Pooled sample-based GWAS: a cost-effective alternative for identifying colorectal and prostate cancer risk variants in the Polish population

Background

Prostate cancer (PCa) and colorectal cancer (CRC) are the most commonly diagnosed cancers and cancer-related causes of death in Poland. To date, numerous single nucleotide polymorphisms (SNPs) associated with susceptibility to both cancer types have been identified, but their effect on disease risk may differ among populations.

Methods

To identify new SNPs associated with PCa and CRC in the Polish population, a genome-wide association study (GWAS) was performed using DNA sample pools on Affymetrix Genome-Wide Human SNP 6.0 arrays. A total of 135 PCa patients and 270 healthy men (PCa sub-study) and 525 patients with adenoma (AD), 630 patients with CRC and 690 controls (AD/CRC sub-study) were included in the analysis. Allele frequency distributions were compared with t-tests and χ²-tests. Only those significantly associated SNPs with a proxy SNP (p<0.001; distance of 100 kb; r²>0.7) were selected. GWAS marker selection was conducted using PLINK. The study was replicated using extended cohorts of patients and controls. The association with previously reported PCa and CRC susceptibility variants was also examined. Individual patients were genotyped using TaqMan SNP Genotyping Assays.

Results

The GWAS selected six and 24 new candidate SNPs associated with PCa and CRC susceptibility, respectively. In the replication study, 17 of these associations were confirmed as significant in additive model of inheritance. Seven of them remained significant after correction for multiple hypothesis testing. Additionally, 17 previously reported risk variants have been identified, five of which remained significant after correction.

Conclusion

Pooled-DNA GWAS enabled the identification of new susceptibility loci for CRC in the Polish population. Previously reported CRC and PCa predisposition variants were also identified, validating the global nature of their associations. Further independent replication studies are required to confirm significance of the newly uncovered candidate susceptibility loci.     

Temperature-triggered self-assembly of elastin-like block co-recombinamers:the controlled formation of micelles and vesicles in an aqueous medium

The possibility of obtaining different self-assembled nanostructures in reversible systems based on elastin-like block corecombinamers is explored in this work. The results obtained show how an evolution from a more common micellar structure to a hollow vesicle can be attained simply by changing the block arrangements and lengths, even when other molecular properties, such as molecular weight or mean polarity, remain essentially unchanged. This work sheds light on the possibility of obtaining hollow nano-objects, based on elastin-like recombinamers, which can assemble and disassemble in response to a change in their surroundings. This kind of system can be an example of how high precision in the genetic production of synthetic macro-molecules can be used, on an exclusive basis, to control the shape and size of their derived nano-objects.     

Cell-type specific roles for PTEN in establishing a functional retinal architecture

Background

The retina has a unique three-dimensional architecture, the precise organization of which allows for complete sampling of the visual field. Along the radial or apicobasal axis, retinal neurons and their dendritic and axonal arbors are segregated into layers, while perpendicular to this axis, in the tangential plane, four of the six neuronal types form patterned cellular arrays, or mosaics. Currently, the molecular cues that control retinal cell positioning are not well-understood, especially those that operate in the tangential plane. Here we investigated the role of the PTEN phosphatase in establishing a functional retinal architecture.

Methodology/Principal Findings

In the developing retina, PTEN was localized preferentially to ganglion, amacrine and horizontal cells, whose somata are distributed in mosaic patterns in the tangential plane. Generation of a retina-specific Pten knock-out resulted in retinal ganglion, amacrine and horizontal cell hypertrophy, and expansion of the inner plexiform layer. The spacing of Pten mutant mosaic populations was also aberrant, as were the arborization and fasciculation patterns of their processes, displaying cell type-specific defects in the radial and tangential dimensions. Irregular oscillatory potentials were also observed in Pten mutant electroretinograms, indicative of asynchronous amacrine cell firing. Furthermore, while Pten mutant RGC axons targeted appropriate brain regions, optokinetic spatial acuity was reduced in Pten mutant animals. Finally, while some features of the Pten mutant retina appeared similar to those reported in Dscam-mutant mice, PTEN expression and activity were normal in the absence of Dscam.

Conclusions/Significance

We conclude that Pten regulates somal positioning and neurite arborization patterns of a subset of retinal cells that form mosaics, likely functioning independently of Dscam, at least during the embryonic period. Our findings thus reveal an unexpected level of cellular specificity for the multi-purpose phosphatase, and identify Pten as an integral component of a novel cell positioning pathway in the retina.     

Initial Characterization of the Pf-Int Recombinase from the Malaria Parasite Plasmodium falciparum

Background

Genetic variation is an essential means of evolution and adaptation in many organisms in response to environmental change. Certain DNA alterations can be carried out by site-specific recombinases (SSRs) that fall into two families: the serine and the tyrosine recombinases. SSRs are seldom found in eukaryotes. A gene homologous to a tyrosine site-specific recombinase has been identified in the genome of Plasmodium falciparum. The sequence is highly conserved among five other members of Plasmodia.

Methodology/Principal Findings

The predicted open reading frame encodes for a ∼57 kDa protein containing a C-terminal domain including the putative tyrosine recombinase conserved active site residues R-H-R-(H/W)-Y. The N-terminus has the typical alpha-helical bundle and potentially a mixed alpha-beta domain resembling that of λ-Int. Pf-Int mRNA is expressed differentially during the P. falciparum erythrocytic life stages, peaking in the schizont stage. Recombinant Pf-Int and affinity chromatography of DNA from genomic or synthetic origin were used to identify potential DNA targets after sequencing or micro-array hybridization. Interestingly, the sequences captured also included highly variable subtelomeric genes such as var, rif, and stevor sequences. Electrophoretic mobility shift assays with DNA were carried out to verify Pf-Int/DNA binding. Finally, Pf-Int knock-out parasites were created in order to investigate the biological role of Pf-Int.

Conclusions/Significance

Our data identify for the first time a malaria parasite gene with structural and functional features of recombinases. Pf-Int may bind to and alter DNA, either in a sequence specific or in a non-specific fashion, and may contribute to programmed or random DNA rearrangements. Pf-Int is the first molecular player identified with a potential role in genome plasticity in this pathogen. Finally, Pf-Int knock-out parasite is viable showing no detectable impact on blood stage development, which is compatible with such function.     

Sex, Lies and fMRI-Gender Differences in Neural Basis of Deception

Deception has always been a part of human communication as it helps to promote self-presentation. Although both men and women are equally prone to try to manage their appearance, their strategies, motivation and eagerness may be different. Here, we asked if lying could be influenced by gender on both the behavioral and neural levels. To test whether the hypothesized gender differences in brain activity related to deceptive responses were caused by differential socialization in men and women, we administered the Gender Identity Inventory probing the participants' subjective social sex role. In an fMRI session, participants were instructed either to lie or to tell the truth while answering a questionnaire focusing on general and personal information. Only for personal information, we found differences in neural responses during instructed deception in men and women. The women vs. men direct contrast revealed no significant differences in areas of activation, but men showed higher BOLD signal compared to women in the left middle frontal gyrus (MFG). Moreover, this effect remained unchanged when self-reported psychological gender was controlled for. Thus, our study showed that gender differences in the neural processes engaged during falsifying personal information might be independent from socialization.     

Host Defense Peptides of Thrombin Modulate Inflammation and Coagulation in Endotoxin-Mediated Shock and Pseudomonas aeruginosa Sepsis

Gram-negative sepsis is accompanied by a disproportionate innate immune response and excessive coagulation mainly induced by endotoxins released from bacteria. Due to rising antibiotic resistance and current lack of other effective treatments there is an urgent need for new therapies. We here present a new treatment concept for sepsis and endotoxin-mediated shock, based on host defense peptides from the C-terminal part of human thrombin, found to have a broad and inhibitory effect on multiple sepsis pathologies. Thus, the peptides abrogate pro-inflammatory cytokine responses to endotoxin in vitro and in vivo. Furthermore, they interfere with coagulation by modulating contact activation and tissue factor-mediated clotting in vitro, leading to normalization of coagulation responses in vivo, a previously unknown function of host defense peptides. In a mouse model of Pseudomonas aeruginosa sepsis, the peptide GKY25, while mediating a modest antimicrobial effect, significantly inhibited the pro-inflammatory response, decreased fibrin deposition and leakage in the lungs, as well as reduced mortality. Taken together, the capacity of such thrombin-derived peptides to simultaneously modulate bacterial levels, pro-inflammatory responses, and coagulation, renders them attractive therapeutic candidates for the treatment of invasive infections and sepsis.     

Synthesis of a natural chalcone and its prenyl analogs--evaluation of tumor cell growth-inhibitory activities, and effects on cell cycle and apoptosis

Six prenyl (=3-methylbut-2-en-1-yl) chalcones (=1,3-diphenylprop-2-en-1-ones), 2-7, and one natural non-prenylated chalcone, 1, have been synthesized and evaluated for their in vitro growth-inhibitory activity against three human tumor cell lines. A pronounced dose-dependent growth-inhibitory effect was observed for all prenylated derivatives, except for 7. The chalcone possessing one prenyloxy group at C(2'), i.e., 2, was the most active derivative against the three human tumor cell lines (5.9相似文献   

Remote sensing to map influence of light pollution on Cory’s shearwater in São Miguel Island,Azores Archipelago

Global economic and population growth increase the extent and intensity of artificial night lighting. From an ecological perspective, this is light pollution, which causes changes in reproductive physiology, migration and foraging of many species and ultimately leads to loss of biodiversity. Some seabirds are intimately linked with the light features of their environments because they are nocturnally active. We report light-induced groundings of Cory’s shearwater (Calonectris diomedea) during a 2-year study (2008 and 2009) in São Miguel Island, in the Azores archipelago, and investigate the spatial correlation of locations of grounded birds with an annual composite of remotely sensed stable lights. Results indicate that 16.7% of fledglings are attracted to lights. The exposure of shearwater colonies in the study area to artificial night lighting is low overall. Four colonies account for 87% of the grounded birds. The distance each bird was found from the closest colony was best explained by the ratio of the satellite-measured light levels at the grounding spot to the light levels at the assigned colony of origin. These results demonstrate that satellite-observed nighttime lights are sufficient to assess risk to marine birds at the scale of oceanic islands and indicate their utility for monitoring the effectiveness of programs to manage lighting to reduce risk for these species and conducting global assessments of species vulnerability. To minimize the impact on Cory’s shearwater and other marine birds, we recommend measures such as reduction and control of lighting intensity near colony locations, while continuing and re-enforcing rescue campaigns.     

Simplifier: a web tool to eliminate redundant NGS contigs

Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions. Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome assembly in tests with data from Prokaryotic organisms.

Availability

Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher.