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Summer Research  Scholarship  Program   Genomics  and  Computational  Biology     Hamilton  group   Project  Titles:   Methods  in  bio-­‐image  analysis  and  classification   Modelling  biological  systems   Project  Description:  Biological  imaging  is  undergoing  rapid  growth  and   development  in  microscope  technology.  High-­‐throughput  screens  for  drug  and   genomic  discovery  are  leading  to  massive  image  sets  in  need  of  new  methods  of   quantification,  modelling,  analysis,  classification,  feature  extraction,   organisation,  visualisation,  comparison,  hypothesis  testing  and  inference.  The   core  of  the  group’s  research  is  to  develop  the  methodologies,  algorithms  and   tools  to  maximise  the  benefit  of  the  new  data  sources  becoming  available.  The   group  collaborates  closely  with  cell  biology,  bioinformatics  and  mathematics   groups  in  creating  these  methodologies  and  utilises  and  develops  techniques  in   areas  such  as  machine  learning,  data  clustering,  graph  algorithms,  image   segmentation,  statistical  testing  and  mathematical  modelling.   Project  duration:  10  weeks   Primary  Supervisor:  Dr  Nick  Hamilton   Further  info:  Please  contact  Dr  Nick  Hamilton  on                      

Ragan group   We  use  advanced  computing  and  bioinformatics  to  make  quantitative  inferences   inferences  about  how  genomes,  gene  families,  protein  families  and  biomolecular   networks  evolve,  diversify  and  function  in  mammalian  cells  and  in  bacteria.   Project  Title:  Gene  exchange  and  genetic  recombination  in  pathogenic  bacteria,   particularly  multidrug-­‐resistant  Staphylococcus  aureus   Description:  Application  of  bioinformatic  and  computational  methods  including   multiple  sequence  alignment,  phylogenetic  inference  and  topology  comparison   to  detect  instances  of  lateral  genetic  transfer  among  hundreds  of  S.  aureus   genomes,  and  correlation  with  genetic  determinants  of  infectivity,  multidrug   resistance  and  virulence.   Expected  outcomes  and  deliverables:  Experience  with  important  methods  in   bioinformatics  and  molecular  phylogenetics  /  phylogenomics  including   automated  workflows,  multiple  sequence  alignment,  tree  inference  and   comparison,  computing  and  data  management.   Suitable  for:  Year  3-­‐4  students  with  interest  in  bioinformatics,  molecular   phylogenetics  and/or  computational  analysis  of  infectious  disease   microorganisms,  with  solid  fundamentals  in  Unix/Linux,  a  modern  scripting   language  (preferably  Python)  and  R.   Primary  Supervisor:  Dr  Cheong  Xin  Chan   Further  info:  Interested  students  please  contact  Dr  Cheong  Xin  Chan  and/or  Professor  Mark  Ragan     Project  Title:  Networks  of  gene  exchange  across  entire  microbial  ecosystems   Description:  Application  of  advanced  statistical,  informatic  and  computational   approaches  to  model  the  transfer  of  genetic  material  across  the  microbial   biosphere.   Expected  outcomes  and  deliverables:  Experience  with  bioinformatic  and   computational  workflows,  non-­‐standard  methods  based  on  k-­‐mer  frequency   spectra,  and  D2  statistics;  new  insights  into  the  world  of  microbial  genomes.   Suitable  for:  Masters-­‐level  or  adventurous  Year  3-­‐4  students  with  strong   grounding  in  frequentist  statistics  and  scripting  (preferably  Python),  and   familiarity  with  Unix/Linux.   Primary  Supervisor:  Dr  Leanne  Haggerty  

Further info:  Interested  students  please  contact  Dr  Leanne  Haggerty  and/or   Professor  Mark  Ragan         Project  Title:  Genes  for  adaptation  to  extreme  environments  in  algal  genomes   Description:  Application  of  bioinformatic  and  computational  methods  including   sequence  clustering,  multiple  sequence  alignment,  phylogenetic  inference  and   statistical  analyses  to  understand  genomic  adaptation  to  temperature  and/or   environmental  stress.  For  some  datasets,  also  structural  and  functional   annotation.   Expected  outcomes  and  deliverables:  Experience  with  important  methods  in   bioinformatics,  evolutionary  biology  and  molecular  phylogenetics  including  data   management,  automated  workflows  and  computing.   Suitable  for:  Year  3-­‐4  students  with  interest  in  bioinformatics,  molecular   evolution  and/or  molecular  phylogenetics  /  phylogenomics  particularly  of   marine  organisms,  with  solid  fundamentals  in  Unix/Linux,  a  modern  scripting   language  (preferably  Python)  and  R.   Primary  supervisor:  Dr  Cheong  Xin  Chan   Further  info:  Interested  students  please  contact  Dr  Cheong  Xin  Chan  and/or  Professor  Mark  Ragan       Project  Title:  Genes  for  brain  development,  social  behaviour  and  cognition  in   the  Neandertal  genome   Description:  Exploratory  project  examining  adaptive  genetic  selection  of  genes   potentially  involved  in  brain  development,  social  behaviour  and/or  cognition  in   the  published  Neandertal  and  Denisovan  genomes.   Expected  outcomes  and  deliverables:  Experience  with  important  methods  in   bioinformatics  and  evolutionary  biology;  understanding  of  brain  and  related   gene  systems  in  human  evolution.   Suitable  for:  Year  3-­‐4  or  Masters  students  able  to  work  semi-­‐independently  in  a   supportive  research  environment.  Must  be  familiar  with  Unix/Linux  and  a   modern  scripting  language  (preferably  Python);  experience  with  the  UCSC   Genome  Browser,  Java,  Matlab  and/or  R  would  be  beneficial.   Primary  supervisor:  Professor  Mark  Ragan   Further  info:  Interested  students  please  contact  Professor  Mark  Ragan  

Project Title:  Networks  of  molecular  interactions  and  genetic  regulation  in   cancer   Description:  Application  of  methods  from  bioinformatics,  knowledge   engineering  and/or  machine  learning  to  infer  and  analyse  networks  of   biomolecular  interaction  based  on  large  gene-­‐expression  and  other  datasets  in   breast,  pancreatic,  prostate  and  other  cancers.   Expected  outcome  and  deliverables:  Experience  with  important  methods  in   bioinformatics  and  computational  biology  as  applied  to  mechanistic   understanding  of  cancer,  including  cancer  subtypes  and  metastasis.  Experience   with  computational  workflows,  data  management  and  specialised  methods  e.g.   ontologies,  knowledge  engineering,  or  machine  learning.   Suitable  for:  Year  3-­‐4  or  Masters  students  with  interest  in  cancer  or  other   complex  disease,  and  strong  grounding  in  statistics.  Familiarity  with  either  bio-­‐ ontologies,  or  machine  learning  techniques  (e.g.  SVMs,  random  forests),  is   strongly  recommended.   Primary  supervisor:  Dr  Melissa  Davis  (knowledge  engineering)  and/or  Dr   Sriganesh  Srihari  (machine  learning).   Further  info:  Interested  students  please  contact  Professor  Mark  Ragan  for  initial   discussion  ,  then  either  Dr  Melissa  Davis  or  Dr  Sriganesh  Srihari                          

Molecular Genetics  and  Development     Little  group   Project  Title:  Mechanism  regulating  tubular  formation  in  a  3D  culture  system   Project  duration:  8  weeks   Description:  Kidney-­‐derived  stromal  cells  can  form  tubular  structures  in  3D   culture  and  this  project  is  to  Investigate  the  potential  signalling  pathways   involved  in  this  process.   Expected  outcomes  and  deliverables:  For  example,  scholars  may  gain  skills  in   data  collection,  or  have  an  opportunity  to  generate  publications  from  their   research.    Students  may  also  be  asked  to  produce  a  report  or  oral  presentation  at   the  end  of  their  project.   Suitable  for:  This  project  will  involve  3D  cell  culture,  immunofluorescence  and   possibly  confocal  microscopy  and  images  processing.  It  is  suitable  for  3rd  or  4th   year  student.   Primary  Supervisor:  Dr  Joan  Li   Further  info:  Please  contact  Dr  Joan  Li  if  you  would  like  further  information                        

Hogan group   Project  Title:  Characterization  of  a  novel  transgenic  reporter  for  snail2   expression   Project  Description:  In  the  Hogan  lab  we  study  the  formation  of  the  vertebrate   vascular  network,  consisting  of  both  blood  and  lymphatic  vessels,  using  the   zebrafish  as  a  model  organism.  New  vessels  form  largely  via  sprouting  of  vessels   from  pre-­‐existing  vasculature,  which  is  termed  angiogenesis  for  blood  vessels   and  lymphangiogenesis  in  the  case  of  lymphatic  vessels.  In  zebrafish  embryos   angiogenic  sprouting  of  arterial  vessel  initiates  at  approximately  22  hours  post   fertilization  (hpf),  followed  by  sprouting  of  venous  vessels  that  will  later   comprise  the  lymphatic  system.  While  zebrafish  embryos  are  highly  transparent,   these  processes  can  be  imaged  live.   Recently,  we  have  established  a  novel  transgenic  line  in  the  lab  that  functions  as   a  reporter  for  snail2  transcription.  Snail2  is  a  well-­‐established  transcription   factor  that  functions  as  an  inducer  of  a  process  referred  to  as  epithelial-­‐to-­‐ mesenchymal  transition  (EMT).  We  would  like  to  use  the  transgenic  zebrafish   embryos  to  visualize  which  endothelial  cells  undergo  EMT  during  sprouting   angiogenesis.  Expression  analysis  will  include  live  confocal  microscopy,  antibody   stainings  and  in  situ  hybridization  experiments.   Project  duration:  10  weeks   Primary  Supervisor:  Dr  Anne  Lagendijk     Further  info:  Please  contact  Dr  Anne  Lagendijk  if  you  would  like  further   information       Project  Title:  The  influence  of  blood  flow  on  endothelial  morphogenesis   Project  Description:  With  this  project  we  would  like  to  perform  a  detailed   analysis  of  the  morphogenetic  events  prior  and  after  the  onset  of  blood  flow.  We   will  make  use  of  a  great  variety  of  transgenic  lines  available  in  the  lab  that  will   differentiate  between  components  of  the  blood  vasculature  like  arteries,  veins   and  lymphatics.  We  will  perform  transient  knock-­‐down  approaches  to  eliminate   blood  flow  during  development  and  also  study  zebrafish  mutants  which  lack   blood  flow.   Project  duration:  8-­‐10  weeks   Primary  Supervisor:  Dr  Anne  Lagendijk   Further  info:  Please  contact  Dr  Anne  Lagendijk  if  you  would  like  further   information  

Molecular Cell  Biology   Parton  group   Our  research  focuses  on  the  cell  surface  in  health  and  disease,  specifically  the   organisation,  dynamics,  and  functions  of  the  plasma  membrane.  We  use  electron   microscopy,  live  confocal  microscopy,  molecular  biology,  and  biochemistry  to   examine  membrane  dynamics  and  microdomain  organisation,  in  particular  the   function  of  caveolae.  These  domains  are  involved  in  signal  transduction  and  lipid   regulation  and  have  been  linked  to  disease  states  such  as  muscular  dystrophy   and  cancer.  We  use  a  range  of  model  systems  including  cultured  cells,  the   zebrafish  and  mouse.   Project  Title:  Membrane  dynamics  in  zebrafish  models  of  muscular  dystrophies.   Project  duration:  8-­‐10  weeks   Description:  We  are  interested  specifically  in  the  role  of  the  Junctophilin  gene  in   the  development  of  the  early  muscle  membrane  systems.  We  believe  that   perturbation  of  junctophilin  expression  results  in  compromised  muscle   development  and  function.  The  optically  transparent  zebrafish  provides  an  ideal   model  to  test  this  hypothesis,  using  gene-­‐knockdown,  expression  analysis  by   insitu  hybridisation,  and  live  imaging  of  fluorescent  transgenic  lines  using   confocal  microscopy.   Expected  outcomes  and  deliverables:  Students  will  be  given  training  in   expression  analysis  and  the  use  of  zebrafish  as  a  model  system.  This  project  has   the  potential  to  be  developed  into  a  larger,  more  in-­‐depth  study  down  the  track   Suitable  for:  This  project  would  be  suitable  for  third  year  students  looking  for   experience  and  training  before  considering  honours  and/or  a  PhD.   Primary  Supervisor:  Dr  Thomas  Hall   Further  info:  Please  contact  Dr  Thomas  Hall  on                  

Teasdale group   Project  Title:  Defining  host-­‐pathogen  interactions  during  Salmonella  infection   Project  duration:  10  weeks   Description:  This  project  will  investigate  the  molecular  details  of  various   pathways  and  how  they  are  modulated  in  response  to  infection  with  Salmonella,   a  leading  cause  of  human  gastroenteritis.   Primary  Supervisor:  Dr  Rohan  Teasdale   Further  info:  Please  contact  Dr  Rohan  Teasdale  on       Project  Title:  Defining  how  Chlamydia  manipulates  the  hosts  membrane   trafficking  pathways  during  infections   Project  duration:  10  weeks   Description:  This  project  will  investigate  the  molecular  details  of  various   membrane  trafficking  pathways  and  there  contribution  to  the  formation  of  the   inclusion  generated  during  infection  with  Chalmydia,  the  most  common  bacterial   sexually  transmitted  disease.   Primary  Supervisor:  Dr  Rohan  Teasdale   Further  info:  Please  contact  Dr  Rohan  Teasdale  on       Project  Title:  Characterisation  of  the  mammalian  endosomal  protein  complex   called  the  retromer   Project  duration:  10  weeks   Description:  Retromer  is  a  central  regulator  of  early  endosome  protein   trafficking  that  has  recently  been  implicated  in  the  progressive  neurological   disorders  such  as  Alzheimer’s  and  Parkinson’s  diseases.  This  project  will   examine  the  known  cellular  biochemical  properties  of  retromer  to  determine  the   molecular  mechanisms  underlying  these  disease  states.   Primary  Supervisor:  Dr  Rohan  Teasdale   Further  info:  Please  contact  Dr  Rohan  Teasdale  on      

Yap group   Project  Title:  Characterization  of  biomechanical  properties  of  epithelial  cells   grown  on  stretchable  substrates   Project  duration:  10  weeks   Description:  This  project  will  investigate  how  mechanical  forces  contribute  to   the  biology  of  cadherin  based  cell-­‐cell  junctions.  By  using  cells  grown  on   stretchable  substrates  combined  with  high  resolution  imaging  and  fluorescence   energy  resonance  transfer  measurements,  this  interdisciplinary  project  study   how  cadherin  receptors  sense  force  and,  transduce  mechanical  stress  into   biochemical  signals.  The  results  of  this  project  will  shed  light  on  the  role  of   cellular  forces  on  in  tissue  organisation  and  how  its  (dys)regulation  can  derive  in   disease,  such  as  cancer.   Primary  Supervisor:  Dr  Guillermo  Gomez   Further  info:  Please  contact  Dr  Guillermo  Gomez  on                                  

Schroder group   Project  Title:  Construction  of  plasmids  for  the  expression  of  inflammasome   reporter  genes   Project  duration:  10  weeks   Description:  The  immune  system  is  critical  to  defence  against  infection,  but  also   drives  unhealthy  processes  in  disease.  An  important  emerging  player  in  innate   immunity  in  both  of  these  settings  is  the  ‘inflammasome’  pathway.   Inflammasomes  are  molecular  machines  that  trigger  immune  system  activation   in  response  to  infection  or  tissue  damage.  Inflammasomes  enable  immune   defences  to  fight  infection,  but  also  drive  unhealthy  inflammation  in  a  wide   variety  of  human  diseases,  including  hereditary  fever  syndromes,  gout,  diabetes,   arthritis,  asbestosis  and  Alzheimer’s  disease.  Pathway  antagonists  already  show   great  clinical  promise  for  the  treatment  of  these  debilitating  diseases.  The  NLRC4   inflammasome  mediates  host  defence  against  Gram-­‐negative  pathogenic  bacteria   such  as  Salmonella,  however  the  cellular  mechanisms  enabling  this  critical   immune  response  are  unclear.  This  project  addresses  this  important  knowledge   gap,  by  cloning  constructs  encoding  fluorescently  tagged  inflammasome   components  to  enable  imaging  of  inflammasome  pathway  activation  in  real  time.   Insight  into  such  mechanisms  of  host  defence  may  enable  the  future  design  of   anti-­‐infective  or  anti-­‐inflammatory  drugs.   Primary  Supervisor:  Dr  Kate  Schroder   Further  info:  Please  contact  Dr  Kate  Schroder  on                          

Chemistry and  Structural  Biology   Alewood  group   Project  Title:  Conotoxins  that  target  chronic  pain  receptors   Project  duration:  10  weeks   Description:  Conotoxins  are  small  bioactive  highly  structured  peptides  from  the   venom  of  marine  cone  snails  (genus  Conus).  Over  the  past  50  million  years  these   molluscs  have  developed  a  complex  venom  cocktail  for  each  species  with  each   venom  comprised  of  1000-­‐10000  distinct  cysteine-­‐rich  peptides  for  prey  capture   and  defence.  This  project  will  focus  on  smaller  conotoxins  which  were  isolated   from  our  transcriptome  /  proteome  program  and  contain  2  or  3  disulfide   bridges.  In  this  project  we  will  chemically  synthesise  two  of  these  conotoxins  and   characterize  them  in  vitro  against  a  panel  of  ion  channel  receptors.   Expected  outcomes  and  deliverables:  Applicants  will  gain  skills  in  learning  to   use  hplc  chromatography,  mass  spectrometry,  transcriptomics  /proteomics   analysis  and  solid  phase  peptide  synthesis.  This  work  will  underpin  future   publications  in  this  field.   Students  will  also  learn  how  to  present  their  work  in  Group  Meetings  using   Powerpoint  presentations.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry  or  biochemistry  preferably  in  their  3rd  or  4th  year.   Primary  Supervisor:  Professor  Paul  Alewood   Further  info:  Please  contact  Paul  Alewood  beforehand  at     Project  Title:  Bioactive  molecules,  chemical  protein  synthesis  and  proteomics   Project  duration:  10  weeks   Description:  The  research  interests  of  our  group  include  the  discovery  and  total   synthesis  of  peptide  toxins  from  Australia’s  venomous  creatures,  the  chemical   synthesis  of  proteins  and  bioactive  peptides,  development  of  new  synthetic  and   analytical  methods,  heterocyclic  chemistry,  proteomics  and  bio-­‐organic  and   medicinal  chemistry.  Special  emphasis  is  placed  on  determining  the  structure-­‐ function  relationships  of  natural  and/or  designed  molecules.   Expected  outcomes  and  deliverables:  Applicants  will  gain  skills  in  learning  to   use  hplc  chromatography,  mass  spectrometry,  transcriptomics  /proteomics  

analysis and  solid  phase  peptide  synthesis.  This  work  will  underpin  future   publications  in  this  field.   Students  will  also  learn  how  to  present  their  work  in  Group  Meetings  using   Powerpoint  presentations.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry  or  biochemistry  preferably  in  their  3rd  or  4th  year.   Primary  Supervisor:  Professor  Paul  Alewood   Further  info:  Please  contact  Paul  Alewood  beforehand  at                                        

Cooper group   Further  information  can  be  found  at  the  Cooper  Group  website:     Project  title:  Anti-­‐inflammatory  small  molecules  for  Alzheimers  and  Parkinsons   Project  duration:  8-­‐10  weeks   Description:  Interleukin  1β  is  a  key  component  of  the  innate  immune  response   vital  for  host  protection  against  invading  pathogens  and  aiding  in  cellular  and   tissue  repair.  However,  IL-­‐1β  is  also  a  potent  pyrogen  and  dysregulation  leads  to   a  wide  variety  of  diseases  including  auto  inflammatory  disorders.  We  are   developing  a  series  of  compounds  which  modulate  IL-­‐1β  through  targeting  the   NLRP3  inflammasome  signalling  cascade.  This  project  will  involve  synthesis  of   novel  members  of  this  compound  series  for  testing  against  our  lead  compound   with  the  aim  to  generate  molecules  with  activity  in  disorders  of  the  CNS   (multiple  sclerosis,  Alzheimers  and  Parkinsons  disease).   Expected  outcomes  and  deliverables:  This  project  is  oriented  in  the  field  of   medicinal  chemistry  and  will  develop  the  synthetic  and  analytical  skills  of  the   successful  applicant.  The  student  will  generate  a  number  of  small  molecules   using  solution  phase  chemistry  contributing  to  our  series  for  future  patent   and/or  publication.  This  project  works  across  many  disciplinary  areas  and   molecules  generated  will  be  tested.  The  student  can  expect  to  complete  the  work   with  a  good  understanding  of  the  underlying  biology  and  the  structure   activity/property  relationships  within  the  series  they  are  working.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry,  3-­‐4  year  students.   Primary  Supervisor:  Dr  Avril  Robertson.  Co-­‐supervisor:  Professor  Matthew   Cooper   Further  Info:  For  further  information  please  contact  the  Cooper  group  enquires   email:  info-­‐   Please  ensure  contact  is  made  prior  to  submitting  an  application.       Project  title:  Lipopeptide  antibiotics  to  treat  multidrug  resistant  bacterial   infections   Project  duration:  8-­‐10  weeks   Description:  There  is  an  urgent  medical  need  for  new  antibiotics  to  treat   infections  caused  by  multidrug-­‐resistant  (MDR)  Gram-­‐negative  pathogens,  which   is  exacerbated  by  the  paucity  of  drug  candidates  in  the  pharmaceutical  

pipeline.  Based  on  our  established  methods,  this  project  will  use  solid  phase   synthesis  to  make  naturally  occurring  and  novel  octapeptin  derivatives  for   testing  using  an  in-­‐house  collection  of  drug  resistant  bacterial  strains  as  well  as   NDM-­‐1  producing  Gram-­‐negative  bacteria.   Expected  outcomes  and  deliverables:  The  successful  applicant  will  generate  a   number  of  small  molecules  using  solid  phase  chemistry  in  order  to  complete  our   set  of  molecules  for  publication.  Molecules  generated  will  be  tested  against  a   panel  of  bacteria  but  will  also  be  tested  for  antifungal  activity  giving  likelihood  of   2  publications.  The  motivated  student  can  expect  to  complete  the  work  with  a   good  understanding  of  the  underlying  biology  and  the  structure   activity/property  relationships  within  the  series  they  are  working.  This  project   is  oriented  in  the  field  of  medicinal  chemistry  and  will  develop  the  synthetic  and   analytical  skills  of  the  successful  applicant.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry,  3-­‐4  year  students.   Primary  Supervisor:  Dr  Avril  Robertson.  Co-­‐supervisor:  Professor  Matthew   Cooper   Further  Info:  For  further  information  please  contact  the  Cooper  group  enquires   email:  info-­‐   Please  ensure  contact  is  made  prior  to  submitting  an  application.       Project  Title:  Natural  product  anti-­‐infective  drug  discovery   Project  duration:  8-­‐10  weeks   Description:  Natural  products  have  been  a  valuable  source  of  new  drugs  leads   for  hundreds  of  years.  We  have  initiated  a  research  collaboration  to  screen   plants  from  South  East  Queensland,  which  is  home  to  a  large  diversity  of  species,   for  anti-­‐infective  activity.  We  will  also  undertake  chemotaxonomy  analyses  of   selected  plant  species  using  LC-­‐MS.   Expected  outcomes  and  deliverables:  This  project  aims  to  identify  new  anti-­‐ infective  active  compounds  from  plants,  as  well  as  helping  to  resolve  plant   taxonomy  issues  using  a  chemotaxonomy  approach.    This  project  will  enable  the   student  to  get  hands  on  experience  with  analytical  chemistry  equipment  and   techniques,  as  well  as  undertake  preparative  scale  compound  isolation  and   structure  elucidation  with  NMR  and  MS.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry,  2-­‐4  year  students.    This  project  will  suit  students  who   are  interested  in  natural  products  chemistry,  analytical  chemistry  and/or  anti-­‐ infective  drug  discovery.  

Primary Supervisor:  Dr  Mark  Butler.  Co-­‐supervisor:  Prof  Matt  Cooper   Further  info:  For  further  information  please  contact  the  Cooper  Group  enquires   email:  info-­‐   Please  ensure  contact  is  made  prior  to  submitting  an  application.       Project  Title:  Tackling  Gram-­‐Negative  Bacterial  Infections  One  Residue  at  a   Time   Project  duration:  8-­‐10  weeks   Description:  The  polymyxin  (PMB)  class  of  antibiotics  (Polymyxin  B  and   colistin),  identified  in  1947  as  secondary  metabolite  nonribosomal  peptides   produced  by  the  soil  bacterium  Bacillus  polymyxa,  are  the  last-­‐resort  therapeutic   option  to  treat  Gram-­‐negative  infections  that  fail  to  respond  to  all  other  currently   available  treatments.  The  polymyxins  are  cyclic  hepapeptides  highly  decorated   with  diaminobutyric  acid  (Dab)  residues  that  are  important  for  the  biological   activity  and  solution-­‐state  NMR  has  revealed  that  PMBs  exhibit  a  conformational   preference  toward  a  type  II’  b-­‐turn.  This  project  will  involve  the  solution-­‐phase   synthesis  of  Fmoc-­‐protected  amino  acid  peptidomimetics  and  their   incorporation  into  PMB  via  solid  phase  peptide  synthesis.   Expected  outcomes  and  deliverables:  The  applicant  will  apply  several   medicinal  chemistry  principles,  namely  organic/solid-­‐phase  peptide  synthesis,   peptidomimetic  design,  and  SAR  analysis,  to  further  our  understanding  of  how   this  important  class  of  antibiotics  interact  with  their  biological  targets.  This   project  will  strengthen  the  applicant’s  skills  in  the  areas  of  organic  synthesis  and   analytical  analysis,  and  will  allow  the  opportunity  to  see  how  chemistry  and   biology  interface  in  a  drug  discovery  setting.    The  research  outcomes  will  lead  to   future  publications,  and  will  contribute  to  a  high  impact  research  area.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry,  preferably  3-­‐4  year  students.   Primary  Supervisor:  Dr  Karl  Hansford.  Co-­‐supervisor:  Prof  Matt  Cooper   Further  info:  For  further  information  please  contact  the  Cooper  Group  enquires   email:  info-­‐     Please  ensure  contact  is  made  prior  to  submitting  an  application.       Project  Title:  Is  Two  Better  than  One?  Vancomycin  Dimers  to  Treat   Glycopeptide-­‐Resistant  Bacteria  

Project Duration:  8-­‐10  weeks   Description:  Glycopeptide  antibiotics  such  as  vancomycin  are  a  last  line  of   defence  in  the  treatment  of  serious  infections  caused  by  drug  resistant  Gram-­‐ positive  bacteria  such  as  MRSA.  They  inhibit  a  key  step  in  the  biosynthesis  of  the   bacterial  cell  wall  peptidoglycan.  Mutations  in  the  peptidoglycan  structure  have   led  to  widespread  vancomycin  resistance  in  recent  years.  We  have  developed   novel  vancomycin  derivatives  containing  additional  functional  groups  that  are   highly  active  against  Gram-­‐positive  bacteria.    One  recent  analogue  incorporated   two  vancomycin  molecules  and  exhibited  a  very  different  antibacterial  profile,   with  selectivity  for  vancomycin  resistant  species.   Expected  outcomes  and  deliverables:  The  project  will  focus  on  the  design  and   synthesis  of  analogues  of  this  novel  vancomycin  dimer.  The  applicant  will  apply   several  medicinal  chemistry  principles,  namely  organic/solid-­‐phase  peptide   synthesis,  characterisation,  drug  design,  and  SAR  analysis,  to  increase  our   understanding  of  what  structural  features  contribute  to  overcoming  vancomycin   resistance.    While  primarily  synthesis-­‐focused,  the  student  will  have  the   opportunity  to  observe  and  learn  antimicrobial  testing  and  mode  of  action   studies.  The  research  outcomes  will  lead  to  future  publications,  and  will   contribute  to  a  high  impact  research  area.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry,  preferably  3-­‐4  year  students.   Primary  Supervisor:  Dr  Mark  Blaskovich.  Co-­‐supervisor:  Prof  Matt  Cooper   Further  info:  For  further  information  please  contact  the  Cooper  Group  enquires   email:  info-­‐   Please  ensure  contact  is  made  prior  to  submitting  an  application.       Project  Title:  Synthesis  of  compounds  used  as  fatty  acid  tales  for  antibiotic   development.   Project  duration:  8-­‐10  weeks   Description:  One  of  the  main  areas  of  expertise  in  the  Cooper  Group  is  the   development  of  new  antibiotics  to  treat  multidrug-­‐resistant  (MDR)  gram-­‐ negative  pathogens.  The  aim  of  the  summer  research  project  will  be  to   synthesize  a  variety  of  small  molecules  to  be  used  as  fatty  acids  tales  for  the   polymyxin  cyclopeptide  antibiotic  scaffold.  Changing  the  fatty  acid  moieties  is   one  of  the  most  direct  routes  to  modify  activity  and  cytotoxicity.   Expected  outcomes  and  deliverables:  After  8-­‐10  weeks  of  work  the  student   will  be  expected  to  deliver  a  set  of  compounds  in  order  to  complete  a  small   library  of  Polymyxin  derivatives.    After  the  summer  research  project  is  complete,  

the student  can  expect  to  have  a  basic  knowledge  of  synthetic  chemistry,   analytical  techniques  used  in  chemistry:  Thin  Layer  Chromatography  (TLC),   Nuclear  Magnetic  Resonance  (NMR),  and  Liquid  Chromatography  Mass   Spectrometry  (LCMS)  among  others.  This  project  is  oriented  in  the  field  of   Organic  Chemistry/Medicinal  Chemistry.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry,  2-­‐3  year  students.   Primary  Supervisor:  Alejandra  Gallardo-­‐Godoy,  Ph.D.  Co-­‐supervisor:  Prof  Matt   Cooper   Further  info:  For  further  information  please  contact  the  Cooper  Group  enquires   email:  info-­‐   Please  ensure  contact  is  made  prior  to  submitting  an  application.                                    

Craik group   Project  Title:  Disulfide-­‐rich  peptides  as  templates  for  the  treatment  of   amyloidosis   Project  duration:  8  weeks   Description:  Alzheimer's  disease  is  the  primary  form  of  dementia,  a  disease  that   affects  the  cognitive  faculties  of  over  250,000  Australians  but  has  no  effective   cure.  The  disease,  and  others  including  diabetes,  is  associated  with  the   aggregation  of  proteins  in  the  body.  A  possible  strategy  to  treat  the  disease  is  to   prevent  the  aggregation  of  those  proteins.  In  this  project,  the  aim  is  to  use   peptides,  a  promising  class  of  compounds  that  offers  many  advantages  over   small  molecules,  such  as  specificity  and  low  toxicity.  In  particular,  the  project  will   focus  on  the  use  of  cyclic  disulfide-­‐rich  peptides  because  they  can  be  used  as   ultra-­‐stable  templates  for  drug  design.  The  approach  is  to  use  a  rational   structure-­‐informed  approach  to  design  inhibitors  of  aggregation.  The  project  will   involve  chemical  synthesis  and  purification  of  peptides,  NMR  spectroscopy  to   characterise  their  structures,  and  in  vitro  assays  to  characterise  their  activity.   Expected  outcomes  and  deliverables:  Scholars  may  gain  skills  in  use  of   equipment  for  the  purification  and  characterisation  of  peptides  (i.e.  reverse-­‐ phase  HPLC,  NMR  spectroscopy,  fluorescence  spectrometer),  data  collection  and   analysis.  Students  will  also  have  the  opportunity  to  produce  an  oral  presentation   at  the  end  of  their  project.   Suitable  for:  This  project  is  open  to  applications  from  students  with  a   background  in  chemistry,  3-­‐4  year  students,  UQ  enrolled  students  only.   Primary  Supervisor:  Dr  Conan  Wang   Further  info:  Please  contact  me  if  you  require  further  information  at                    

Hankamer group   Project  Title:  Structural  studies  of  endosomal  sorting  complexes  hijacked   during  enveloped  virus  infection.   Project  duration:  10  weeks   Description:  Endsomal  sorting  complexes  (ESCRTs)  are  a  family  of  multi-­‐ protein  assemblies,  conserved  from  yeast  to  higher  eukaryotes,  that  regulate   three  fundamental  biological  processes:  the  terminal  stages  of  cytokinesis;  the   biogenesis  of  multivesicular  bodies,  and  the  fission  of  nascent  enveloped  viruses   from  the  plasma  membrane  of  infected  cells.    In  all  three  processes,  the  ESCRT   machinery  mediates  the  deformation  of  cell  membranes,  leading  to  the   formation  of  a  budded  membrane  structures,  and  ultimately  membrane   fission.    This  project  is  focused  on  using  structural  and  molecular  biology   techniques  to  acquire  a  better  understanding  of  the  molecular  mechanisms  that   drive  this  membrane  remodelling  process.    A  particular  focus  is  on   understanding  how  a  wide  range  of  enveloped  viruses  (including  HIV)  hijack  the   ESCRT  machinery  during  infection,  opening  up  the  potential  to  develop  novel   anti-­‐viral  therapies.   Expected  outcomes  and  deliverables:  A  number  of  functionally  important   ESCRT  complexes  are  currently  being  targeted,  and  it  is  expected  that  scholars   would  be  given  the  opportunity  to  focus  their  studies  on  one  such  complex  of   interest.   Scholars  will  develop  skills  in  recombinant  protein  expression,  protein   purification  and  biophysical  analyses  of  protein-­‐protein  interactions  and  multi-­‐ protein  complex  formation.    It  is  also  expected  that  students  will  work  closely   with  microscope  technicians  to  analyse  the  structure  of  these  complexes  using   high  resolution  electron  cryo-­‐microscopy  (Cryo-­‐EM),  which  will  then  give  the   students  opportunities  to  develop  skills  in  image  processing  and  protein   structure  determination.   Suitable  for:  Suited  to  3rd  year  students  with  a  background  in  Biochemistry  and   Molecular  Biology,  although  students  from  other  backgrounds  are  also  welcome   to  apply.   Primary  Supervisor:  Dr  Michael  Landsberg   Further  info:  For  further  info,  please  contact  Michael  Landsberg          

King group   Project  Title:  Venoms  to  drugs:  translating  venom  peptides  into  human   therapeutics   Project  duration:  10  weeks   Description:  The  primary  focus  of  this  project  will  be  structure-­‐function   characterisation  and  therapeutic  development  of  venom  peptides  that  modulate   the  activity  of  neuronal  ion  channels  involved  in  pain  signalling  in  humans.   Molecules  that  antagonise  these  ion  channels  have  the  potential  to  be  developed   as  analgesics  without  the  side-­‐effects  of  current-­‐generation  pain  killers.   Expected  outcomes  and  deliverables:  Students  will  gain  skills  in  a  wide   variety  of  biochemical  and  biophysical  techniques,  including  recombinant   protein  production,  HPLC,  NMR  and  electrophysiology,  and  they  will    have  an   opportunity  to  generate  publications  from  their  research.    Students  will  be   required  to  produce  a  brief  report  and  an  oral  presentation  at  the  end  of  their   project.   Suitable  for:  This  project  is  open  to  UQ-­‐enrolled  students  only,  with  a   background  in  chemistry  and  biochemistry.   Primary  Supervisor:  Professor  Glenn  F.  King   Further  info:  Only  one  position  is  available  for  this  project.  Applicants  must   contact  Prof.  King  by  email  at                          

Smythe group   Project  Title:  The  Development  of  HPGD2S  Inhibitors  for  Asthma   Project  duration:  8  weeks   Description:  The  prevalence,  complexity  and  severity  of  allergic  disease  and   asthma  are  increasing  worldwide,  particularly  in  developed  countries.  Currently,   most  asthma  patients  manage  the  disease  through  a  combination  of  fast-­‐acting   relief,  including  beta2-­‐agonists,  and  long  term  medications,  such  as   corticosteroids.  However,  these  therapies  provide  non-­‐specific,  anti-­‐ inflammatory  treatment  of  the  underlying  disease  and  only  offer  patients   symptomatic  relief.  Prostaglandin  D2  (PGD2)  is  a  well  recognized  pro-­‐ inflammatory  modulator  of  asthma  and  allergic  disease.  Hematopoietic   prostaglandin  D2  synthase  (HPGD2S)  is  the  enzyme  responsible  for  the   overproduction  of  PGD2  and  is  a  well  validated  target  for  therapeutic   intervention.   Expected  outcomes  and  deliverables:  Our  research  team  is  focused  on  drug   design  using  a  plethora  of  medicinal  chemistry  techniques.  Successful  applicants   will  synthesize  an  array  of  small  molecule  inhibitors  using  a  combination  of   synthetic  organic  chemistry  and  peptide  chemistry  techniques.  Students  will  test   these  inhibitors  in  an  enzyme  assay  and  develop  a  structure-­‐activity  relationship   between  the  molecules  and  their  biological  activity.  Throughout  the  project,   students  will  be  given  the  opportunity  to  develop  and  design  their  own   inhibitors.  The  overall  aim  of  the  project  will  be  to  improve  the  potency  of  a  lead   compound.   Suitable  for:  The  project  is  open  to  applications  from  motivated  students  with  a   background  in  chemistry.   Primary  Supervisor:  A/Prof  Mark  Smythe  Co-­‐supervisor:  Dr  Christina  Kulis   Further  info:  Please  contact  Christina  Kulis  before   submitting  an  application.    

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