The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Evolution of Protein Molecules

Glutathione peroxidase (GPx) is a widespread protein superfamily found in many organisms throughout all kingdoms of life. Although it was initially thought to use only glutathione as reductant, recent evidence suggests that the majority of GPxs have specificity for thioredoxin. We present a thorough in silico analysis performed on 724 sequences and 12 structures aimed to clarify the evolutionary, structural, and sequence determinants of GPx specificity. Structural variability was found to be limited to only two regions, termed oligomerization loop and functional helix, which modulate both reduced substrate specificity and oligomerization state. We show that mammalian GPx-1, the canonic selenocysteine-based tetrameric glutathione peroxidase, is a recent “invention” during evolution. Contrary to common belief, cysteine-based thioredoxin-specific GPx, which we propose the TGPx, are both more common and more ancient. This raises interesting evolutionary considerations regarding oligomerization and the use of ...

Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily.

Mechanisms by which pesticides affect insect immunity.

Glutathione peroxidases (GPXs, EC 1.11.1.9) were first discovered in mammals as key enzymes involved in scavenging of activated oxygen species (AOS). Their efficient antioxidant activity depends on the presence of the rare amino-acid residue selenocysteine (SeCys) at the catalytic site. Nonselenium GPX-like proteins (NS-GPXs) with a Cys residue instead of SeCys have also been found in most organisms. As SeCys is important for GPX activity, the function of the NS-GPX can be questioned. Here, we highlight the evolutionary link between NS-GPX and seleno-GPX, particularly the evolution of the SeCys incorporation system. We then discuss what is known about the enzymatic activity and physiological functions of NS-GPX. Biochemical studies have shown that NS-GPXs are not true GPXs; notably they reduce AOS using reducing substrates other than glutathione, such as thioredoxin. We provide evidence that, in addition to their inefficient scavenging action, NS-GPXs act as AOS sensors in various signal-transduction pathways.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1742-4658.2007.05774.x

Seleno-independent glutathione peroxidases. More than simple antioxidant scavengers.

Molecular cloning of a phospholipid-hydroperoxide glutathione peroxidase gene from the tick, Boophilus microplus (Acari: Ixodidae).

Theileria buffeli infection of a Michigan cow confirmed by small subunit ribosomal RNA gene analysis

Bovine anaplasmosis prevalence in northern Veracruz state, Mexico

Perturbation of tyraminergic/octopaminergic function inhibits oviposition in the cattle tick Rhipicephalus (Boophilus) microplus

Three organophosphate resistant Boophilus microplus Canestrini cell lines were generated by exposing B. microplus VIII-SCC cell line to incrementally increased toxic concentrations of the acaricide coumaphos. The development of resistance was evidenced by LC50 values elevated over those of control cells. The resistant cell lines selected in higher concentrations of organophosphate, designated C44 and C54, also had significantly slower duplication rates than a resistant cell line selected in lower concentrations of coumaphos (C34) and the nonresistant control cells. Resistant cell lines C44 and C54 also had significantly higher levels of esterase after exposure to coumaphos than resistant cell line C34 and the nonresistant controls. These in vitro results agree with reports of increased esterase activity associated with organophosphate resistance in B. microplus ticks in vivo.

Raquel Cossío-Bayúgar

Papers

Molecular cloning of a phospholipid-hydroperoxide glutathione peroxidase gene from the tick, Boophilus microplus (Acari: Ixodidae).

Theileria buffeli infection of a Michigan cow confirmed by small subunit ribosomal RNA gene analysis

Bovine anaplasmosis prevalence in northern Veracruz state, Mexico

Perturbation of tyraminergic/octopaminergic function inhibits oviposition in the cattle tick Rhipicephalus (Boophilus) microplus

In vitro generation of organophosphate resistant boophilus microplus (Acari: Ixodidae) cell lines.