Seminars | This Week

CASB Seminar

Date/Time: Monday 30th April 2018 11:30

Location: IMB Auditorium

Title of talk: Integration of informatics and metabolic engineering for the discovery and analysis of novel antibiotics
Speaker's name: Prof Tilmann Weber
Speaker's organisation: Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark
Talk abstract: Genome analyses of many microorganisms indicate that the genetic potential to synthesize secondary metabolites is far beyond the number of molecules observed in traditional chemical screenings. Thus, genome mining for natural products biosynthetic pathways has emerged as an important technology complementing the chemical approaches. This trend was supported by the public availability of powerful genome mining bioinformatics software that allow microbiologists or chemists to carry out such analyses. In collaboration with the group of M. Medema at Wageningen University, we are coordinating the development of the comprehensive genome mining platform antiSMASH (http://antismash.secondarymetabolites.org), which allows users to easily mine microbial (and plant) genomic sequences for the presence of secondary metabolite biosynthetic gene clusters. We have also recently released the antiSMASH database (http://antismash-db.secondarymetabolites.org), a user-friendly web-based application featuring >3000 annotated bacterial genomes. These genome mining technologies build the foundations of our experimental work on actinomycetes, a group of organisms that historically have been - and still are - among the most important producers of natural antibiotics. In response to severe limitations concerning the efficiency of mutagenesis protocols essential to metabolic engineering and synthetic biology approaches, we developed a CRISPR/Cas9-based toolkit for streptomycetes and other actinomycetes. This toolkit was extended with our software CRISPy-web (http://crispy.secondarymetabolites.org), which enables users to design the sgRNAs required for the CRISPR/Cas9 experiments for any user-submitted microbial genome in a user-friendly web-interface. Having such tools at hand, it is not only possible to identify the biosynthetic pathways, but also to engineer them directly. Based on knowledge of the biosynthesis of the antibiotic kirromycin, we were recently able to engineer a strain to incorporate non-natural polyketide extender units enabling easily accessible Click-chemistry modifications.

Host name: Prof Rob Capon
Host phone number: 334 62979
Host email: r.capon@imb.uq.edu.au

Seminars | This Week

IMB Seminar Series

Date/Time: Friday 27th April 2018 12:30

Location: QBP Auditorium, Bld 80

Title of talk: New insights into subnuclear paraspeckles: where long noncoding RNA meets phase separation
Speaker's name: Dr Archa Fox
Speaker's organisation: The University of Western Australia
Talk abstract: Paraspeckles are protein-rich nuclear organelles built around a specific long noncoding RNA scaffold. New discoveries show how paraspeckles are formed through multiple RNA-protein and protein-protein interactions, some of which involve multivalent interactions driving phase separation. Once formed, paraspeckles influence gene regulation through sequestration of component proteins and RNAs, with subsequent depletion in other compartments. Here I will focus on the dual aspects of paraspeckle structure and function, revealing an emerging role for these dynamic bodies in a multitude of cellular settings, including, in particular, cancer.

Host name: Associate Professor Brett Collins
Host email: imbevents@uq.edu.au

Seminars | This Week

IMB Seminar Series

Date/Time: Friday 4th May 2018 12:30

Location: QBP Auditorium, Bld 80

Title of talk: Origin of animal multicellularity and complex differentiation landscapes
Speaker's name: Professor Bernie Degnan
Speaker's organisation: School of Biological Sciences, UQ
Talk abstract: The shared ancestor of all living animals minimally possessed epithelial and mesenchymal cell types that could transdifferentiate over an ontogenetic life cycle. This capacity to develop and differentiate required a regulatory capacity to control spatial and temporal gene expression, and included a diversified set of signaling pathways, transcription factors, distal enhancers, promoters and noncoding RNAs. In this seminar, I track the evolution of the regulatory architecture underlying cell differentiation in multicellular animals and provide evidence consistent with the first animal cell having a stem-like capacity to transition between multiple differentiated states.

Host name: Professor Peter Koopman
Host email: imbevents@uq.edu.au

Seminars | This Week

Chemistry and Structural Biology Division Seminar

Date/Time: Thursday 3rd May 2018 12:30

Location: Seminar Room 3.142, QBP Bldg 80, UQ St Lucia

Title of talk: Inhibition of the biosynthesis of branched chain amino acids: Herbicides, fungicides and antibacterials
Speaker's name: Dr Luke Guddat
Speaker's organisation: SCMB, University of Queensland
Talk abstract: Acetohydroxyacid synthase (AHAS) is the first enzyme in the branched chain amino acid (i.e. leucine, valine and isoleucine) biosynthesis pathway, whose activity is essential for the survival of plants, fungi and bacteria. However, humans do not have this pathway and instead rely on dietary intake to supply these essential metabolites. Due to this difference in metabolism been animals and other organisms AHAS is an excellent target for both herbicide and antimicrobial drug discovery. Indeed, more than 50 inhibitors of AHAS have been developed as commercial herbicides, with some of these compounds also exhibiting antifungal and antituberculosis activity. Our group has used X-ray crystallography, mass spectrometry and enzyme kinetics to provide a comprehensive understanding as to how the five different chemical classes exert their activity as inhibitors of AHAS and as herbicides. Furthermore, we have shown that it is a combination of direct inhibition to AHAS and their ability to accelerate the production of reactive oxygen species due to a side reaction of AHAS that accounts for their extraordinary biological activity. Insights from the structural investigations provide new ideas as to how to overcome the development of herbicide resistance and how to design new compounds that could be repurposed as antimicrobial agents.

Host name: Professor David Fairlie
Host phone number: 62989
Host email: d.fairlie@imb.uq.edu.au

Seminars | This Week

QAAFI Science Seminar

Date/Time: Tuesday 24th April 2018 12:00

Location: 3.142, Level 3

Title of talk: Ecological risk assessment of nanopesticides
Speaker's name: Dr Melanie Kah
Speaker's organisation: University of Vienna/CSIRO
Talk abstract: The presentation will build on the results of a series of workshops organised with a group drawn from regulatory agencies, academia, research, and the agrochemicals industry, and aiming to establish guiding principles for the regulatory evaluation of nano-enabled pesticides. The talk will also include the results of experiments looking at how nano carrier systems affect the transport and degradation of pesticides in the environment, and how this can be measured and incorporated into ecological assessment.

Host name: QAAFI Communications
Host phone number: 0733462168
Host email: qaaficomms@uq.edu.au

Seminars | This Week

Genomics of Development and Disease Seminar Series

Date/Time: Thursday 26th April 2018 11:00

Location: Large Seminar Room

Title of talk: Phenotypic prediction in human complex traits and diseases using big data
Speaker's name: Ying Wang
Speaker's organisation: IMB, UQ (Visscher Group)

Title of talk: Evaluating the Klebsiella pneumoniae resistome via Oxford Nanopore Technologies MinION sequencing
Speaker's name: Miranda Pitt
Speaker's organisation: IMB, UQ (Coin Group)

Host name: Quan Nguyen
Host email: quan.nguyen@imb.uq.edu.au

Seminars | This Week

SBMS Seminar

Date/Time: Monday 30th April 2018 13:00

Location: QBI auditorium

Title of talk: Complexities in angiotensin receptor signalling and implications for cardiovascular control
Speaker's name: Professor Wally Thomas
Speaker's organisation: School of Biomedical Sciences, The University of Queensland

Host name: Dr Niwanthi Rajapakse
Host email: n.rajapakse@uq.edu.au

Seminars | This Week

UQ Genomics Initiative

Date/Time: Tuesday 24th April 2018 14:30

Location: QBP Small Seminar Room 80-3-146

Title of talk: The Use of Confirmation Capture Technology for Genome Assembly, Genome Wide Structural Variation and TAD Analysis
Speaker's name: Veronica Mankinen
Speaker's organisation: Dovetail Genomics
Talk abstract: Proximity ligation, a library prep technique that enables visualization of regions of the genome that although distant in genomic space are in close proximity when the genome is in its native 3-dimensional state, can be used for a variety of applications including Scaffolding of de-novo genome assemblies up to full chromosomes, visualization of genome wide Structural Variation and evaluation of
TADs, Topologically Associated Domains.
Dovetail Genomics is focused on the use of Proximity Ligation in all of these applications through our services and our new kits. During this seminar we will present an overview of the techniques and case studies of each of these applications for use in human, agricultural and evolutionary biology applications.

Title of talk: The Story of the Brahman Genome: from contigs to chromosomes
Speaker's name: Elizabeth Ross
Speaker's organisation: Queensland Alliance for Agriculture and Food Innovation
Talk abstract: Just 15 years after the massive undertaking that was the Human Genome Project, we have now
reached a point where technological advances make it possible to sequence and assemble a de-novo
genome in under one year to a reference standard. This may be the tipping point where it is now viable
for economically important species to have a reference quality genome sequence. Sequencing of a
Brahman genome (Bos indicus) for use a reference was identified as an industry goal, to ensure that
cattle with B. indicus genomic content can fully benefit from the full suite of genomics technologies (e.g.
GWAS) that are available for trait improvement and understanding. Here we present the Brahman
reference genome. In total 195GB of sequence data was obtained from the PacBio Sequel. The
sequence reads were error corrected using the DAZZler scrubber suite and then assembled with the
Falcon assembler. The assembly yielded 1867 contigs, with an N50 of 6MB. The assembled contigs
were error corrected with Arrow, and then scaffolded using Hi-C and Chicago data. After scaffolding the assembly consisted of 843 scaffolds with an N50 of 62MB, and L50 of 13 with 1106 gaps. The scaffolds then underwent several rounds of gap filling using PBJelly and Arrow. After gap filling and polishing the assembly consists of 835 scaffolds, which contain only 443 gaps in total. Eighteen of the
30 chromosomes are present at >95% length in a single scaffold, including the notoriously hard to assemble X chromosome. The X chromosome scaffold contains 83 gaps and shows a high level of agreement with other recent cattle assemblies. By using independent scaffolding methods it will be possible to compare the B. indicus and Bos taurus genomes with the aim of identifying structural variation and other genomic differences.

Host name: Brooke Gardiner & Yuanyuan Cheng
Host phone number: 0403126221
Host email: brooke.gardiner@uq.edu.au

Seminars | This Week

QBI Neuroscience Seminar

Date/Time: Tuesday 1st May 2018 11:00

Location: QBI, Level 7 Auditorium

Title of talk: CNTN4, a candidate gene for autism spectrum disorders, affects hippocampal neuronal function and behaviour
Speaker's name: Dr Asami Oguro-Ando
Speaker's organisation: University of Exeter Medical School Exeter, UK
Talk abstract: Autism spectrum disorders (ASD) are neurodevelopmental disorders that are clinically detected by impairments in social interaction and restricted, repetitive behaviour. Learning and memory behaviour is one of the endophenotypes that can be studied to simplify the heterogeneity in ASD. Contactin4 (CNTN4), an Ig cell adhesion molecule (IgCAM) gene, has been reported as a strongly associated gene with ASD. We target the functional analysis of CNTN4 and how it changes hippocampal brain functions. The goal of this study is to understand how CNTN4 loss-of-function impacts brain development and behaviour. To this end we used a Cntn4-knockout (KO) mouse model and determined hippocampal neuronal morphology, subjected mice to fear conditioning and hippocampal long-term potentiation.
First, we tested if Cntn4 gene expression affects CA1 synaptic transmission and the ability to induce LTP in hippocampal slices. Stimulation in CA1 stratum radiatum with 900 pulses at 10 Hz and 1 pulse at 100 Hz significantly decreased synaptic potentiation in Cntn4 KO mice.
Next, we investigated brain morphological changes in Cntn4 KO mice. Golgi analyses showed abnormal dendritic arborisation of hippocampal CA1 neurons and an increased hippocampal volume. Furthermore, it was also investigated whether these changes correlated with deficits in learning and memory behaviour. For that purpose, short- and long-term recognition memory, spatial memory and fear conditioning responses were assessed. These behavioural studies showed increased contextual fear conditioning in Cntn4 heterozygous and homozygous KO mice, quantified by a gene-dose dependent increase in freezing response. In comparison to wild-type mice, Cntn4-deficient animals froze significantly less and groomed more, indicative of increased stress responsiveness under the test conditions. Our neuro-anatomical behavioural and electrophysiological results in Cntn4 KO mice suggest that CNTN4 has important functions for fear memory through the neuronal morphological and synaptic plasticity changes in hippocampus CA1.

Host name: Deirdre Wilson
Host email: d.wilson5@uq.edu.au