An ensemble approach to accurately detect somatic mutations using SomaticSeq

SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. The workflow currently incorporates five state-of-the-art somatic mutation callers, and extracts over 70 individual genomic and sequencing features for each candidate site. A training set is provided to an adaptively boosted decision tree learner to create a classifier for predicting mutation statuses. We validate our results with both synthetic and real data. We report that SomaticSeq is able to achieve better overall accuracy than any individual tool incorporated.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0758-2) contains supplementary material, which is available to authorized users.     

Fate of Zinc Oxide Nanoparticles Coated onto Macronutrient Fertilizers in an Alkaline Calcareous Soil

Zinc oxide (ZnO) nanoparticles may provide a more soluble and plant available source of Zn in Zn fertilizers due to their greater reactivity compared to equivalent micron- or millimetre-sized (bulk) particles. However, the effect of soil on solubility, spatial distribution and speciation of ZnO nanoparticles has not yet been investigated. In this study, we examined the diffusion and solid phase speciation of Zn in an alkaline calcareous soil following application of nanoparticulate and bulk ZnO coated fertilizer products (monoammonium phosphate (MAP) and urea) using laboratory-based x-ray techniques and synchrotron-based μ-x-ray fluorescence (μ–XRF) mapping and absorption fine structure spectroscopy (μ–XAFS). Mapping of the soil-fertilizer reaction zones revealed that most of the applied Zn for all treatments remained on the coated fertilizer granule or close to the point of application after five weeks of incubation in soil. Zinc precipitated mainly as scholzite (CaZn₂(PO₄)₂.2H₂O) and zinc ammonium phosphate (Zn(NH₄)PO₄) species at the surface of MAP granules. These reactions reduced dissolution and diffusion of Zn from the MAP granules. Although Zn remained as zincite (ZnO) at the surface of urea granules, limited diffusion of Zn from ZnO-coated urea granules was also observed for both bulk and nanoparticulate ZnO treatments. This might be due to either the high pH of urea granules, which reduced solubility of Zn, or aggregation (due to high ionic strength) of released ZnO nanoparticles around the granule/point of application. The relative proportion of Zn(OH)₂ and ZnCO₃ species increased for all Zn treatments with increasing distance from coated MAP and urea granules in the calcareous soil. When coated on macronutrient fertilizers, Zn from ZnO nanoparticles (without surface modifiers) was not more mobile or diffusible compared to bulk forms of ZnO. The results also suggest that risk associated with the presence of ZnO NPs in calcareous soils would be the same as bulk sources of ZnO.     

Genipin induces cell death via intrinsic apoptosis pathways in human glioblastoma cells

Genipin, a compound derived from Gardenis jasminoides Ellis fruits, was demonstrated to be the specific uncoupling protein 2 (UCP2) inhibitor. UCP2 is a mitochondrial carrier protein that creates proton leaks across the inner mitochondrial membrane, thus uncoupling oxidative phosphorylation from adenosine triphosphate (ATP) synthesis. Several studies revealed that UCP2 is broadly over-expressed in leukemia, colorectal, lung, ovarian, prostate, testicular, and bladder cancers. However, the effect of genipin still needs to be elucidated in neurological malignancies. In this study, we investigated the anticancer effect of genipin in U87MG and A172 cell lines. The anticancer effect of genipin on these cell lines was measured by microculture tetrazoliumtest (MTT), Trypan blue exclusion, and colony formation assays, in the presence of various concentrations of genipin at different time intervals. We assessed apoptosis and measure intracellular reactive oxygen species (ROS) by flow cytometry. Expression of UCP2 and some of the genes involved in apoptosis was analyzed by real-time quantitative polymerase chain reaction (PCR). Results of the MTT assay showed that genipin moderately reduced metabolic activity of both cell lines in dose- and time-dependent manner. Result of Trypan blue exclusion test indicated that the viable cell count decreased in the treated group in a concentration-dependent manner. Genipin also significantly decreased colony formation ability of these cells in a concentration-dependent manner. Result of morphological changes showed that there were significant differences in cell number and morphology in treated groups as compared with the untreated groups. Flow cytometric analysis of U87MG and A172 cells with annexin V/propidium iodide staining, 48 hours after treatment with genipin, displays 22.4% and 26.1% apoptotic population, respectively, in treated cells, in comparison to 7.42% and 9.31% apoptotic cells of untreated cells. After treatment, UCP2 and B-cell lymphoma 2 (BCL ₂) genes are downregulated, and BCL ₂ associated X protein, BCL ₂ antagonist/killer, BCL ₂ interacting killer, and Cytochrome c genes are upregulated. Genipin treatment increased mitochondrial ROS levels and also induced apoptosis through caspase-3 upregulation. In conclusion, the antiproliferative effects of genipin on the growth of both glioblastoma cell lines have been shown in all of these assays, and genipin profoundly induced apoptosis in both cell lines via the UCP2-related mitochondrial pathway through the induction of intracellular ROS.     

Defining the role of 17β-estradiol in human endometrial stem cells differentiation into neuron-like cells

Human endometrial stem cells (hEnSCs) that can be differentiated into various neural cell types have been regarded as a suitable cell population for neural tissue engineering and regenerative medicine. Considering different interactions between hormones, growth factors, and other factors in the neural system, several differentiation protocols have been proposed to direct hEnSCs towards specific neural cells. The 17β-estradiol plays important roles in the processes of development, maturation, and function of nervous system. In the present research, the impact of 17β-estradiol (estrogen, E2) on the neural differentiation of hEnSCs was examined for the first time, based on the expression levels of neural genes and proteins. In this regard, hEnSCs were differentiated into neuron-like cells after exposure to retinoic acid (RA), epidermal growth factor (EGF), and also fibroblast growth factor-2 (FGF2) in the absence or presence of 17β-estradiol. The majority of cells showed a multipolar morphology. In all groups, the expression levels of nestin, Tuj-1 and NF-H (neurofilament heavy polypeptide) (as neural-specific markers) increased during 14 days. According to the outcomes of immunofluorescence (IF) and real-time PCR analyses, the neuron-specific markers were more expressed in the estrogen-treated groups, in comparison with the estrogen-free ones. These findings suggest that 17β-estradiol along with other growth factors can stimulate and upregulate the expression of neural markers during the neuronal differentiation of hEnSCs. Moreover, our findings confirm that hEnSCs can be an appropriate cell source for cell therapy of neurodegenerative diseases and neural tissue engineering.     

A review of drug therapy for sporadic fatal insomnia

Background: Sporadic fatal insomnia (sFI) is a rapid progressive neurodegenerative disease characterised by gradual to perpetual insomnia, followed by dysautonomia, coma and death.¹ Lugaresi E, Medori R, Montagna P, Baruzzi A, Cortelli P, Lugaresi A, Tinuper P, Zucconi M, Gambetti P. Fatal familial insomnia and dysautonomia with selective degeneration of thalamic nuclei. New England J of Med. 1986;315:997–1003. doi:10.1056/NEJM198610163151605.[Crossref], [PubMed], [Web of Science ®] [Google Scholar] The cause of sFI was recently mapped to a mutation in a protein, the prion, found in the human brain. It is the unfolding of the prion that leads to the generation of toxic oligomers that destroy brain tissue and function. Recent studies have confirmed that a methionine mutation at codon 129 of the human Prion is characteristic of sFI. Current treatment slows down the progression of the disease, but no cure has been found, yet. Methods: We used Molecular Docking and Molecular Dynamics simulation methods, to study the toxic Fatal-Insomnia-prion conformations at local unfolding. The idea was to determine these sites and to stabilise these regions against unfolding and miss-folding, using a small ligand, based on a phenothiazine "moiety". Conclusion: As a result we here discuss current fatal insomnia therapy and present seven novel possible compounds for in vitro and in vivo screening.     

Curcumin can prevent the loss of sinoatrial node cells in methionine-treated rats: A stereological study

Methionine (MET) rich diets, smoking, coffee and alcohol consumption, low physical activity, and aging are related to high plasma concentrations of homocysteine, which can jeopardize the heart health. Although hyperhomocysteinemia has been considered a recognized risk factor for cardiac dysrhythmia, the structural changes of the conductive system, including Sinoatrial (SA) node of the heart involved in the disorder, have not been completely clarified. Curcumin is the main component of turmeric and has shown some cardioprotective effects.This study aimed to evaluate the effect of curcumin on the structural changes of the SA node in L-MET-treated rats. These alterations were evaluated by means of stereological techniques, namely cavalieri principle for volume estimation and optical disector counting technique for cell counting. Both techniques used two-dimensional images for obtaining three-dimensional parameters. The rats were divided into four groups, including control, MET-treated (1 g/kg/day), curcumin-treated, (100 mg/kg/day), and MET + curcumin. The treatments were performed for 28 days. On the final day, SA nodes were dissected out for stereological investigation. Compared to the control rats, the volume of SA node, total volume of grape-like cell clusters, and number of SA node cells were respectively decreased by 42%, 34%, and 37% in the MET-treated group (p < 0.04). However, collagen density remained constant in all the study groups. Furthermore, treatment with curcumin could protect the SA node from cellular decline in the MET + curcumin group (p < 0.01).It can be concluded that curcumin could prevent the structural changes of the SA node in the rats treated with methionine.     

Synthesis, antibacterial activity, and quantitative structure-activity relationships of new (Z)-2-(nitroimidazolylmethylene)-3(2H)-benzofuranone derivatives

A new series of (Z)-2-(1-methyl-5-nitroimidazole-2-ylmethylene)-3(2H)-benzofuranones (11a-p) and (Z)-2-(1-methyl-4-nitroimidazole-5-ylmethylene)-3(2H)-benzofuranones (12a-m) were synthesized and assayed for their antibacterial activity against Gram-positive and Gram-negative bacteria. Most of the 5-nitroimidazole analogues (11a-p) showed a remarkable inhibition of a wide spectrum of Gram-positive bacteria (Staphylococcus aureus, Streptococcus epidermidis, MRSA, and Bacillus subtilis) and Gram-negative Klebsiella pneumoniae, whereas 4-nitroimidazole analogues (12a-m) were not effective against selected bacteria. The quantitative structure-activity relationship investigations were applied to find out the correlation between the experimentally evaluated activities with various parameters of the compounds studied. The QSAR models built in this work had reasonable predictive power and could be explained by the observed trends in activities.     

Biomechanical and Structural Features of CS2 Fimbriae of Enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrhea worldwide, and infection of children in under-developed countries often leads to high mortality rates. Isolated ETEC expresses a plethora of colonization factors (fimbriae/pili), of which CFA/I and CFA/II, which are assembled via the alternate chaperone pathway (ACP), are among the most common. Fimbriae are filamentous structures whose shafts are primarily composed of helically arranged single pilin-protein subunits, with a unique biomechanical ability to unwind and rewind. A sustained ETEC infection, under adverse conditions of dynamic shear forces, is primarily attributed to this biomechanical feature of ETEC fimbriae. Recent understanding about the role of fimbriae as virulence factors points to an evolutionary adaptation of their structural and biomechanical features. In this work, we investigated the biophysical properties of CS2 fimbriae from the CFA/II group. Homology modeling of its major structural subunit, CotA, reveals structural clues related to the niche in which they are expressed. Using optical-tweezers force spectroscopy, we found that CS2 fimbriae unwind at a constant force of 10 pN and have a corner velocity (i.e., the velocity at which the force required for unwinding rises exponentially with increased speed) of 1300 nm/s. The biophysical properties of CS2 fimbriae assessed in this work classify them into a low-force unwinding group of fimbriae together with the CFA/I and CS20 fimbriae expressed by ETEC strains. The three fimbriae are expressed by ETEC, colonize in similar gut environments, and exhibit similar biophysical features, but differ in their biogenesis. Our observation suggests that the environment has a strong impact on the biophysical characteristics of fimbriae expressed by ETEC.     

Prevalence of congenital hypothyroidism in Isfahan, Iran: results of a survey on 20,000 neonates

AIMS: To evaluate the prevalence of congenital hypothyroidism (CH) in a screening program performed for the first time in Isfahan, Iran. METHODS: From May 2002 to December 2002, T4 and TSH serum concentrations of 20,000 3- to 7-day-old newborns, born in all 17 hospitals of the city, were measured by radioimmunoassay and immunoradiometric assay, respectively. The newborns with abnormal screening results (TSH >20 mIU/l, T4 <6.5 microg/dl and based on the weight) were re-examined. RESULTS: Of 531 recalled subjects (recall rate 2.6%), 54 were confirmed to be hypothyroid, showing a prevalence of 1:370 for CH. CONCLUSION: Considering the high frequency of CH, the necessity of implementing a routine screening program in the healthcare system of Isfahan Province is emphasized.