1 Alistat 4 report, under the name of 1bbiA.msf. Its statistics, from the alistat 4.3.2 CE 4 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-71 in 1bbiA colored by their relative importance. (See Appendix, Fig.5, for the coloring scheme.) Format: MSF Number of sequences: 27 Total number of residues: 1816 Smallest: 60 Largest: 71 Average length: 67.3 Alignment length: 71 Average identity: 63% Most related pair: 99% Most unrelated pair: 40% Most distant seq: 60% Furthermore, 25% of residues show as conserved in this alignment. Fig. 2. Residues in 1bbiA, colored by their relative importance. Clockwise: The alignment consists of 96% eukaryotic ( 96% plantae) front, back, top and bottom views. sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 1bbiA.descr. 2.3 Residue ranking in 1bbiA The 1bbiA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1bbiA can be found in the file called 1bbiA.ranks sorted in the attachment. 2.4 Top ranking residues in 1bbiA and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 2 shows residues in 1bbiA colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.3 are composed of the residues listed in Table 1. Table 1. cluster size member Fig. 3. Residues in 1bbiA, colored according to the cluster they belong to: color residues red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The red 7 8,9,12,14,22,58,62 corresponding Pymol script is attached. blue 3 36,39,51 yellow 3 17,19,20 green 2 44,46 purple 2 41,49 2.4.2 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1bbiA surface, away from (or Table 1. Clusters of top ranking residues in 1bbiA. susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1bbi. It is shown in Fig. 4. The residues belonging to this surface ”patch” are listed in Table 2, while Table 2 Table 3. continued res type disruptive mutations 17 S (KR)(FQMWH)(NYELPI)(D) 19 P (YR)(TH)(SKECG)(FQWD) 20 P (YR)(TH)(SKECG)(FQWD) 22 C (KER)(FQMWHD)(NYLPI)(SVA) 33 H (E)(TQMD)(SNKVCLAPIG)(YR) 36 C (KER)(FQMWHD)(NYLPI)(SVA) 39 C (KER)(FQMWHD)(NYLPI)(SVA) 41 C (KER)(FQMWHD)(NYLPI)(SVA) 49 C (KER)(FQMWHD)(NYLPI)(SVA) 51 C (KER)(FQMWHD)(NYLPI)(SVA) 58 C (KER)(FQMWHD)(NYLPI)(SVA) 62 C (KER)(FQMWHD)(NYLPI)(SVA) Table 3. Disruptive mutations for the surface patch in 1bbiA. 3 NOTES ON USING TRACE RESULTS Fig. 4. A possible active surface on the chain 1bbiA. 3.1 Coverage Trace results are commonly expressed in terms of coverage: the resi- due is important if its “coverage” is small - that is if it belongs to 3 suggests possible disruptive replacements for these residues (see some small top percentage of residues [100% is all of the residues Section 3.6). in a chain], according to trace. The ET results are presented in the form of a table, usually limited to top 25% percent of residues (or Table 2. to some nearby percentage), sorted by the strength of the presumed res type substitutions(%) cvg antn evolutionary pressure. (I.e., the smaller the coverage, the stronger the 8 C C(100) 0.25 S-S pressure on the residue.) Starting from the top of that list, mutating a 9 C C(100) 0.25 S-S couple of residues should affect the protein somehow, with the exact 12 C C(100) 0.25 S-S effects to be determined experimentally. 14 C C(100) 0.25 S-S 17 S S(100) 0.25 site 3.2 Known substitutions 19 P P(100) 0.25 20 P P(100) 0.25 One of the table columns is “substitutions” - other amino acid types 22 C C(100) 0.25 S-S seen at the same position in the alignment. These amino acid types 33 H H(100) 0.25 may be interchangeable at that position in the protein, so if one wants 36 C C(100) 0.25 S-S to affect the protein by a point mutation, they should be avoided. For 39 C C(100) 0.25 S-S example if the substitutions are “RVK” and the original protein has 41 C C(100) 0.25 S-S an R at that position, it is advisable to try anything, but RVK. Conver- n 49 C C(100) 0.25 S-S sely, when looking for substitutions which will ot affect the protein, 51 C C(100) 0.25 S-S one may try replacing, R with K, or (perhaps more surprisingly), with 58 C C(100) 0.25 S-S V. The percentage of times the substitution appears in the alignment 62 C C(100) 0.25 S-S is given in the immediately following bracket. No percentage is given in the cases when it is smaller than 1%. This is meant to be a rough guide - due to rounding errors these percentages often do not add up Table 2. Residues forming surface ”patch” in 1bbiA. to 100%. 3.3 Surface Table 3. res type disruptive To detect candidates for novel functional interfaces, first we look for mutations residues that are solvent accessible (according to DSSP program) by A˚ 2 8 C (KER)(FQMWHD)(NYLPI)(SVA) at least 10 , which is roughly the area needed for one water mole- 9 C (KER)(FQMWHD)(NYLPI)(SVA) cule to come in the contact with the residue. Furthermore, we require 12 C (KER)(FQMWHD)(NYLPI)(SVA) that these residues form a “cluster” of residues which have neighbor A˚ 14 C (KER)(FQMWHD)(NYLPI)(SVA) within 5 from any of their heavy atoms. Note, however, that, if our picture of protein evolution is correct, continued in next column the neighboring residues which are not surface accessible might be equally important in maintaining the interaction specificity - they 3 should not be automatically dropped from consideration when choo- sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) 3.4 Number of contacts COVERAGE Another column worth noting is denoted “noc/bb”; it tells the num- ber of contacts heavy atoms of the residue in question make across V the interface, as well as how many of them are realized through the 100% 50% 30% 5% backbone atoms (if all or most contacts are through the backbone, mutation presumably won't have strong impact). Two heavy atoms are considered to be “in contact” if their centers are closer than 5A˚ . 3.5 Annotation If the residue annotation is available (either from the pdb file or V from other sources), another column, with the header “annotation” RELATIVE IMPORTANCE appears. Annotations carried over from PDB are the following: site (indicating existence of related site record in PDB ), S-S (disulfide bond forming residue), hb (hydrogen bond forming residue, jb (james Fig.
Load more

Recommended publications
  • Use of Organelle Markers to Study Genetic Diversity in Soybean
    Chapter 26 Use of Organelle Markers to Study Genetic Diversity in Soybean Lidia Skuza, Ewa Filip and Izabela Szućko Additional information is available at the end of the chapter http://dx.doi.org/10.5772/52028 1. Introduction Soybean is the most important crop provider of proteins and oil used in animal nutrition and for human consumption. Plant breeders continue to release improved cultivars with en‐ hanced yield, disease resistance, and quality traits. It is also the most planted genetically modified crop. The narrow genetic base of current soybean cultivars may lack sufficient al‐ lelic diversity to counteract vulnerability to shifts in environmental variables. An investiga‐ tion of genetic relatedness at a broad level may provide important information about the historical relationship among different genotypes. Such types of study are possible thanks to different markers application, based on variation of organelle DNA (mtDNA or cpDNA). 2. Mitochondrial genome 2.1. Genomes as markers Typically, all sufficiently variable DNA regions can be used in genetic studies of popula‐ tions and in interspecific studies. Because of in seed plants chloroplasts and mitochondria are mainly inherited uniparentally, organelle genomes are often used because they carry more information than nuclear markers, which are inherited biparentally. The main benefit is that there is only one allele per cell and per organism, and, consequently, no recombina‐ tion between two alleles can occur. With different dispersal distances, genomes inherited bi‐ parentally, maternally and paternally, also reveal significant differences in their genetic variability among populations. In particular, maternally inherited markers show diversity within a population much better [1].
    [Show full text]
  • Jervis Bay Territory Page 1 of 50 21-Jan-11 Species List for NRM Region (Blank), Jervis Bay Territory
    Biodiversity Summary for NRM Regions Species List What is the summary for and where does it come from? This list has been produced by the Department of Sustainability, Environment, Water, Population and Communities (SEWPC) for the Natural Resource Management Spatial Information System. The list was produced using the AustralianAustralian Natural Natural Heritage Heritage Assessment Assessment Tool Tool (ANHAT), which analyses data from a range of plant and animal surveys and collections from across Australia to automatically generate a report for each NRM region. Data sources (Appendix 2) include national and state herbaria, museums, state governments, CSIRO, Birds Australia and a range of surveys conducted by or for DEWHA. For each family of plant and animal covered by ANHAT (Appendix 1), this document gives the number of species in the country and how many of them are found in the region. It also identifies species listed as Vulnerable, Critically Endangered, Endangered or Conservation Dependent under the EPBC Act. A biodiversity summary for this region is also available. For more information please see: www.environment.gov.au/heritage/anhat/index.html Limitations • ANHAT currently contains information on the distribution of over 30,000 Australian taxa. This includes all mammals, birds, reptiles, frogs and fish, 137 families of vascular plants (over 15,000 species) and a range of invertebrate groups. Groups notnot yet yet covered covered in inANHAT ANHAT are notnot included included in in the the list. list. • The data used come from authoritative sources, but they are not perfect. All species names have been confirmed as valid species names, but it is not possible to confirm all species locations.
    [Show full text]
  • Ecology of Pyrmont Peninsula 1788 - 2008
    Transformations: Ecology of Pyrmont peninsula 1788 - 2008 John Broadbent Transformations: Ecology of Pyrmont peninsula 1788 - 2008 John Broadbent Sydney, 2010. Ecology of Pyrmont peninsula iii Executive summary City Council’s ‘Sustainable Sydney 2030’ initiative ‘is a vision for the sustainable development of the City for the next 20 years and beyond’. It has a largely anthropocentric basis, that is ‘viewing and interpreting everything in terms of human experience and values’(Macquarie Dictionary, 2005). The perspective taken here is that Council’s initiative, vital though it is, should be underpinned by an ecocentric ethic to succeed. This latter was defined by Aldo Leopold in 1949, 60 years ago, as ‘a philosophy that recognizes[sic] that the ecosphere, rather than any individual organism[notably humans] is the source and support of all life and as such advises a holistic and eco-centric approach to government, industry, and individual’(http://dictionary.babylon.com). Some relevant considerations are set out in Part 1: General Introduction. In this report, Pyrmont peninsula - that is the communities of Pyrmont and Ultimo – is considered as a microcosm of the City of Sydney, indeed of urban areas globally. An extensive series of early views of the peninsula are presented to help the reader better visualise this place as it was early in European settlement (Part 2: Early views of Pyrmont peninsula). The physical geography of Pyrmont peninsula has been transformed since European settlement, and Part 3: Physical geography of Pyrmont peninsula describes the geology, soils, topography, shoreline and drainage as they would most likely have appeared to the first Europeans to set foot there.
    [Show full text]
  • Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2006-12-01 Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation Ashley N. Egan Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Egan, Ashley N., "Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation" (2006). Theses and Dissertations. 1294. https://scholarsarchive.byu.edu/etd/1294 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. by Brigham Young University in partial fulfillment of the requirements for the degree of Brigham Young University All Rights Reserved BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL and by majority vote has been found to be satisfactory. ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the format, citations and
    [Show full text]
  • Viewed by [11,12])
    BMC Biology BioMed Central Research article Open Access Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change Ashley N Egan*1 and Keith A Crandall2,3 Address: 1Department of Microbiology & Molecular Biology, Brigham Young University, 773 WIDB, Provo UT 84602, USA, 2Department of Biology, Brigham Young University, Provo, UT 84602, USA and 3Monte L Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA Email: Ashley N Egan* - [email protected]; Keith A Crandall - [email protected] * Corresponding author Published: 17 December 2008 Received: 17 November 2008 Accepted: 17 December 2008 BMC Biology 2008, 6:55 doi:10.1186/1741-7007-6-55 This article is available from: http://www.biomedcentral.com/1741-7007/6/55 © 2008 Egan and Crandall; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Past studies in the legume family (Fabaceae) have uncovered several evolutionary trends including differential mutation and diversification rates across varying taxonomic levels. The legume tribe Psoraleeae is shown herein to exemplify these trends at the generic and species levels. This group includes a sizable diversification within North America dated at approximately 6.3 million years ago with skewed species distribution to the most recently derived genus, Pediomelum, suggesting a diversification rate shift. We estimate divergence dates of North American (NAm) Psoraleeae using Bayesian MCMC sampling in BEAST based on eight DNA regions (ITS, waxy, matK, trnD-trnT, trnL-trnF, trnK, trnS-trnG, and rpoB-trnC).
    [Show full text]
  • WO 2017/202946 Al 30 November 2017 (30.11.2017) W !P O PCT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/202946 Al 30 November 2017 (30.11.2017) W !P O PCT (51) International Patent Classification: Published: C12N 9/5 (2006.01) — with international search report (Art. 21(3)) (21) International Application Number: — before the expiration of the time limit for amending the PCT/EP2017/062598 claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (22) International Filing Date: — with sequence listing part of description (Rule 5.2(a)) 24 May 2017 (24.05.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 16170964.7 24 May 2016 (24.05.2016) EP (71) Applicant: NOVOZYMES A/S [DK/DK]; Krogshoejvej 36, 2880 Bagsvaerd (DK). (72) Inventors: CARSTENSEN, Lone; Krogshoejvej 36, 2880 Bagsvaerd (DK). SPODSBERG, Nikolaj; Krogshoejvej 36, 2880 Bagsvaerd (DK). GJERMANSEN, Morten; Krogshoejvej 36, 2880 Bagsvaerd (DK). SALOMON, Jes- per; Krogshoejvej 36, 2880 Bagsvaerd (DK). KROGH, Kristian, B,R,M,; Krogshoejvej 36, 2880 Bagsvaerd (DK). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY,TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Darkwood Reserve NSW Report, 2010
    Bush Blitz s pecies Discovery p r o g r a m Darkwood reserve NsW 12–16 February 2010 REPORT What is contents Bush Blitz? Bush Blitz is a three- What is Bush Blitz 2 year, multi-million dollar Executive summary 3 partnership between the Introduction 3 australian government, Reserve Overview 4 Bhp Billiton, earthwatch Methods 5 australia, and ausplots- Results 6 rangelands to document plants and animals in selected Discussion 7 properties across australia’s Appendix A: Species Lists 9 National reserve system. Fauna Taxa 10 Flora Taxa 16 Appendix B: Listed Species 19 this innovative partnership Fauna Taxa 20 harnesses the expertise of many Appendix C: Exotic Pest Species 21 of australia’s top scientists from Fauna Taxa 22 museums, herbaria, universities, Flora Taxa 22 and other institutions and organisations across the country. 2 Bush Blitz survey report Executive Introduction summary A short (six day) Bush Blitz was The Bush Blitz program aims to survey the flora and fauna of conducted on Darkwood Reserve in recent additions to the National Reserve System (NRS). Bush New South Wales during February 2010 Blitz is an initiative of the Australian Government, through the in conjunction with the Bush Blitz Australian Biological Resources Study (ABRS) in partnership with Media Launch. In total, 363 species were BHP Billiton, Earthwatch Australia and AusPlots-Rangelands. The identified on the reserve. With previous Bush Blitz objectives are: records for the Reserve, the total number ++ to promote, publicise and demonstrate the importance of of species known from Darkwood is taxonomy through the vehicle of species discovery; now 392.
    [Show full text]
  • Incongruence in Plant Hybrid and Phylogenetic Trees
    Acta Bot. Neerl. 45(3), September 1996, p. 243-262 Review Molecular marker incongruence in plant hybrid zones and phylogenetic trees Loren+H. Rieseberg Jeannette Whitton and C.+Randal Linder Department of Biology, Indiana University, Bloomington, IN 47404, USA CONTENTS Introduction 243 Patterns of marker incongruence 246 Potential explanations for these patterns 248 Differential introgression in Helianthus 250 Conclusions 258 References 258 Key-words: molecular markers, hybridization, introgression, molecular cytoplasmic gene flow, phylogeny. INTRODUCTION One of the striking observations from the young field of molecular evolutionary biology has been the high frequency of cases where taxon-specific markers are found differ in both and distribution. to widely phylogenetic geographic This pattern has been observed most frequently when cytoplasmic markers are compared with those of nuclear origin (Rieseberg & Soltis 1991), but similar observations are often made for comparisons among markers of nuclear origin only (Rieseberg & Ellstrand 1993). These observations are important to phylogenists because they provide ‘footprints’ of past evolutionary events, information that may be critical to elucidating true organismal phylogeny. Marker incongruence also is significant to the evolutionist because it into differences in may provide insights the the evolutionary biology of organellar versus nuclear genes (as well as differences among nuclear genes), the role of selection, linkage and recombination in controlling the frequency and spatial distribution of effects introgressed genes, and the of introgression on the maintenance of species differences. this we list of the best of molecular marker In paper, some examples incongruence from both hybrid zones and phylogenetic trees in plants. General patterns emerging from this tabulation are discussed, and possible explanations are briefly summarized.
    [Show full text]
  • Thesis Sci 2016 Bello Abubakar.Pdf
    Taxonomy and evolutionary studies on the genus Psoralea L. (Psoraleeae, Fabaceae) Abubakar Bello Thesis presented for the degree of Doctor of Philosophy in the Department of Biological Sciences, University of Cape Town Supervisors: A. Prof A. Muthama Muasya and Dr Samson B.M. Chimphango University of Cape Town December, 2015 The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town DEDICATION This study is dedicated to my late father, Alhaji Muhammadu Bello Sule who answered the call of his Lord on the cold morning of Tuesday, 2nd June, 2014 for his patience especially during his trying times on his sick bed when he was extremely in need of my presence but could not be with him as a result of this study. My Lord! Bestow on him Your Mercy as he did bring me up when I was young. Page | ii DECLARATION I Abubakar Bello, hereby declare that the work on which this thesis is based is my original work (except where acknowledgements indicate otherwise) and that neither the whole nor any part of it has been, is being, or is to be submitted for another degree in this or any other university. I authorise the University of Cape Town to reproduce for the purpose of research either the whole or a portion of the content in any manner whatsoever.
    [Show full text]
  • Genetic Analyses for Resistance to Soybean Rust (Phakopsora Pachyrhizi) and Yield Stability Among Soybean Genotypes in Kenya By
    Genetic analyses for resistance to soybean rust ( Phakopsora pachyrhizi) and yield stability among soybean genotypes in Kenya By Susan Wothaya Wanderi B.Sc. Agriculture, M.Sc. Agronomy, University of Nairobi, Kenya A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (PhD) in Plant Breeding African Centre for Crop Improvement (ACCI) School of Agricultural, Earth and Environmental Sciences University of KwaZulu-Natal Republic of South Africa. December, 2012 Thesis abstract Soybean ( Glycine max (L.) Merr.) occupies an important position in the world economy of the feedstock of high quality protein and vegetable oils. However, its production is threatened by, Asian soybean rust (ASR), caused by the rust fungus Phakopsora pachyrhizi Syd. & P. Syd. This fungus is highly dependent on environmental conditions, has a wide range of hosts, and evolves rapidly into novel races, making it difficult to control. In addition, most commercial varieties are susceptible to rust, the rust has already developed resistance to triazole fungicides, and most small-scale farmers cannot afford expensive systemic fungicides to control the disease. The use of resistant varieties is the most viable, long-term option to manage ASR, especially in the small-holder soybean farming sector. This study was therefore designed to undertake the following goals: (i) to identify farmers’ preferred varieties and desired traits, their knowledge of ASR, and other key constraints affecting soybean production in Kenya; (ii) to evaluate soybean accessions for rust resistance, and to determine the correlation of rust resistance with other agronomic traits; (iii) to determine the mode of inheritance for ASR resistance and selected agronomic traits; and (iv) to determine yield stability of soybean advanced lines at multiple sites in Central and Eastern Kenya.
    [Show full text]
  • VOL4 Appendix 10
    Appendix 10 Flora and Fauna Assessment South East Open Cut Project & Modification to the Existing ACP Consent Ashton Coal South East Open Cut Flora and Fauna Assessment Ashton Coal Operations Pty Ltd November 2009 0092509 Final 2 www.erm.com Delivering sustainable solutions in a more competitive world Approved by: Naomi Buchhorn Ashton Coal Position: Project Manager South East Open Cut Signed: Flora and Fauna Assessment Date: 5 November 2009 Ashton Coal Operations Pty Ltd Mike Shelly Partner November 2009 0092509 Final 2 Date: 5 November 2009 www.erm.com Environmental Resources Management Australia Pty Ltd Quality System This report has been prepared in accordance with the scope of services described in the contract or agreement between Environmental Resources Management Australia Pty Ltd ABN 12 002 773 248 (ERM) and the Client. The report relies upon data, surveys, measurements and results taken at or under the particular times and conditions specified herein. Any findings, conclusions or recommendations only apply to the aforementioned circumstances and no greater reliance should be assumed or drawn by the Client. Furthermore, the report has been prepared solely for use by the Client and ERM accepts no responsibility for its use by other parties. CONTENTS 1 INTRODUCTION 1.1 INTRODUCTION 1 1.2 PURPOSE OF THE REPORT 1 1.3 SEOC AREA DESCRIPTION 2 1.4 LEGISLATIVE REQUIREMENTS 3 1.4.1 ENVIRONMENT PROTECTION AND BIODIVERSITY CONSERVATION ACT 1999 3 1.4.2 ENVIRONMENTAL PLANNING AND ASSESSMENT ACT 1979 4 1.4.3 STATE ENVIRONMENTAL PLANNING POLICY
    [Show full text]
  • Terrestrial Ecological Assessment
    DOCUMENT REGISTER/TRANSMITTAL Date of Issue Day 27 25 3 Shute Harbour Marina EIS, Terrestrial Project Title : Ecological Assessment Month 9027 Project No. : SHU01 Year 07 08 08 Distribution No. of Copies Dave Quinlan 11 Shute Harbour Marina Developments Pty Ltd , PO Box 1001, SPRING HILL Q 4004 Erin Young 1 Cardno (Qld) Pty Ltd, PO Box 388, TOOWONG Q 4066 Document No. Document Title Issue 1 SHU01_Eco Assess_002_270907 2 SHU01_Eco Assess_003_250208 X 3 SHU01_Eco Assess_004_03072008 X A=As Requested B=As Built CA=Council Approval Purpose C=Construction I=Information Update R=Review T=Tender B=Black & White Copy C=Colour Copy D=Disk Medium DDE E=Electronic Transfer O=Original OT=Other Size PLACE Design Group Pty. Ltd. A.C.N. 082 370 063 Suite 1, 139 Gotha Street, Fortitude Valley, Brisbane, Qld 4006, PO Box 498 Albion BC, QLD, 4010 T/ 617 3852 3922 ● F/617 3852 4766 ● Brisbane ● Sydney ● Gold Coast ● Sunshine Coast ● China 03.07.2008 SHU01 Version 004 Shute Harbour Marina Development SHUTE HARBOUR MARINA DEVELOPMENT EIS, TERRESTRIAL ECOLOGICAL ASSESSMENT Prepared by Place Design Group for Shute Harbour Marina Development Pty Ltd PLANNING DESIGN ENVIRONMENT Level 1, 282 Wickham Street Fortitude Valley, Queensland, 4006 PO Box 419, Fortitude Valley, 4006 Queensland, Australia Telephone +61 7 3852 3922 Facsmile +61 7 3852 4766 Email: [email protected] Web: www.placedesigngroup.com ACKNOWLEDGEMENTS This report has been prepared by the following persons and organisations: PLACE Environmental Staff Wayne Moffitt Review Andrew Dickinson
    [Show full text]