Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.     

Redescription of the species of Passalus Fabricius, 1792 (Coleoptera: Passalidae) described by Walter Douglas Hincks (1906–1961) deposited in the Museum of the University of Manchester

ABSTRACT

As part of the effort to study Passalus Fabricius, 1792, we are redescribing and re-illustrating the species of the genus described by Walter Douglas Hincks deposited the Museum of the University of Manchester. Applying characters not yet described for these species as well as morphometric measures we hope to support future taxonomic and phylogenetic studies.     

Incremental Tree-Based Missing Data Imputation with Lexicographic Ordering

In the framework of incomplete data analysis, this paper provides a nonparametric approach to missing data imputation based on Information Retrieval. In particular, an incremental procedure based on the iterative use of tree-based method is proposed and a suitable Incremental Imputation Algorithm is introduced. The key idea is to define a lexicographic ordering of cases and variables so that conditional mean imputation via binary trees can be performed incrementally. A simulation study and real data applications are carried out to describe the advantages and the performance with respect to standard approaches.     

Tunable pKa values and the basis of opposite charge selectivities in nicotinic-type receptors

Among ion channels, only the nicotinic-receptor superfamily has evolved to generate both cation- and anion-selective members. Although other, structurally unrelated, neurotransmitter-gated cation channels exist, no other type of neurotransmitter-gated anion channel, and thus no other source of fast synaptic inhibitory signals, has been described so far. In addition to the seemingly straightforward electrostatic effect of the presence (in the cation-selective members) or absence (in the anion-selective ones) of a ring of pore-facing carboxylates, mutational studies have identified other features of the amino-acid sequence near the intracellular end of the pore-lining transmembrane segments (M2) that are also required to achieve the high charge selectivity shown by native channels. However, the mechanism underlying this more subtle effect has remained elusive and a subject of speculation. Here we show, using single-channel electrophysiological recordings to estimate the protonation state of native ionizable side chains, that anion-selective-type sequences favour whereas cation-selective-type sequences prevent the protonation of the conserved, buried basic residues at the intracellular entrance of the pore (the M2 0' position). We conclude that the previously unrecognized tunable charge state of the 0' ring of buried basic side chains is an essential feature of these channels' versatile charge-selectivity filter.     

Taxonomic review of the Amazonian millipede genus Parastenonia Hoffman, 1977 and description of a new species from iron-ore caves (Polydesmida: Chelodesmidae)

ABSTRACT

The Amazonian genus Parastenonia Hoffman, 1977 is here revised. The species P. carajas sp. nov. is described from Brazilian iron-ore caves and P. aurae (Schubart, 1947) is considered junior synonym of P. parae (Cook, 1895). In addition, the known geographic distribution of the genus is presented with the inclusion of new occurrence data.

http://www.zoobank.org/urn:lsid:zoobank.org:act:CCBEED10-DCB4-48C9-A71D-CED3462DD72A     

Solving the factorization problem with P systems

P systems have been used many times to face with computationally difficult problems, such as NP-complete decision problems and NP-hard optimization problems. In this paper we focus our attention on another computationally intractable problem: factorization. In particular, we first propose a simple method to encode binary numbers using multisets. Then, we describe three families of P systems: the first two allow to add and to multiply two binary encoded numbers, respectively, and the third solves the factorization problem.     

A mirror-symmetric cell division that orchestrates neuroepithelial morphogenesis

The development of cell polarity is an essential prerequisite for tissue morphogenesis during embryogenesis, particularly in the development of epithelia. In addition, oriented cell division can have a powerful influence on tissue morphogenesis. Here we identify a novel mode of polarized cell division that generates pairs of neural progenitors with mirror-symmetric polarity in the developing zebrafish neural tube and has dramatic consequences for the organization of embryonic tissue. We show that during neural rod formation the polarity protein Pard3 is localized to the cleavage furrow of dividing progenitors, and then mirror-symmetrically inherited by the two daughter cells. This allows the daughter cells to integrate into opposite sides of the developing neural tube. Furthermore, these mirror-symmetric divisions have powerful morphogenetic influence: when forced to occur in ectopic locations during neurulation, they orchestrate the development of mirror-image pattern formation and the consequent generation of ectopic neural tubes.     

Genome-wide association study identifies susceptibility loci for IgA nephropathy

We carried out a genome-wide association study of IgA nephropathy, a major cause of kidney failure worldwide. We studied 1,194 cases and 902 controls of Chinese Han ancestry, with targeted follow up in Chinese and European cohorts comprising 1,950 cases and 1,920 controls. We identified three independent loci in the major histocompatibility complex, as well as a common deletion of CFHR1 and CFHR3 at chromosome 1q32 and a locus at chromosome 22q12 that each surpassed genome-wide significance (P values for association between 1.59 × 10?2? and 4.84 × 10?? and minor allele odds ratios of 0.63-0.80). These five loci explain 4-7% of the disease variance and up to a tenfold variation in interindividual risk. Many of the alleles that protect against IgA nephropathy impart increased risk for other autoimmune or infectious diseases, and IgA nephropathy risk allele frequencies closely parallel the variation in disease prevalence among Asian, European and African populations, suggesting complex selective pressures.