Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. However, the fungi rich in SM production are taxonomically restricted to Dikarya, two phyla of Kingdom Fungi, Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus . Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont

SpBase: the sea urchin genome database and web site

SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It is exposed to the public through a web site served with open source software (http://spbase.org/). The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful research models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple sea urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple sea urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided

Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions. The accuracy of our splice site recognition function is 97% for donor splice sites and 96% for acceptor splice sites. For exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. This corresponds to a correlation coefficient for exon prediction of 0.87. The precision of this approach is better than other methods and has been tested on a larger data set. We have also developed a means for predicting exon-exon junctions in cDNA sequences, which can be useful for selecting optimal PCR primers

Study of the Anthropogenic Impact on the Change of Geoecological Conditions of the Khojahasan Lake, Azerbaijan

The  paper  considers  the  results  of  geoecological  and  geophysical  studies  conducted   in   the   Khojahasan Lake basin in the Western part of Baku. The main purpose of the work was to study the anthropogenic impact on geoecological conditions of the lake. To assess the development of exogenous geological processes in the coastal zone of the lake and their impact on the environment, geophysical studies were carried out by the vertical electric sounding (VES). From 1990 to 2014, the physical and chemical characteristics of water and sediments were studied in a representative section of the lake. Metal concentrations, including such toxic elements as Cu, Zn, Cd, Sr, Ba, Pb, Cr, and Ni, were determined in the trace element composition of bottom sediments. It was revealed that since the mid-XIX century and especially since the second half of the XX century the high rate of population growth and urbanization in the territory of the Absheron Peninsula (in the Republic of Azerbaijan the name Apsheron was changed to Absheron) led to intensive use of natural resources and increased anthropogenic load on the environment. Technogenesis actively violates the natural cycle of matter and energy in lakes (limnogenesis), along with other natu- ral media, as lake basins are located in lowlands and often accumulate industrial, municipal, agricultural, and other discharges. Pollutants accumulated in the lake basin affect hydrobiochemical conditions, transform quantitative and qualitative indicators of the aquatic environment and bottom sediments. Factors affecting the lake landscape are ge- netically different, unequal in the degree and nature of the impact, as well as induration

The Effect of the Pairing Interaction on the Energies of Isobar Analog Resonances in 112−124^{112-124}Sb and Isospin Admixture in 100−124^{100-124}Sn Isotopes

In the present study, the effect of the pairing interaction and the isovector correlation between nucleons on the properties of the isobar analog resonances (IAR) in $^{112-124}$Sb isotopes and the isospin admixture in $^{100-124}$Sn isotopes is investigated within the framework of the quasiparticle random phase approximation (QRPA). The form of the interaction strength parameter is related to the shell model potential by restoring the isotopic invariance of the nuclear part of the total Hamiltonian. In this respect, the isospin admixtures in the $^{100-124}$Sn isotopes are calculated, and the dependence of the differential cross section and the volume integral $J_{F}$ for the Sn($^{3}$He,t)Sb reactions at E($^{3}$He)$=200$ MeV occurring by the excitation of IAR on mass number A is examined. Our results show that the calculated value for the isospin mixing in the $^{100}$Sn isotope is in good agreement with Colo et al.'s estimates $(4-5$, and the obtained values for the volume integral change within the error range of the value reported by Fujiwara et al. (53$\pm$5 MeV fm$^{3}$). Moreover, it is concluded that although the differential cross section of the isobar analog resonance for the ($^{3}$He,t) reactions is not sensitive to pairing correlations between nucleons, a considerable effect on the isospin admixtures in $N\approx Z$ isotopes can be seen with the presence of these correlations.Comment: 16 pages, 5 EPS figures and 2 tables, Late

mGene.web: a web service for accurate computational gene finding

We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp)

mGene.web: a web service for accurate computational gene finding

We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp)

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost andduringmushroomformation.The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation aremore highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics