Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences

Motivation

Paired-end sequencing protocols, offered by next generation sequencing (NGS) platforms like Illumia, generate a pair of reads for every DNA fragment in a sample. Although this protocol has been utilized for several metagenomics studies, most taxonomic binning approaches classify each of the reads (forming a pair), independently. The present work explores some simple but effective strategies of utilizing pairing-information of Illumina short reads for improving the accuracy of taxonomic binning of metagenomic datasets. The strategies proposed can be used in conjunction with all genres of existing binning methods.

Results

Validation results suggest that employment of these “Binpairs” strategies can provide significant improvements in the binning outcome. The quality of the taxonomic assignments thus obtained are often comparable to those that can only be achieved with relatively longer reads obtained using other NGS platforms (such as Roche).

Availability

An implementation of the proposed strategies of utilizing pairing information is freely available for academic users at https://metagenomics.atc.tcs.com/binning/binpairs.     

The search for common anthropogenic impacts on biodiversity: a global network

We introduce an initiative to assess and compare landscape changes related to human activities on a global scale, using a single group of invertebrates. The GLOBENET programme uses common field methodology (pitfall trapping), to appraise assemblages of ground beetles (Coleoptera, Carabidae) in visually-similar land-mosaics (urban-rural gradients). Carabids were selected as the focal taxon as they are sufficiently varied (both taxonomically and ecologically), abundant and sensitive to the environment. However, work on other taxa is comparable with the GLOBENET framework. The continuum of decreasing human pressure from city centres into the surrounding countryside was selected to represent human-caused disturbance for this initial stage of GLOBENET because these gradients can be found virtually all over the world. Through the broad-scale assessment envisioned in the GLOBENET programme, we seek to separate general, repeated effects on biodiversity from those that depend on local environments or particular biotic assemblages. Based on this understanding we aim to develop simple tools and protocols for assessing ecological effects of human-caused landscape changes, which could help to sustainably manage landscapes for biodiversity and for human requirements. For instance, the response of different functional groups of carabids to these landscape changes may help guide management practices. Further GLOBENET developments and information are available at our website: http://www.helsinki.fi/science/globenet/     

The early stages of Ptenopsila Enderlein (Psocoptera,Caeciliidae)

All early stages of Ptenopsila, a characteristic psocid genus of southern South America, are described and features of taxonomic value are illustrated. Examination of early stages confirms the placement of this genus in the Caeciliidae.     

Routing of thylakoid lumen proteins by the chloroplast twin arginine transport pathway

Thylakoids are complex sub-organellar membrane systems whose role in photosynthesis makes them critical to life. Thylakoids require the coordinated expression of both nuclear- and plastid-encoded proteins to allow rapid response to changing environmental conditions. Transport of cytoplasmically synthesized proteins to thylakoids or the thylakoid lumen is complex; the process involves transport across up to three membrane systems with routing through three aqueous compartments. Protein transport in thylakoids is accomplished by conserved ancestral prokaryotic plasma membrane translocases containing novel adaptations for the sub-organellar location. This review focuses on the evolutionarily conserved chloroplast twin arginine transport (cpTat) pathway. An overview is provided of known aspects of the cpTat components, energy requirements, and mechanisms with a focus on recent discoveries. Some of the most exciting new studies have been in determining the structural architecture of the membrane complex involved in forming the point of passage for the precursor and binding features of the translocase components. The cpTat system is of particular interest because it transports folded protein domains using only the proton motive force for energy. The implications for mechanism of translocation by recent studies focusing on interactions between membrane Tat components and with the translocating precursor will be discussed.     

Anti-Müllerian hormone in three intersex conditions.

Anti-Müllerian hormone (AMH), secreted by embryonic testicular Sertoli cells, inhibits the development of Müllerian ducts in the male. An enzyme-linked immunoassay (ELISA) for AMH was used to investigate three intersex infants. The AMH level was correlated with each patient's degree of Müllerian duct development. Complete inhibition of Müllerian structures correlated with the normal levels of AMH in the infant with testicular feminization. Detectable levels of AMH were found in the hermaphroditic infant; however, these low levels reflected Sertoli cell inadequacy of the ovotestis, which was documented by a right rudimentary Fallopian tube and a normal uterus. In the infant with persistent Müllerian duct syndrome, (PMDS), the normal Müllerian derivatives are compatible with 1) an AMH receptor defect; 2) a biologically and immunologically abnormal AMH molecule, or 3) a functional AMH deletion. The lack of detectable AMH in this infant excluded the AMH receptor abnormality and thus directed authors' search for the specific defect to the AMH gene. Thus, this ELISA for AMH is as valuable a tool to the molecular biologist studying a precise genetic error as it is to the physician making a precise clinical diagnosis.