Zanoni Dias

Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.

Reversal and transposition distance of linear chromosomes

In recent years we are seeing increasing interest in research on mutational events acting on large portions of chromosomes. Among these events, a reversal acts on a fragment of a chromosome, reversing the order and orientation of the genes, and a transposition moves fragments from one region to another within a chromosome. We analyze genomes evolving by reversals and transpositions. We present approximation algorithms to compute the reversal and transposition distance for linear permutations, and a lower bound on the reversal and transposition diameter of signed linear permutations.

Image Phylogeny by Minimal Spanning Trees

Nowadays, digital content is widespread and also easily redistributable, either lawfully or unlawfully. Images and other digital content can also mutate as they spread out. For example, after images are posted on the Internet, other users can copy, resize and/or re-encode them and then repost their versions, thereby generating similar but not identical copies. While it is straightforward to detect exact image duplicates, this is not the case for slightly modified versions. In the last decade, some researchers have successfully focused on the design and deployment of near-duplicate detection and recognition systems to identify the cohabiting versions of a given document in the wild. Those efforts notwithstanding, only recently have there been the first attempts to go beyond the detection of near-duplicates to find the structure of evolution within a set of images. In this paper, we tackle and formally define the problem of identifying these image relationships within a set of near-duplicate images, what we call Image Phylogeny Tree (IPT), due to its natural analogy with biological systems. The mechanism of building IPTs aims at finding the structure of transformations and their parameters if necessary, among a near-duplicate image set, and has immediate applications in security and law-enforcement, forensics, copyright enforcement, and news tracking services. We devise a method for calculating an asymmetric dissimilarity matrix from a set of near-duplicate images and formally introduce an efficient algorithm to build IPTs from such a matrix. We validate our approach with more than 625000 test cases, including both synthetic and real data, and show that when using an appropriate dissimilarity function we can obtain good IPT reconstruction even when some pieces of information are missing. We also evaluate our solution when there are more than one near-duplicate sets in the pool of analysis and compare to other recent related approaches in the literature.

First steps toward image phylogeny

In this paper, we introduce and formally define a new problem, Image Phylogeny Tree (IPT): to find the structure of transformations, and their parameters, that generate a given set of near duplicate images. This problem has direct applications in security, forensics, and copyright enforcement. We devise a method for calculating an asymmetric dissimilarity matrix from a set of near duplicate images. We also describe a new algorithm to build an IPT. We also analyze our algorithms computational complexity. Finally, we perform experiments that show near-perfect reconstructed IPT results when using an appropriate dissimilarity function.

Sorting by Prefix Transpositions

A transposition is an operation that exchanges two consecutive, adjacent blocks in a permutation. A prefix transposition is a transposition that moves the first element in the permutation. In this work we present the first results on the problem of sorting permutations with the minimum number of prefix transpositions. This problem is a variation of the transposition distance problem, related to genome rearrangements. We present approximation algorithms with performance ratios of 2 and 3. We conjecture that the maximum prefix transposition distance is D(n) = n-?n/4? and present the results of several computational tests that support this. Finally, we propose an algorithm that decides whether a given permutation can be sorted using just the number of transpositions indicated by the breakpoint lower-bound.

AN ALTERNATIVE ALGEBRAIC FORMALISM FOR GENOME REARRANGEMENTS

Here we relate the recent theory of genome rearrangements to the theory of permutation groups in a new way and hope to set the ground for further advances in the area. This work was motivated by the fact that many arguments in genome rearrangements are of the form “look at the figure”, and lack more formal algebraic derivation. We intend to give the area a strong algebraic formalism, much as analytic geometry provided an alternative geometric arguments based on pictures.

Genome rearrangements distance by fusion, fission, and transposition is easy

Given two genomes represented as circularly ordered sequences of genes, we show a polynomial time algorithm for the minimum weight series of fusion, jissions, and transpositions (with transpositions weighing twice as much as fusions and

A new approach for approximating the transposition distance

ssions) that transforms one genome into the other. The algorithm is based on classical results ofpermutation group theory and is the jirst polynomial result for a genome rearrangement problem involving transpositions. It has been observed in real biological instances that transpositions occur with about ha&- the frequency of reversals. Although we are not using reversals in this study, this observation motivated the double weight assigned to transpositions.

SIS: a program to generate draft genome sequence scaffolds for prokaryotes

One of the proposed ways to compare genomes or other large DNA molecules is by computing a rearrangement distance, defined as the minimum number of rearrangement events necessary to transform one molecule into another taking into account only the relative order of similar genes. In this work, we study the problem of computing the transposition distance between two linear gene orders, represented by permutations. To help solve it, we present a very simple structure, the breakpoint diagram, and a 2.25-approximation algorithm for the problem based on this structure. While there are better approximation algorithms, they are based on more complex data structures. Our algorithm was implemented in the C programming language and we show experimental results obtained with it on all permutations of up to 11 genes, plus selected permutations of higher size.

Exploring heuristic and optimum branching algorithms for image phylogeny

BackgroundDecreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome.ResultsWe present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of sis, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that sis has overall better performance.Conclusionssis is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of sis in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.