CRM Genome Rearrangements Symposium

--- Biological, Computational, Algebraic/Combinatorial Perspectives ---

Thursday April 23rd 2015,  9am - 6pm

UWS, Parramatta (Main/South) Campus

Please register your interest and whether you'd like to join for the post-symposium dinner ASAP, preferably by Thursday April 16th with Dr. Shona Yu <s.yu@uws.edu.au>.

Everyone is welcome!

Confirmed speakers:

 

Talk Schedule

Morning session (EB.3.21)

  9:00 -- 10:00   Welcoming coffee 
10:00 -- 10:40   Pedro Feijão 
10:40 -- 11:20   Aaron Darling 
11:20 -- 11:40   Stephen Cameron

Lunch              (Provided in the River bar/cafe, directly below the CRM, in the EN building)

Afternoon session (EB.3.36)

 1:30 -- 2:10     Ian Grainge 
 2:10 -- 2:30     Stuart Serdoz 
 2:30 -- 3:10     Jeremy Sumner
 3:10 -- 3:30     Sangeeta Bhatia

 3:30 -- 4:00     Coffee

 4:00 -- 4:20     Shoba Ranganathan
 4:20 -- 4:40     Mark Tanaka
 4:40 -- 5:20     Andrew Francis

 5:20 -- 6++      Mass discussion pit / Wine + Cheese Reception (CRM), followed by dinner outing near Parramatta train station/ferry wharf.

 

Titles and Abstracts

Sangeeta Bhatia (University of Western Sydney)

"TBA"

Abstract: TBA.

Stephen Cameron (Queensland University of Technology)

"Mitochondrial genome rearrangements in lice: A model system for ground-truthing methods?"

Abstract:   The mitochondrial (mt) genome of animals is the smallest extant genome with just 37 genes and whose composition is conserved across the Bilateria, representing over 500 million years of evolution. The arrangement of genes within the mt genome is often highly conserved for higher animal taxa (such as phyla) but varies between them. Insects (after vertebrates) are the second most widely studied group for mt genomics with almost 1000 species having been sequenced. Almost all major insect lineages retain the ancestral genome arrangement, which is also shared with crustaceans. Of the small number of insect groups that depart from this conservative pattern, lice (Phthiraptera) display the greatest levels of genome variability both in terms of genome structure and gene rearrangements. Comparisons of genome rearrangement rate and type against objective evolutionary trees constructed for lice allow us to test the frequency of rearrangement classes and assumptions about convergent genome structures. Perhaps such approaches can also be used to train/test software used to infer the evolutionary patterns of genome rearrangement in the absence of a "known" evolutionary history.

Aaron Darling (University of Technology Sydney)

"Inference of genome rearrangement histories: a perspective on the  challenges and implications for biology"

Abstract:   Genome evolution, including the evolution of genome arrangement, has  been studied for decades. In this time we have witnessed great  technological advances in our ability to generate genome sequence data,  along with corresponding advances in theorems and algorithms to  reconstruct the history of events that led to modern genomes. In some  cases, these analysis techniques have uncovered patterns in genome  evolution that appear to be pervasive in living organisms. However, in  many cases, the actual history of evolutionary events remains poorly  informed by the data. Not only is the order in which events took place  usually poorly informed, but so are the actual events themselves in most  cases. In this seminar I will review the current state of the art in  genome evolution inference, identifying some areas current algorithms  and theorems are inadequate, along with suggestions for how the field  might contribute important biological insight in the future.

Pedro Feijão (Universität Bielefeld, Germany)

"Permutation groups applied to genome rearrangement problems"

Abstract:   Genome evolution occurs in many ways, from small mutations that change individual nucleotides, to large scale events, such as genome rearrangements, that move large pieces of DNA to different positions and even different chromosomes.

The first formal approaches for comparing genomes considering rearrangement events were proposed in the 1990's, with genomes modelled as permutations, but initial results are based on graph and combinatorial approaches.
A different approach, proposed by Meidanis and Dias in 2000, aims to solve genome rearrangement problems algebraically, using permutations groups. In this talk, I will give an overview of our groups' research in this field, with results and current challenges of using permutations groups in genome rearrangements.

Andrew Francis (University of Western Sydney)

"Affine symmetric groups, coloured diagram algebras and bacterial genome evolution"

Abstract:   The inversion process in bacteria arises through the same biological process as knotting, and yet their modelling has been done with totally disjoint toolkits. In this talk I will report on some recent work modelling the inversion process with affine symmetric groups, and briefly report on our progress towards a unified algebraic framework for the biology using coloured diagram algebras.

Joint work with: Sangeeta Bhatia, Attila Egri-Nagy, Volker Gebhardt, Stuart Serdoz, Mark Tanaka, Shona Yu.

Ian Grainge (University of Newcastle)

"Simple topology: FtsK directed recombination at dif sites"

Abstract:   Bacteria generally have circular chromosomes, and circular chromosomes have many advantages during replication and segregation before cell division. One disadvantage, though, is that DNA repair mechanisms can lead to a genetic crossover between the two circles of DNA resulting in them being joined into a single circular dimer, which cannot be divided equally to the two daughter cells at division. To resolve the chromosome dimer back to monomers bacteria have evolved a site-specific recombination system which acts at a site called dif. Two tyrosine recombinases, XerC and XerD, each cut and exchange one pair of DNA strands at the two dif sites in a dimeric chromosome, but this reaction is further controlled by a DNA translocase protein, FtsK. Reactions on model substrates show that when FtsK is present the reaction products are exclusively unlinked circular products rather than catenanes. How exactly FtsK directs reactions to a simple topological outcome remains an interesting question.

Shoba Ranganathan (Macquarie University)

"Biomarkers for ovarian cancer using an integrated approach in a Boolean framework"

Abstract:   Cancer is a complex disease where molecular mechanism remains elusive. A systems approach is needed to integrate diverse biological information for the prognosis and therapy risk assessment using mechanistic approach to understand gene interactions in pathways and networks and functional attributes to unravel the biological behaviour of tumors.

We weighted the functional attributes based on various functional properties observed between cancerous and non-cancerous genes reported from literature. This weighing schema was then encoded in a Boolean logic framework to rank differentially expressed genes. We have identified 17 genes to be differentially expressed from a total of 11,173 genes, where ten genes are reported to be down-regulated via epigenetic inactivation and seven genes are up-regulated. Here, we report that the overexpressed genes IRAK1, CHEK1 and BUB1 may play an important role in ovarian cancer. We also show that these 17 genes can be used to form an ovarian cancer signature, to distinguish normal from ovarian cancer subjects and that the set of three genes, CHEK1, AR, and LYN, can be used to classify good and poor prognostic tumors.

We have developed a workflow using a Boolean logic schema for the identification of differentially expressed genes by integrating diverse biological information. This integrated approach resulted in the identification of genes as potential biomarkers in ovarian cancer.

Stuart Serdoz (University of Western Sydney)

"Bacterial genome rearrangements and expected distance"

Abstract:   The aim of many rearrangement algorithms is to attempt to find the minimum number of rearrangements to explain the change between two genomes. These pairwise distances are used in phylogenetic reconstruction methods such as NJ, UPGMA, and the Fitch-Margoliash method. The key criticism of minimal distance is that it underestimates the true length of the evolutionary path. Our approach takes into account the underlying group structure to provide a weighted average distance over all possible histories with the idea of providing an expected distance. This talk will introduce the development of the expected distance with a focus on walks on Cayley graphs.

Jeremy Sumner (University of Tasmania)

"A representation-theoretic approach to the calculation of genome rearrangement distances"

Abstract:      A simple model of circular genome rearrangements is obtained by taking a restricted set of gene permutations S and considering the distance between two genomes to be related to the number of permutations required to convert one genome into the other. Stochastically, we consider genome evolution as a Poisson process where each permutation in S is applied with uniform rate, with the distance between two genomes defined as the maximum likelihood time passed. Algebraically, the set of permutations S generates a group G and we need to compute the number of ways of expressing a given element of G as a word of length k in "letters" S. Unfortunately, this algebraic task is combinatorially intensive (factorial in the number of genes/regions) but must be solved in order for the stochastic analysis to proceed. I will present some recent ponderings taking a representation-theoretic approach which converts the combinatorial problem into linear algebra and the computation of certain eigenvalues. This improves the complexity of the problem a little (by a square root!), but is by no means a silver bullet (square root of factorial complexity is still terrible!)

Mark Tanaka (University of New South Wales)

"Mobile genes in evolving genomes: do bursts of transposition help insertion sequences persist?"

Abstract:       It is unclear why mobile genes called insertion sequences (ISs) occur widely among bacteria despite being mostly harmful to their host genomes. Rates of horizontal gene transfer are likely to be too low to maintain ISs. Beneficial mutations induced by ISs are likely to be too rare to sustain them in the long run. Stressful environments can cause rates of IS transposition to be elevated. We ask whether these bursts of
transposition can facilitate the persistence of ISs. We consider an evolutionary model of IS dynamics in which a transient transposition burst occurs. Here I will describe how ISs increase variation in reproductive fitness thereby allowing host populations to adapt to new environments; I will discuss the implications of our findings for the persistence of ISs on evolutionary timescales.


How to get here

The symposium is held at the Main Parramatta (South) campus [map]; 

Talks + coffee are all in the EB building and lunch will be provided in the River bar/cafe below the Centre for Research in Mathematics division of the EN building (next to Subway).

Flying:

Unfortunately UWS does not have a private helipad/airport (that I have access to). 

The nearest airport is Sydney (Kingsford-Smith) airport -- From here you can catch the Airport Link train then change at Central train station for another train to Parramatta/Rydalmere train station. 

Train/public transport: 

Please look up the TransportNSW website, for Airport Link train times and public transport (trains, buses, ferries, light rail) in Sydney in general.

Rydalmere station is ~11 minutes walk from the EB building.

OR

Parramatta station is ~36 minutes walk from the EB building; there are several regular buses (e.g., M52, 521, 525; bus ride <10 mins) though from the Stand A2 bus stop just outside the train station.

Parking:

There are, e.g., 4 carparks next to the EB building (between it and James Ruse Drive; see map link above).

Warning: It is apparently extremely stress-inducing to try and find a parking after 8:43am, during teaching term!

A bit more information can be found here .

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