Atomic force microscopy characterization of silver nanoparticles interactions with marine diatom cells and extracellular polymeric substance

This study highlights the capacity of atomic force microscopy (AFM) for investigating nanoparticle (NP) algal cell interaction with a subnanometer resolution. We designed a set of AFM experiments to characterize NP size, shape, and structure to visualize changes in the cell morphology induced by NPs and to characterize NP interaction with the extracellular polymeric substance (EPS). Samples for AFM imaging were prepared using the same protocol-drop deposition on mica and imaged in air. Here we address the interactions of Ag NPs with ubiquitous, lightly silicified marine diatoms Cylindrotheca fusiformis and Cylindrotheca closterium and their EPS. In natural seawater used throughout this study, the single Ag NPs adopted truncated tetrahedron morphology with particle heights of 10, 20, 30, and 40 nm. This size class Ag NPs penetrates the cell wall through the valve region built of silica NPs embedded in organic matrix. The Ag NPs cause a local damage inside the cell without disintegration of the cell wall. The EPS production has been shown to increase as a feedback response to Ag NP exposure and may contribute to detoxification mechanisms. Imaging EPS at high resolution revealed the incorporation of Ag NPs and their aggregates into the EPS-gel matrix, proving their detoxifying capacity.     

Effects of diet and temperature on condition, proximate composition and three major macro elements, Ca, P and Mg, in barbel Barbus barbus juveniles

Six feeding groups of 60 early juveniles (0.6?g) of a rheophilic cyprinid barbel Barbus barbus were reared in triplicate in 18?glass aquaria. Fish fed a commercial formulated dry diet Aller Futura were compared with those on natural food??commercially available frozen Chironomidae larvae at 17, 21 and 25°C. Daily food rations were adjusted according to fish biomass, differences in hydration between the two diets, and rearing temperature. No mortality occurred during experiment. Temperature, and especially diet, both affected whole body proximate and mineral composition of B. barbus juveniles. Under conditions of this experiment the formulated diet Aller Futura seems to satisfy the demands for calcium and magnesium, while an elevated lipid content in this diet was found and marginally deficient phosphorus content can be concluded. These resulted in a depressed content of phosphorus and total minerals in the body, and in elevated lipid content and condition coefficient in the Futura-fed fish, but no visible body deformities occurred. Advantages and limitations of the condition coefficient K were discussed. This is a non-destructive, express indicator that can be used as a supplementary tool for estimation of changes in body proximate composition in fish juveniles of similar size within a population.     

An alternative theoretical approach to escape decision-making: the role of visual cues

Escape enables prey to avoid an approaching predator. The escape decision-making process has traditionally been interpreted using theoretical models that consider ultimate explanations based on the cost/benefit paradigm. Ultimate approaches, however, suffer from inseparable extra-assumptions due to an inability to accurately parameterize the model's variables and their interactive relationships. In this study, we propose a mathematical model that uses intensity of predator-mediated visual stimuli as a basic cue for the escape response. We consider looming stimuli (i.e. expanding retinal image of the moving predator) as a cue to flight initiation distance (FID; distance at which escape begins) of incubating Mallards (Anas platyrhynchos). We then examine the relationship between FID, vegetation cover and directness of predator trajectory, and fit the resultant model to experimental data. As predicted by the model, vegetation concealment and directness of predator trajectory interact, with FID decreasing with increased concealment during a direct approach toward prey, but not during a tangential approach. Thus, we show that a simple proximate expectation, which involves only visual processing of a moving predator, may explain interactive effects of environmental and predator-induced variables on an escape response. We assume that our proximate approach, which offers a plausible and parsimonious explanation for variation in FID, may serve as an evolutionary background for traditional, ultimate explanations and should be incorporated into interpretation of escape behavior.     

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.     

Inhibition of post-synaptic Kv7/KCNQ/M channels facilitates long-term potentiation in the hippocampus

Activation of muscarinic acetylcholine receptors (mAChR) facilitates the induction of synaptic plasticity and enhances cognitive function. In the hippocampus, M(1) mAChR on CA1 pyramidal cells inhibit both small conductance Ca(2+)-activated KCa2 potassium channels and voltage-activated Kv7 potassium channels. Inhibition of KCa2 channels facilitates long-term potentiation (LTP) by enhancing Ca(2+)calcium influx through postsynaptic NMDA receptors (NMDAR). Inhibition of Kv7 channels is also reported to facilitate LTP but the mechanism of action is unclear. Here, we show that inhibition of Kv7 channels with XE-991 facilitated LTP induced by theta burst pairing at Schaffer collateral commissural synapses in rat hippocampal slices. Similarly, negating Kv7 channel conductance using dynamic clamp methodologies also facilitated LTP. Negation of Kv7 channels by XE-991 or dynamic clamp did not enhance synaptic NMDAR activation in response to theta burst synaptic stimulation. Instead, Kv7 channel inhibition increased the amplitude and duration of the after-depolarisation following a burst of action potentials. Furthermore, the effects of XE-991 were reversed by re-introducing a Kv7-like conductance with dynamic clamp. These data reveal that Kv7 channel inhibition promotes NMDAR opening during LTP induction by enhancing depolarisation during and after bursts of postsynaptic action potentials. Thus, during the induction of LTP M(1) mAChRs enhance NMDAR opening by two distinct mechanisms namely inhibition of KCa2 and Kv7 channels.     

Elevated cerebral spinal fluid cytokine levels in boys with cerebral adrenoleukodystrophy correlates with MRI severity

Background

X-linked adrenoleukodystrophy (ALD) is a metabolic, peroxisomal disease that results from a mutation in the ABCD1 gene. The most severe course of ALD progression is the cerebral inflammatory and demyelinating form of the disease, cALD. To date there is very little information on the cytokine mediators in the cerebral spinal fluid (CSF) of these boys.

Methodology/Principal Findings

Measurement of 23 different cytokines was performed on CSF and serum of boys with cerebral ALD and patients without ALD. Significant elevations in CSF IL-8 (29.3±2.2 vs 12.8±1.1 pg/ml, p = 0.0001), IL-1ra (166±30 vs 8.6±6.5 pg/ml, p = 0.005), MCP-1 (610±47 vs 328±34 pg/ml, p = 0.002), and MIP-1b (14.2±1.3 vs 2.0±1.4 pg/ml, p<0.0001) were found in boys with cALD versus the control group. The only serum cytokine showing an elevation in the ALD group was SDF-1 (2124±155 vs 1175±125 pg/ml, p = 0.0001). The CSF cytokines of IL-8 and MCP-1b correlated with the Loes MRI severity score (p = 0.04 and p = 0.008 respectively), as well as the serum SDF-1 level (p = 0.002). Finally, CSF total protein was also significantly elevated in boys with cALD and correlated with both IL-8, MCP-1b (p = 0.0001 for both), as well as Loes MRI severity score (p = 0.0007).

Conclusions/Significance

IL-8, IL-1ra, MCP-1, MIP-1b and CSF total protein were significantly elevated in patients with cALD; IL-8, MCP-1b, and CSF total protein levels correlated with disease severity determined by MRI. This is the largest report of CSF cytokine levels in cALD to date, and identification of these key cytokines will provide further insight into disease progression and perhaps lead to improved targeted therapies.     

Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs

Nucleotide modifications to microRNAs or their precursors can influence their processing and/or activity. A challenge to their analysis is the lack of independent references for the termini generated by primary processing; typically, these are empirically assigned as the most abundant mapped reads. Mirtrons offer such an independent measure since these microRNA hairpins are defined by splicing. Consequently, mirtron-derived reads that deviate from splice sites reflect modification following primary processing. Analysis in Drosophila revealed multiple modification patterns, including select alterations of 5' termini, many 3' resection events, and unexpectedly abundant 3' untemplated monouridylation. Resections occur on mature AGO1-loaded species, whereas uridylation occurs on pre-miRNAs but is compatible with dicing and AGO1 loading. Strikingly, we found many mirtrons whose modified reads are more abundant than those produced by primary processing. In some cases, these abundant modified reads matched the genome owing to fortuitous uridines in downstream flanking exons, thus highlighting the value of an independent reference for the primary-processed sequence. We could further extend the principle of abundant and preferred uridylation of mirtrons, relative to canonical pre-miRNAs, to Caenorhabditis elegans, mouse, and human. Finally, we found that 3' resection occurs broadly across AGO1-loaded canonical miRNA and star species. Altogether, these findings substantially broaden the complexity of terminal modification pathways acting upon small regulatory RNAs.     

Effect of climate,topography and habitat on species-richness of breeding birds in Poland

We developed predictive maps of farmland and forest species richness which are based on the “focal species concept” and remote sensing data. We explored environmental preferences of 17 farmland and 33 forest species in Poland, using data from the Pan-European Monitoring Scheme. The largest number of farmland species was noted in the central and eastern parts, while the opposite trend was observed in the case of forest species, where the preferred areas were in the north and south-east. The most important environmental component affecting the bird faunas of farmland and forest was a gradient from arable fields to forest. This relationship is unimodal, which means that on a meso-geographical scale the highest species richness occurred in heterogeneous landscapes where fields are interspersed with forest. Our results also indicate that the geographical gradient in Poland's bird fauna can simply be attributed to the habitat-based distinction: western and central parts are dominated by large agricultural habitats and coniferous forest, while in other areas predominate mixed forests and extensively used farmland. Among the climatic factors, only rainfall influenced the farmland bird species. Its effect is non-linear, but positive, which means that in areas with higher rainfall more species are recorded.Our predictive maps are complementary to research on population trends, and can be an essential tool for effective management and conservation of species populations on a trans-national scale.