Are we degenerate tetraploids? More genomes, new facts

<p>Abstract</p> <p>Background</p> <p>Within the bilaterians, the appearance and evolution of vertebrates is accompanied by enormous changes in anatomical, morphological and developmental features. This evolution of increased complexity has been associated with two genome duplications (2R hypothesis) at the origin of vertebrates. However, in spite of extensive debate the validity of the 2R hypothesis remains controversial. The paucity of sequence data in early years of genomic era was an intrinsic obstacle in tracking the genome evolutionary history of chordates.</p> <p>Hypothesis</p> <p>In this article I review the 2R hypothesis by taking into account the recent availability of genomic sequence data for an expanding range of animals. I argue here that genetic architecture of lower metazoans and representatives of major vertebrate and invertebrate lineages provides no support for the hypothesis relating the origin of vertebrates with widespread gene or genome duplications.</p> <p>Conclusion</p> <p>It appears that much of the genomic complexity of modern vertebrates is very ancient likely predating the origin of chordates or even the Bilaterian-Nonbilaterian divergence. The origin and evolution of vertebrates is partly accompanied by an increase in gene number. However, neither can we take this subtle increase in gene number as an only causative factor for evolution of phenotypic complexity in modern vertebrates nor we can take it as a reflection of polyplodization events early in their history.</p> <p>Reviewers</p> <p>This article was reviewed by Eugene Koonin, Joshua Cherry (nominated by David Lipman), and Jerzy Jurka.</p

An insight into the phylogenetic history of HOX linked gene families in vertebrates

<p>Abstract</p> <p>Background</p> <p>The human chromosomes 2q, 7, 12q and 17q show extensive intra-genomic homology, containing duplicate, triplicate and quadruplicate paralogous regions centered on the HOX gene clusters. The fact that two or more representatives of different gene families are linked with HOX clusters is taken as evidence that these paralogous gene sets might have arisen from a single chromosomal segment through block or whole chromosome duplication events. This would imply that the constituent genes including the HOX clusters reflect the architecture of a single ancestral block (before vertebrate origin) where all of these genes were linked in a single copy.</p> <p>Results</p> <p>In the present study we have employed the currently available set of protein data for a wide variety of vertebrate and invertebrate genomes to analyze the phylogenetic history of 11 multigene families with three or more of their representatives linked to human HOX clusters. A topology comparison approach revealed four discrete co-duplicated groups: group 1 involves the genes from GLI, HH, INHB, IGFBP (cluster-1), and SLC4A families; group 2 involves ERBB, ZNFN1A, and IGFBP (cluster-2) gene families; group 3 involves the HOX clusters and the SP gene family; group 4 involves the integrin beta chain and myosine light chain families. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups may not share their evolutionary history and may not have duplicated simultaneously.</p> <p>Conclusion</p> <p>We conclude that co-duplicated groups may themselves be remnants of ancient small-scale duplications (involving chromosomal segments or gene-clusters) which occurred at different time points during chordate evolution. Whereas the recent combination of genes from distinct co-duplicated groups on different chromosomal regions (human chromosomes 2q, 7, 12q, and 17q) is probably the outcome of subsequent rearrangement of genomic segments, including syntenic groups of genes.</p

Non-Markovian Modeling of Nonequilibrium Fluctuations and Dissipation in Active Viscoelastic Biomatter

Based on a Hamiltonian that incorporates the elastic coupling between a tracer particle and the embedding active viscoelastic biomatter, we derive a generalized non-Markovian Langevin model for the nonequilibrium mechanical tracer response. Our analytical expressions for the frequency-dependent tracer response function and the tracer positional autocorrelation function agree quantitatively with experimental data for red blood cells and actomyosin networks with and without adenosine triphosphate over the entire frequency range and in particular reproduce the low-frequency violation of the fluctuation-dissipation theorem. The viscoelastic power laws, the elastic constants and effective friction coefficients extracted from the experimental data allow straightforward physical interpretation

Evolution and Functional Diversification of the GLI Family of Transcription Factors in Vertebrates

Background: In vertebrates the “SONIC HEDGEHOG” signalling pathway has been implicated in cell-fate determination, proliferation and the patterning of many different cell types and organs. As the GLI family members (GLI1, GLI2 and GLI3) are key mediators of hedgehog morphogenetic signals, over the past couple of decades they have been extensively scrutinized by genetic, molecular and biochemical means. Thus, a great deal of information is currently available about the functional aspects of GLI proteins in various vertebrate species. To address the roles of GLI genes in diversifying the repertoire of the Hh signalling and deploying them for the vertebrate specifications, in this study we have examined the evolutionary patterns of vertebrate GLI sequences within and between species. Results: Phylogenetic tree analysis suggests that the vertebrate GLI1, GLI2 and GLI3 genes diverged after the separation of urochordates from vertebrates and before the tetrapods-bony fishes split. Lineage specific duplication events were also detected. Estimation of mode and strength of selection acting on GLI orthologs demonstrated that all members of the GLI gene family experienced more relaxed selection in teleost fish than in the mammalian lineage. Furthermore, the GLI1 gene appeared to have been exposed to different functional constraints in fish and tetrapod lineages, whilst a similar level of functional constraints on GLI2 and GLI3 was suggested by comparable average non-synonymous (Ka) substitutions across the lineages. A relative rate test suggested that the majority of the paralogous copies of the GLI family analyzed evolve

Brain Activation During Maximum Concentric and Eccentric Knee Extension Muscle Contractions

Purpose: In spite of mounting evidence indicating that concentric and eccentric knee extensor muscle contractions might have special nervous system control strategies, the differentiation of brain frequencies between concentric and eccentric movements and how the motor cortex programs this contraction has been less studied. In this study, the brain and muscle activation differences during maximum concentric and eccentric contractions were compared. Methods: Nine healthy volunteers performed 20 maximum eccentric and 20 maximum concentric knee extensor contractions. Electroencephalography (EEG) signals from sensorimotor-related cortical areas were recorded simultaneous with the electromyography (EMG) of the knee extensor muscles. In the spectral analysis the performance related power values were calculated for Theta (4-7 Hz) and Alpha (7-12 Hz). Results: The time-domain results revealed, longer time and greater cortical activity is required for the preparation of an eccentric contraction. For the eccentric task, the cortical activity was greater, but the EMG was lower in comparison to the concentric task values. Statistical analysis showed significant higher and lower Theta and Alpha power in both types of contractions compared to the resting state, respectively. Conclusion: These findings suggest that increased Theta power is associated with task complexity and focused attention and decreased Alpha power values with increased information processing in the somatosensory cortex

Shear-induced bimodality and stability analysis of chiral spheroidal swimmers

We study the shear-induced behavior of chiral (circle-swimming) and nonchiral swimmers in a planar channel subjected to Poiseuille (pressure-driven) flow. The swimmers are modeled as active Brownian spheroids, self-propelling with a fixed-magnitude velocity, pointing along their axis of symmetry. We consider both cases of prolate and oblate swimmers and focus primarily on swimmers that possess an intrinsic, or active, counterclockwise angular velocity, in addition to the shear-induced angular velocity they acquire within the channel flow (Jeffery orbits). The probabilistic results are established using a Smoluchowski equation within the position orientation phase space that is solved numerically. We show that the interplay between shear- and chirality-induced angular velocities, combined with the effects due to particle self-propulsion and steric particle-wall interactions, lead to an interesting range of effects, including pinning, off-centered and near-wall accumulation of swimmers within the channel. This is further accompanied by the linear stability analysis of swimmers, used to explain the probabilistic results. We discuss the qualitative differences of probabilistic results that emerge due to the different regimes of rotational dynamics of swimmers in channel flow, particularly the shear-trapping/-escaping of prolate/oblate swimmers and the difference in latitudes of fixed points associated with each swimmer shape. Our results point to possible mechanisms for flow-driven separation of active spheroidal particles based on their chirality strength.Comment: 14 Pages, 5 Figure

Antibacterial Effect of Two Nano Zinc Oxide Gel Preparations Compared to Calcium Hydroxide and Chlorhexidine Mixture

Introduction: The aim of this study was to compare the antibacterial effects of two gels containing zinc oxide and zinc oxide/silver nanoparticles and a mixture of calcium hydroxide and 0.12% chlorhexidine as intracanal medicaments in root canals contaminated with Enterococcus faecalis (E. faecalis) at different time intervals. Methods and Materials: After preparation and culturing of E. faecalis in 132 single root teeth, the initial count of bacteria was performed. Then, different materials as intracanal medicaments were used in periods of 3, 7 and 14 days (group 1: calcium hydroxide with 0.12% CHX paste; group 2 zinc oxide nanoparticles gel; group 3: zinc oxide/silver nanoparticles gel; group 4: normal saline as the control group). After the specified time, intracanal medicament was removed and the final count of bacteria was performed. Antibacterial effect of materials was counted by measuring the percentage reduction in the colony counts (RCC). Data were analyzed using the descriptive statistics (Mean±SD) and multi-factorial analysis of variance (by taking into account the effect of the time factor on the dependent variable). Results: There were no statistically significant differences among mean RCC of different time intervals in each group (P=0.09). However, the differences in mean RCC of different dressing materials were significant (P&lt;0.001). The effect of interaction between time and materials was significant (P=0.015). Comparison of the antibacterial effects of experimental agents at different time intervals showed that the mean RCC in group 1 was higher than other groups (P&lt;0.001). The difference in antibacterial effect between groups 2 and 3 was not significant (P&gt;0.05). The minimum antibacterial effect was observed in group 4 (P&lt;0.0001). Conclusions: The mixture of calcium hydroxide/chlorhexidine as an intracanal medicament was more effective than zinc oxide and zinc oxide/silver nanoparticles gels. Keywords: Calcium Hydroxide; Chlorhexidine; E. faecalis; Nanoparticles; Zinc Oxid

Reliability and Availability Improvement in Economic Data Grid Environment Based On Clustering Approach

Abstract - One of the important problems in grid environments is data replication in grid sites. Reliability and availability of data replication in some cases is considered low. To separate sites with high reliability and high availability of sites with low availability and low reliability, clustering can be used. In this study, the data grid dynamically evaluate and predict the condition of the sites. The reliability and availability of sites were calculated and it was used to make decisions to replicate data. With these calculations, we have information on the locations of users in grid with reliability and availability or cost commensurate with the value of the work they did. This information can be downloaded from users who are willing to send them data with suitable reliability and availability. Simulation results show that the addition of the two parameters, reliability and availability, assessment criteria have been improved in certain access patterns