An asymmetric approach to preserve common intervals while sorting by reversals

Background  

The reversal distance and optimal sequences of reversals to transform a genome into another are useful tools to analyse evolutionary scenarios. However, the number of sequences is huge and some additional criteria should be used to obtain a more accurate analysis. One strategy is searching for sequences that respect constraints, such as the common intervals (clusters of co-localised genes). Another approach is to explore the whole space of sorting sequences, eventually grouping them into classes of equivalence. Recently both strategies started to be put together, to restrain the space to the sequences that respect constraints. In particular an algorithm has been proposed to list classes whose sorting sequences do not break the common intervals detected between the two inital genomes A and B. This approach may reduce the space of sequences and is symmetric (the result of the analysis sorting A into B can be obtained from the analysis sorting B into A).     

An easy case of sorting by reversals.

We show that a special case of sorting by reversals can be performed in polynomial time, namely, when the number of breakpoints is twice the distance.     

Perfect sorting by reversals is not always difficult

We propose new algorithms for computing pairwise rearrangement scenarios that conserve the combinatorial structure of genomes. More precisely, we investigate the problem of sorting signed permutations by reversals without breaking common intervals. We describe a combinatorial framework for this problem that allows us to characterize classes of signed permutations for which one can compute, in polynomial time, a shortest reversal scenario that conserves all common intervals. In particular, we define a class of permutations for which this computation can be done in linear time with a very simple algorithm that does not rely on the classical Hannenhalli-Pevzner theory for sorting by reversals. We apply these methods to the computation of rearrangement scenarios between permutations obtained from 16 synteny blocks of the X chromosomes of the human, mouse, and rat     

Evolution under reversals: parsimony and conservation of common intervals

In comparative genomics, gene order data is often modeled as signed permutations. A classical problem for genome comparison is to detect common intervals in permutations, that is, genes that are colocalized in several species, indicating that they remained grouped during evolution. A second largely studied problem related to gene order is to compute a minimum scenario of reversals that transforms a signed permutation into another. Several studies began to mix the two problems and it was observed that their results are not always compatible: Often, parsimonious scenarios of reversals break common intervals. If a scenario does not break any common interval, it is called perfect. In two recent studies, Berard et al. defined a class of permutations for which building a perfect scenario of reversals sorting a permutation was achieved in polynomial time and stated as an open question whether it is possible to decide, given a permutation, if there exists a minimum scenario of reversals that is perfect. In this paper, we give a solution to this problem and prove that this widens the class of permutations addressed by the aforementioned studies. We implemented and tested this algorithm on gene order data of chromosomes from several mammal species and we compared it to other methods. The algorithm helps to choose among several possible scenarios of reversals and indicates that the minimum scenario of reversals is not always the most plausible     

Exploring the solution space of sorting by reversals, with experiments and an application to evolution

In comparative genomics, algorithms that sort permutations by reversals are often used to propose evolutionary scenarios of rearrangements between species. One of the main problems of such methods is that they give one solution while the number of optimal solutions is huge, with no criteria to discriminate among them. Bergeron et al. started to give some structure to the set of optimal solutions, in order to be able to deliver more presentable results than only one solution or a complete list of all solutions. However, no algorithm exists so far to compute this structure except through the enumeration of all solutions, which takes too much time even for small permutations. Bergeron et al. state as an open problem the design of such an algorithm. We propose in this paper an answer to this problem, that is, an algorithm which gives all the classes of solutions and counts the number of solutions in each class, with a better theoretical and practical complexity than the complete enumeration method. We give an example of how to reduce the number of classes obtained, using further constraints. Finally, we apply our algorithm to analyse the possible scenarios of rearrangement between mammalian sex chromosomes.     

The genome and the nucleus: a marriage made by evolution

Genomes are housed within cell nuclei as individual chromosome territories. Nuclei contain several architectural structures that interact and influence the genome. In this review, we discuss how the genome may be organised within its nuclear environment with the position of chromosomes inside nuclei being either influenced by gene density or by chromosomes size. We compare interphase genome organisation in diverse species and reveal similarities and differences between evolutionary divergent organisms. Genome organisation is also discussed with relevance to regulation of gene expression, development and differentiation and asks whether large movements of whole chromosomes are really observed during differentiation. Literature and data describing alterations to genome organisation in disease are also discussed. Further, the nuclear structures that are involved in genome function are described, with reference to what happens to the genome when these structures contain protein from mutant genes as in the laminopathies. Review related to the 15th International Chromosome Conference (ICC XV), held in September 2004, Brunel University, London, UK     

In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting

Water-in-oil (w/o) emulsions can be used to compartmentalize and select large gene libraries for a predetermined function. The aqueous droplets of the w/o emulsion function as cell-like compartments in each of which a single gene is transcribed and translated to give multiple copies of the protein (e.g., an enzyme) it encodes. While compartmentalization ensures that the gene, the protein it encodes, and the products of the activity of this protein remain linked, it does not directly afford a way of selecting for the desired activity. Here we show that re-emulsification of w/o emulsions gives water-in-oil-in-water (w/o/w) emulsions with an external (continuous) water phase through which droplets containing fluorescent markers can be isolated by fluorescence-activated cell sorting (FACS). These w/o/w emulsions can be sorted by FACS, while the content of the aqueous droplets of the primary w/o emulsion remains intact. Consequently, genes embedded in these water droplets together with a fluorescent marker can be isolated and enriched from an excess of genes embedded in water droplets without a fluorescent marker. The ability of FACS instruments to sort up to 40000 events per second may endow this technology a wide potential in the area of high-throughput screening and the directed evolution of enzymes.     

Cache consensus: rapid object sorting by a robotic swarm

We present a new method which allows a swarm of robots to sort arbitrarily arranged objects into homogeneous clusters. In the ideal case, a distributed robotic sorting method should establish a single homogeneous cluster for each object type. This can be achieved with existing methods, but the rate of convergence is considered too slow for real-world application. Previous research on distributed robotic sorting is typified by randomised movement with a pick-up/deposit behaviour that is a probabilistic function of local object density. We investigate whether the ability of each robot to localise and return to remembered places can improve distributed sorting performance. In our method, each robot maintains a cache point for each object type. Upon collecting an object, it returns to add this object to the cluster surrounding the cache point. Similar to previous biologically inspired work on distributed sorting, no explicit communication between robots is implemented. However, the robots can still come to a consensus on the best cache for each object type by observing clusters and comparing their sizes with remembered cache sizes. We refer to this method as cache consensus. Our results indicate that incorporating this localisation capability enables a significant improvement in the rate of convergence. We present experimental results using a realistic simulation of our targeted robotic platform. A subset of these experiments is also validated on physical robots.     

Protein sorting in the Golgi apparatus: a consequence of maturation and triggered sorting

To explain how resident proteins distribute in peak-like patterns at various positions in the secretory pathway, Glick and co-workers postulated that resident proteins comprise different populations (termed kin populations) and that these compete with each other for entering retrograde transport carriers [Glick et al. (1997) FEBS Lett. 414, 177-181]. Using modelling and computer simulation, they could demonstrate that differences in competitiveness sufficed to generate overlapping but distinct peak-like steady state distributions of the different kin populations across the Golgi stack. In this study, we have tested the robustness of the competition model and find that over-expression or changes in the number of kin populations affect their overall steady state distributions. To increase the robustness of the system, we have introduced a milieu-induced trigger for recycling. This allows for a decrease in the coupling between kin populations permitting both over-expression as well as changes in the number of kin populations. We have also extended the model to include a Golgi to endoplasmic reticulum (ER) recycling pathway and find that only a small amount of resident proteins may recycle at any time without upsetting their observed distributions in the Golgi stack. The biological relevance of a trigger-induced sorting mechanism and ER recycling is discussed.     

Common principles in clathrin-mediated sorting at the Golgi and the plasma membrane

Clathrin-mediated vesicular trafficking events underpin the vectorial transfer of macromolecules between several eukaryotic membrane-bound compartments. Classical models for coat operation, focused principally on interactions between clathrin, the heterotetrameric adaptor complexes, and cargo molecules, fail to account for the full complexity of the coat assembly and sorting process. New data reveal that targeting of clathrin adaptor complexes is generally supported by phosphoinositides, that cargo recognition by heterotetrameric adaptors depends on phosphorylation-driven conformational alterations, and that dedicated clathrin-associated sorting proteins (CLASPs) exist to promote the selective trafficking of specific categories of cargo. A host of accessory factors also participate in coat polymerization events, and the independently folded appendage domains that project off the heterotetrameric adaptor core function as recruitment platforms that appear to oversee assembly operations. It is also now clear that focal polymerization of branched actin microfilaments contributes to clathrin-coated vesicle assembly and movement at both plasma membrane and Golgi sites. This improved appreciation of the complex mechanisms governing clathrin-dependent sorting events reveals several common principles of clathrin operation at the Golgi and the plasma membrane.     

Plant glycosyl hydrolases and biofuels: a natural marriage

Much of what is currently known about the structure, properties and biochemical activities of glycosyl hydrolases (GHs) has resulted from detailed studies of microbial enzymes. Conversely, such information is sparse in the plant GH literature, where the focus has traditionally been on studying expression and biological function. However, the current resurgence of interest in lignocellulosic biofuels is catalyzing new interest in this field, and recent reports suggest that some plant GH families have more in common with their microbial counterparts than was previously suspected. The repertoires of plant GHs, with their associated catalytic activities and polysaccharide binding affinities, may have valuable applications in modifying plant cell wall architecture and in the development and characterization of new bioenergy feedstocks.     

PAR proteins and the cytoskeleton: a marriage of equals

The PAR proteins are a group of widely conserved regulators of polarity, many of which are asymmetrically localized in polarized cells. Recent work shows that distinct modes of actomyosin- and microtubule-based transport contribute to the establishment of PAR asymmetries in different cell types. Cross-regulatory interactions among PAR proteins and with other conserved polarity complexes stabilize asymmetries once they form, and shape the evolution of PAR protein distributions in response to cytoskeletal transport or other polarizing inputs. The PAR proteins in turn modulate the actomyosin and microtubule cytoskeletons. In some cases, this is a form of feedback control, central to the establishment and maintenance of PAR asymmetries. In others, it underlies the elaboration of functional cell polarity.     

Sorting by reversals and block-interchanges with various weight assignments

Background  

A classical problem in studying genome rearrangements is understanding the series of rearrangement events involved in transforming one genome into another in accordance with the parsimonious principle when two genomes with the same set of genes differ in gene order. The most studied event is the reversal, but an increasing number of reports have considered reversals along with other genome rearrangement events. Some recent studies have investigated the use of reversals and block-interchanges simultaneously with a weight proportion of 1:2. However, there has been less progress towards exploring additional combinations of weights.     

Improving the biosafety of cell sorting by adaptation of a cell sorting system to a biosafety cabinet.

BACKGROUND: The jet-in-air cell sorters currently available are not very suitable for sorting potentially biohazardous material under optimal conditions because they do not protect operators and samples as recommended in the guidelines for safe biotechnology. To solve this problem we have adapted a cell sorting system to a special biosafety cabinet that satisfies the requirements for class II cabinets. With aid of this unit, sorting can be performed in conformance with the recommendations for biosafety level 2. METHODS: After integrating a modified fluorescence-activated cell sorter (FACS) Vantage into a special biosafety cabinet, we investigated the influence of the laminar air flow (LAF) inside the cabinet on side stream stability and the analytical precision of the cell sorter. In addition to the routine electronic counting of microparticles, we carried out tests on the containment of aerosols, using T4 bacteriophage as indicators, to demonstrate the efficiency of the biosafety cabinet for sorting experiments performed under biosafety level 2 conditions. RESULTS: The experiments showed that LAF, which is necessary to build up sterile conditions in a biosafety cabinet, does not influence the conditions for side stream stability or the analytical precision of the FACS Vantage cell sorting system. In addition, tests performed to assess aerosol containment during operation of the special biosafety cabinet demonstrated that the cabinet-integrated FACS Vantage unit (CIF) satisfies the conditions for class II cabinets. In the context of gene transfer experiments, the CIF facility was used to sort hematopoietic progenitor cells under biosafety level 2 conditions. CONCLUSIONS: The newly designed biosafety cabinet offers a practical modality for improving biosafety for operators and samples during cell sorting procedures. It can thus also be used for sorting experiments with genetically modified organisms in conformance with current biosafety regulations and guidelines.     

Regulatory T cells and infection: a dangerous necessity

Surviving a given infection requires the generation of a controlled immune response. Failure to establish or restore homeostatic conditions during or following the onset of an infection can lead to tissue damage. Investigation of the immunoregulatory network that arises in response to the infectious process or that is induced by the pathogen itself should provide insight into therapeutic approaches for the control of infection and any subsequent immunopathology. In this Review, I discuss current hypotheses and points of polemic associated with the origin, mode of action and antigen specificity of the various populations of regulatory T cells that arise during infection.     

Common intervals and symmetric difference in a model-free phylogenomics, with an application to streptophyte evolution.

The common intervals of two permutations on n elements are the subsets of terms contiguous in both permutations. They constitute the most basic representation of conserved local order. We use d, the size of the symmetric difference (the complement of the common intervals) of the two subsets of 2({1,n}) thus determined by two permutations, as an evolutionary distance between the gene orders represented by the permutations. We consider the Steiner Tree problem in the space (2({1,n}), d) as the basis for constructing phylogenetic trees, including ancestral gene orders. We extend this to genomes with unequal gene content and to genomes containing gene families. Applied to streptophyte phylogeny, our method does not support the positioning of the complex algae Charales as a sister group to the land plants. Simulations show that the method, though unmotivated by any specific model of genome rearrangement, accurately reconstructs a tree from artificial genome data generated by random inversions deriving each genome from its ancestor on this tree.