qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles

Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects the sensitivity of mutation detection, copy number analysis, cancer gene expression and methylation profiling. Tumour cellularity is traditionally estimated by pathological review of sectioned specimens; however this method is both subjective and prone to error due to heterogeneity within lesions and cellularity differences between the sample viewed during pathological review and tissue used for research purposes. In this paper we describe a statistical model to estimate tumour cellularity from SNP array profiles of paired tumour and normal samples using shifts in SNP allele frequency at regions of loss of heterozygosity (LOH) in the tumour. We also provide qpure, a software implementation of the method. Our experiments showed that there is a medium correlation 0.42 (-value = 0.0001) between tumor cellularity estimated by qpure and pathology review. Interestingly there is a high correlation 0.87 (-value 2.2e-16) between cellularity estimates by qpure and deep Ion Torrent sequencing of known somatic KRAS mutations; and a weaker correlation 0.32 (-value = 0.004) between IonTorrent sequencing and pathology review. This suggests that qpure may be a more accurate predictor of tumour cellularity than pathology review. qpure can be downloaded from https://sourceforge.net/projects/qpure/.     

Contribution of Rare Copy Number Variants to Isolated Human Malformations

Background

Congenital malformations are present in approximately 2–3% of liveborn babies and 20% of stillborn fetuses. The mechanisms underlying the majority of sporadic and isolated congenital malformations are poorly understood, although it is hypothesized that the accumulation of rare genetic, genomic and epigenetic variants converge to deregulate developmental networks.

Methodology/Principal Findings

We selected samples from 95 fetuses with congenital malformations not ascribed to a specific syndrome (68 with isolated malformations, 27 with multiple malformations). Karyotyping and Multiplex Ligation-dependent Probe Amplification (MLPA) discarded recurrent genomic and cytogenetic rearrangements. DNA extracted from the affected tissue (46%) or from lung or liver (54%) was analyzed by molecular karyotyping. Validations and inheritance were obtained by MLPA. We identified 22 rare copy number variants (CNV) [>100 kb, either absent (n = 7) or very uncommon (n = 15, <1/2,000) in the control population] in 20/95 fetuses with congenital malformations (21%), including 11 deletions and 11 duplications. One of the 9 tested rearrangements was de novo while the remaining were inherited from a healthy parent. The highest frequency was observed in fetuses with heart hypoplasia (8/17, 62.5%), with two events previously related with the phenotype. Double events hitting candidate genes were detected in two samples with brain malformations. Globally, the burden of deletions was significantly higher in fetuses with malformations compared to controls.

Conclusions/Significance

Our data reveal a significant contribution of rare deletion-type CNV, mostly inherited but also de novo, to human congenital malformations, especially heart hypoplasia, and reinforce the hypothesis of a multifactorial etiology in most cases.     

Honeydew collection by the invasive garden ant Lasius neglectus versus the native ant L. grandis

Honeydew collection performed by the invasive ant Lasius neglectus and by the native ant L. grandis was compared. The invasive ant collected 2.09 kg of honeydew per tree while the native ant collected 0.82 kg. The aphid Lachnus roboris was visited by both ant species. In holm oaks colonized by L. neglectus, aphid abundance tended to increase and its honeydew production increased twofold. The percentage of untended aphids was lower in holm trees occupied by L. neglectus. As tending ants also prey on insects, we estimated the percentage of carried insects. The native ant workers carried more insects than the invasive ant. Both ant species preyed mainly on Psocoptera and the rarely tended aphid, Hoplocallis picta. We conclude that the higher honeydew collection achieved by L. neglectus was the consequence of (1) its greater abundance, which enabled this ant to tend more Lachnus roboris and (2) its greater level of attention towards promoting an increase of honeydew production. Handling editor: Heikki Hokkanen     

Drinking water quality and risk implications for community health: A case study of shallow water wells and boreholes in three major communities in Northern Cross-River,Southern Nigeria

The quality of water sources and its potential health implications to adults and children populations of respective major communities in Northern Cross-River was assessed. Water samples (n = 10/water source/site) were collected from three (Okpoma, Okuku and Ugaga) communities and heavy metal concentrations (Lead (Pb), Cadmium (Cd), Chromium (Cr), Manganese (Mn), Nickel (Ni), Copper (Cu), Cobalt (Co), and Zinc (Zn)) were evaluated using Atomic Absorption Spectrometer (AAS). Overall, Pb, Cd, Ni, and Co were higher than drinking water guidelines, while only Cr, Mn, Cu, and Zn were within the permissible limits. The estimated average daily intake (EADI) and target hazard quotient (THQ) were used to determine risk implications for adult and children consumer populations. The EADI for Pb in adults for borehole water, Pb and Cr by child consumer population for borehole and shallow well water exceeded the reference dose (RfD) by USEPA. The THQ for adult population were >1 for Pb in borehole water and >1 for Pb and Cr across all sites for the child consumer population. Overall, our findings indicate toxicity and higher hazard risk for both adult (Pb) and children (Pb and Cr) populations that source drinking water from borehole and shallow well water in these communities.     

Evaluation of the Hydroxynitrile Lyase Activity in Cell Cultures of Capulin （Prunus serotina）

Enzymatic preparations obtained from young plants and cell cultures of capulin were screened for hydroxynitrile lyase activity. The threeweek old plants, grown under sterile conditions, were used to establish a solid cell culture. Crude preparations obtained from this plant material were evaluated for the transformation of benzaldehyde to the corresponding cyanohydrin (mandelonitrile). The results show that the crude material from roots, stalks, and leaves of young plants and calli of roots, stalks, internodes and petioles biocatalyzed the addition of hydrogen cyanide (HCN) to benzaldehyde with a modest to excellent enantioselectivity.     

East African coastal forest under pressure

The Arabuko Sokoke dryland coastal forest along the East African coastline provides a unique habitat for many endangered endemic animal and plant species. High demographic pressure with subsequent land-splitting, soil depletion in combination with erratic rainfalls and the collapse of the tourism industry are negatively affecting food security and human livelihood quality in this region. Food crops were originally produced by subsistence farming, but have now to be purchased at local- and super-markets, constituting a major financial burden for the local people. In consequence, overexploitation of natural resources from Arabuko Sokoke forest (illegal logging, charcoal burning, poaching of wild animals) increased during the past years. In this commentary we document ecosystem heterogeneity leading to high species richness. We discuss direct and indirect drivers of habitat degradation of the Arabuko Sokoke forest, and critically reflect current and future solutions. Key drivers of habitat destruction and biodiversity loss are (i) illegal timber logging and removal of woody biomass, (ii) poaching of bush-meat, (iii) exceeding of the carrying capacity by the local elephant population, restricted to Arabuko Sokoke by an electric fence, and (iv) weak governance structures and institutional confusion exacerbating illegal exploitation of natural resources. Potential solutions might be: Provisioning of additional income sources; reforestation of the surrounding areas in the framework of REDD+ activities to create a buffer around the remaining primary forest; improving governance structures that formulates clear guidelines on future usage and protection of natural resources within the Arabuko Sokoke forest; and family planning to counteract human demographic pressure and the exploitation of natural resources.     

Mind the gap! Integrating taxonomic approaches to assess ant diversity at the southern extreme of the Atlantic Forest

Understanding patterns of species diversity relies on accurate taxonomy which can only be achieved by long‐term natural history research and the use of complementary information to establish species boundaries among cryptic taxa. We used DNA barcoding to characterize the ant diversity of Iguazú National Park (INP), a protected area of the Upper Paraná Atlantic Forest ecoregion, located at the southernmost extent of this forest. We assessed ant diversity using both cytochrome c oxidase subunit 1 (COI) sequences and traditional morphological approaches, and compared the results of these two methods. We successfully obtained COI sequences for 312 specimens belonging to 124 species, providing a DNA barcode reference library for nearly 50% of the currently known ant fauna of INP. Our results support a clear barcode gap for all but two species, with a mean intraspecific divergence of 0.72%, and an average congeneric distance of 17.25%. Congruently, the library assembled here was useful for the discrimination of the ants of INP and allowed us to link unidentified males and queens to their worker castes. To detect overlooked diversity, we classified the DNA barcodes into Molecular Operational Taxonomic Units (MOTUs) using three different clustering algorithms, and compared their number and composition to that of reference species identified based on morphology. The MOTU count was always higher than that of reference species regardless of the method, suggesting that the diversity of ants at INP could be between 6% and 10% higher than currently recognized. Lastly, our survey contributed with 78 new barcode clusters to the global DNA barcode reference library, and added 36 new records of ant species for the INP, being 23 of them new citations for Argentina.