Genome Assemblies across the Diverse Evolutionary Spectrum of Leishmania Protozoan Parasites

We report the high-quality draft assemblies and gene annotations for 13 species and/or strains of the protozoan parasite genera Leishmania , Endotrypanum , and Crithidia , which span the phylogenetic diversity of the subfamily Leishmaniinae within the kinetoplastid order of the phylum Euglenazoa. These resources will support studies on the origins of parasitism.

Annotating the Insect Regulatory Genome

An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify cis-regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotation of newly sequenced insect genomes is an ongoing challenge. We review here the methods being used to identify CRMs in both model and non-model insect species, and focus on two tools that we have developed, REDfly and SCRMshaw. These resources can be paired together in a powerful combination to facilitate insect regulatory annotation over a broad range of species, with an accuracy equal to or better than that of other state-of-the-art methods.

Classification and Separation of Audio and Music Signals

This chapter addresses the topic of classification and separation of audio and music signals. It is a very important and a challenging research area. The importance of classification process of a stream of sounds come up for the sake of building two different libraries: speech library and music library. However, the separation process is needed sometimes in a cocktail-party problem to separate speech from music and remove the undesired one. In this chapter, some existed algorithms for the classification process and the separation process are presented and discussed thoroughly. The classification algorithms will be divided into three categories. The first category includes most of the real time approaches. The second category includes most of the frequency domain approaches. However, the third category introduces some of the approaches in the time-frequency distribution. The approaches of time domain discussed in this chapter are the short-time energy (STE), the zero-crossing rate (ZCR), modified version of the ZCR and the STE with positive derivative, the neural networks, and the roll-off variance. The approaches of the frequency spectrum are specifically the roll-off of the spectrum, the spectral centroid and the variance of the spectral centroid, the spectral flux and the variance of the spectral flux, the cepstral residual, and the delta pitch. The time-frequency domain approaches have not been yet tested thoroughly in the process of classification and separation of audio and music signals. Therefore, the spectrogram and the evolutionary spectrum will be introduced and discussed. In addition, some algorithms for separation and segregation of music and audio signals, like the independent Component Analysis, the pitch cancelation and the artificial neural networks will be introduced.

The algal selenoproteomes

Background Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec but also the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. There have been some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, has been very limited. Results In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to record these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families. Conclusions This study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to determine the complete evolutionary spectrum of selenoproteins in all life forms.

The algal selenoproteomes

Background: Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec but also the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. There have been some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, has been very limited. Results: In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to record these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families. Conclusions: This study reveals the primordial state of the eukaryotic selenoproteome . It is an important clue to explore the significance of selenium for primordial eukaryotes and to determine the complete evolutionary spectrum of selenoproteins in all life forms.

The algal selenoproteomes

Background:Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec, but also the SECIS element in mRNA and the conservation of the Sec flanking region. These unique features have led to developing a series of bioinformatics methods to predict and research selenoprotein genes. There are some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, is very limited.Results:In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to hold these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families.Conclusions:This study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to build the whole evolutionary spectrum of selenoproteins for all life.

Multiwavelength investigation of extended green object G19.88-0.53: revealing a protocluster

ABSTRACT A multiwavelength analysis of star formation associated with the extended green object, G19.88-0.53 is presented in this paper. With multiple detected radio and millimetre components, G19.88-0.53 unveils as harbouring a protocluster rather than a single massive young stellar object. We detect an ionized thermal jet using the upgraded Giant Meterwave Radio Telescope, India, which is found to be associated with a massive, dense and hot ALMA 2.7 mm core driving a bipolar CO outflow. Near-infrared spectroscopy with UKIRT–UIST shows the presence of multiple shock-excited H2 lines concurrent with the nature of this region. Detailed investigation of the gas kinematics using ALMA data reveals G19.88-0.53 as an active protocluster with high-mass star-forming components spanning a wide evolutionary spectrum from hot cores in accretion phase to cores driving multiple outflows to possible UCH ii regions.