Analysis of septins across kingdoms reveals orthology and new motifs

<p>Abstract</p> <p>Background</p> <p>Septins are cytoskeletal GTPase proteins first discovered in the fungus <it>Saccharomyces cerevisiae </it>where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison.</p> <p>Results</p> <p>In the current work, we identified 162 septins from fungi, microsporidia and animals and analyzed their phylogenetic relationships. There was support for five groups of septins with orthology between kingdoms. Group 1 (which includes <it>S. cerevisiae </it>Cdc10p and human Sept9) and Group 2 (which includes <it>S. cerevisiae </it>Cdc3p and human Sept7) contain sequences from fungi and animals. Group 3 (which includes <it>S. cerevisiae </it>Cdc11p) and Group 4 (which includes <it>S. cerevisiae </it>Cdc12p) contain sequences from fungi and microsporidia. Group 5 (which includes <it>Aspergillus nidulans </it>AspE) contains sequences from filamentous fungi. We suggest a modified nomenclature based on these phylogenetic relationships. Comparative sequence alignments revealed septin derivatives of already known G1, G3 and G4 GTPase motifs, four new motifs from two to twelve amino acids long and six conserved single amino acid positions. One of these new motifs is septin-specific and several are group specific.</p> <p>Conclusion</p> <p>Our studies provide an evolutionary history for this important family of proteins and a framework and consistent nomenclature for comparison of septin orthologs across kingdoms.</p

A standardized kinesin nomenclature

In recent years the kinesin superfamily has become so large that several different naming schemes have emerged, leading to confusion and miscommunication. Here, we set forth a standardized kinesin nomenclature based on 14 family designations. The scheme unifies all previous phylogenies and nomenclature proposals, while allowing individual sequence names to remain the same, and for expansion to occur as new sequences are discovered

Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families

The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that create or disrupt stem base pairing. We analyzed the evolution of stem lengths and constructed substitution matrices describing the changes responsible for the variation in the RNA stem length. In addition, we used principal component analysis of the stem length data to determine the most variable stems in different families of RNA. This data provides new insights into the evolution of RNA secondary structures and patterns of variation in the lengths of double helical regions of RNA molecules. Our findings will facilitate design of improved mutational models for RNA structure evolution

Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds

<p>Abstract</p> <p>Background</p> <p>The computational identification of RNAs in genomic sequences requires the identification of signals of RNA sequences. Shannon base pairing entropy is an indicator for RNA secondary structure fold certainty in detection of structural, non-coding RNAs (ncRNAs). Under the Boltzmann ensemble of secondary structures, the probability of a base pair is estimated from its frequency across all the alternative equilibrium structures. However, such an entropy has yet to deliver the desired performance for distinguishing ncRNAs from random sequences. Developing novel methods to improve the entropy measure performance may result in more effective ncRNA gene finding based on structure detection.</p> <p>Results</p> <p>This paper shows that the measuring performance of base pairing entropy can be significantly improved with a constrained secondary structure ensemble in which only canonical base pairs are assumed to occur in energetically stable stems in a fold. This constraint actually reduces the space of the secondary structure and may lower the probabilities of base pairs unfavorable to the native fold. Indeed, base pairing entropies computed with this constrained model demonstrate substantially narrowed gaps of Z-scores between ncRNAs, as well as drastic increases in the Z-score for all 13 tested ncRNA sets, compared to shuffled sequences.</p> <p>Conclusions</p> <p>These results suggest the viability of developing effective structure-based ncRNA gene finding methods by investigating secondary structure ensembles of ncRNAs.</p

Schools, families, and social reproduction

Neoliberal educational discourse across the Global North is marked by an increasing homogeneity, but this masks significant socio-spatial differences in the enactment of policy. The authors focus on four facets of roll-out neoliberalism in English education policy that have expanded the function of primary schools, and redrawn the boundary between state and family responsibilities. Specifically, these are increased state support for: (1) working parenthood through provision of wraparound childcare; (2) parent-child relationships through school-led provision of parenting classes; (3) parental involvement in children’s learning; and (4) child development through schools’ fostering of extracurricular activities. The politics of policies that both enhance state responsibility for, and influence in, matters that were previously within the purview of families are complex. The collective impact of these developments has been both to reform how the work of daily and generational social reproduction is done, and to reshape the social reproduction of a classed and gendered society