Coalescence computations for large samples drawn from populations of time-varying sizes

We present new results concerning probability distributions of times in the coalescence tree and expected allele frequencies for coalescent with large sample size. The obtained results are based on computational methodologies, which involve combining coalescence time scale changes with techniques of integral transformations and using analytical formulae for infinite products. We show applications of the proposed methodologies for computing probability distributions of times in the coalescence tree and their limits, for evaluation of accuracy of approximate expressions for times in the coalescence tree and expected allele frequencies, and for analysis of large human mitochondrial DNA dataset.

Selective Separation of Chromium Species from Soils by Single-Step Extraction Methods: a Critical Appraisal

A critical appraisal of single-step extraction procedures of chromium species from soil was done in terms of their selectivity towards Cr(III) and Cr(VI) species. Samples of natural mineral and organic soil and samples of soil enriched with different chromium compounds of various solubility (in liquid or solid form) were used to simulate contamination of soil by liquid and solid wastes. The efficiency of extraction of Cr(III) and Cr(VI) species with various reagents, e.g. acetic acid, chelating agents (EDTA, DTPA) or inorganic salts (phosphates and carbonates), was evaluated on the basis of recovery results obtained for enriched samples. None of used reagents allow for quantitative extraction of added Cr(III) form. Procedures based on extraction of soil with Na₂CO₃ at room and elevated temperature (90-95 °C) were suitable for extraction of Cr(VI) species from mineral soil, whereas for organic soil, the procedure based on extraction with Na₂CO₃ at room temperature was recommended. The developed extraction procedures were validated using certified reference material (CRM 041 soil) and applied for analysis of contaminated soil samples. The studies showed that the physical state of waste, initial form and oxidation state of chromium and soil properties influenced the final chromium species and their mobility in soil, which have an impact on contamination of environment. The analysis of contaminated soil samples from a tannery area showed that the share of Cr(VI) was very low (only 0.8-4.5%) despite the high total content of chromium, which confirmed that chromium was present in immobile forms.

Transition from traditional to modern forest management shaped the spatial extent of cattle pasturing in Białowieża Primeval Forest in the nineteenth and twentieth centuries

Pasturing of livestock in forests has had profound consequences for Europe's landscapes. In Białowieża Primeval Forest (BPF), cattle pasturing was a part of traditional forest use that ceased only in the second half of the twentieth century. We collected information on the institutional changes governing forest cattle pasturing and the changes in spatial extent of cattle presence in BPF in last two centuries and information on cattle numbers and their impact on forest regeneration. The spatial extent of cattle pasturing was highly variable, with the distribution of grazing areas frequently changing. Forest near villages (constituting less than 10 % of the area) was most often used for cattle grazing during continued longer time periods. Historical data showed that cattle have had a clear impact on forest regeneration. However, the frequent changes that occurred in the extent of cattle grazing indicate that their impact occurred locally, was smaller in other less intensively used areas, and in the forest as a whole.

Contrasting Patterns of Species Richness and Functional Diversity in Bird Communities of East African Cloud Forest Fragments

Rapid fragmentation and degradation of large undisturbed habitats constitute major threats to biodiversity. Several studies have shown that populations in small and highly isolated habitat patches are prone to strong environmental and demographic stochasticity and increased risk of extinction. Based on community assembly theory, we predict recent rapid forest fragmentation to cause a decline in species and functional guild richness of forest birds combined with a high species turnover among habitat patches, and well defined dominance structures, if competition is the major driver of community assembly. To test these predictions, we analysed species co-occurrence, nestedness, and competitive strength to infer effects of interspecific competition, habitat structure, and species' traits on the assembly of bird species communities from 12 cloud forest fragments in southern Kenya. Our results do not point to a single ecological driver of variation in species composition. Interspecific competition does not appear to be a major driver of species segregation in small forest patches, while its relative importance appears to be higher in larger ones, which may be indicative for a generic shift from competition-dominated to colonisation-driven community structure with decreasing fragment size. Functional trait diversity was independent of fragment size after controlling for species richness. As fragmentation effects vary among feeding guilds and habitat generalists, in particular, tend to decline in low quality forest patches, we plead for taking species ecology fully into account when predicting tropical community responses to habitat change.

Mesoscale atmospheric transport of ragweed pollen allergens from infected to uninfected areas

Allergenic ragweed (Ambrosia spp.) pollen grains, after being released from anthers, can be dispersed by air masses far from their source. However, the action of air temperature, humidity and solar radiation on pollen grains in the atmosphere could impact on the ability of long distance transported (LDT) pollen to maintain allergenic potency. Here, we report that the major allergen of Ambrosia artemisiifolia pollen (Amb a 1) collected in ambient air during episodes of LDT still have immunoreactive properties. The amount of Amb a 1 found in LDT ragweed pollen grains was not constant and varied between episodes. In addition to allergens in pollen sized particles, we detected reactive Amb a 1 in subpollen sized respirable particles. These findings suggest that ragweed pollen grains have the potential to cause allergic reactions, not only in the heavily infested areas but, due to LDT episodes, also in the regions unaffected by ragweed populations.

Familial Alzheimer's Disease Lymphocytes Respond Differently Than Sporadic Cells to Oxidative Stress: Upregulated p53-p21 Signaling Linked with Presenilin 1 Mutants

Familial (FAD) and sporadic (SAD) Alzheimer's disease do not share all pathomechanisms, but knowledge on their molecular differences is limited. We previously reported that cell cycle control distinguishes lymphocytes from SAD and FAD patients. Significant differences were found in p21 levels of SAD compared to FAD lymphocytes. Since p21 can also regulate apoptosis, the aim of this study was to compare the response of FAD and SAD lymphocytes to oxidative stress like 2-deoxy-D-ribose (2dRib) treatment and to investigate the role of p21 levels in this response. We report that FAD cells bearing seven different PS1 mutations are more resistant to 2dRib-induced cell death than control or SAD cells: FAD cells showed a lower apoptosis rate and a lower depolarization of the mitochondrial membrane. Despite that basal p21 cellular content was lower in FAD than in SAD cells, in response to 2dRib, p21 mRNA and protein levels significantly increased in FAD cells. Moreover, we found a higher cytosolic accumulation of p21 in FAD cells. The transcriptional activation of p21 was shown to be dependent on p53, as it can be blocked by PFT-α, and correlated with the increased phosphorylation of p53 at Serine 15. Our results suggest that in FAD lymphocytes, the p53-mediated increase in p21 transcription, together with a shift in the nucleocytoplasmic localization of p21, confers a survival advantage against 2dRib-induced apoptosis. This compensatory mechanism is absent in SAD cells. Thus, therapeutic and diagnostic designs should take into account possible differential apoptotic responses in SAD versus FAD cells.

Genomic findings in patients with clinical suspicion of 22q11.2 deletion syndrome

Chromosome 22q11.2 deletion syndrome, one of the most common human genomic syndromes, has highly heterogeneous clinical presentation. Patients usually harbor a 1.5 to 3 Mb hemizygous deletion at chromosome 22q11.2, resulting in pathognomic TBX1, CRKL and/or MAPK1 haploinsufficiency. However, there are some individuals with clinical features resembling the syndrome who are eventually diagnosed with genomic disorders affecting other chromosomal regions. The objective of this study was to evaluate the additive value of high-resolution array-CGH testing in the cohort of 41 patients with clinical features of 22q11.2 deletion syndrome and negative results of standard cytogenetic diagnostic testing (karyotype and FISH for 22q11.2 locus). Array-CGH analysis revealed no aberrations at chromosomes 22 or 10 allegedly related to the syndrome. Five (12.2 %) patients were found to have other genomic imbalances, namely 17q21.31 microdeletion syndrome (MIM#610443), 1p36 deletion syndrome (MIM#607872), NF1 microduplication syndrome (MIM#613675), chromosome 6pter-p24 deletion syndrome (MIM#612582) and a novel interstitial deletion at 3q26.31 of 0.65 Mb encompassing a dosage-dependent gene NAALADL2. Our study demonstrates that the implementation of array-CGH into the panel of classic diagnostic procedures adds significantly to their efficacy. It allows for detection of constitutional genomic imbalances in 12 % of subjects with negative result of karyotype and FISH targeted for 22q11.2 region. Moreover, if used as first-tier genetic test, the method would provide immediate diagnosis in ∼40 % phenotypic 22q11.2 deletion subjects.

Determination of total arsenic and arsenic species in drinking water, surface water, wastewater, and snow from Wielkopolska, Kujawy-Pomerania, and Lower Silesia provinces, Poland

Arsenic is a ubiquitous element which may be found in surface water, groundwater, and drinking water. In higher concentrations, this element is considered genotoxic and carcinogenic; thus, its level must be strictly controlled. We investigated the concentration of total arsenic and arsenic species: As(III), As(V), MMA, DMA, and AsB in drinking water, surface water, wastewater, and snow collected from the provinces of Wielkopolska, Kujawy-Pomerania, and Lower Silesia (Poland). The total arsenic was analyzed by inductively coupled plasma mass spectrometry (ICP-MS), and arsenic species were analyzed with use of high-performance liquid chromatography inductively coupled plasma mass spectrometry (HPLC/ICP-MS). Obtained results revealed that maximum total arsenic concentration determined in drinking water samples was equal to 1.01 μg L(-1). The highest concentration of total arsenic in surface water, equal to 3778 μg L(-1) was determined in Trująca Stream situated in the area affected by geogenic arsenic contamination. Total arsenic concentration in wastewater samples was comparable to those determined in drinking water samples. However, significantly higher arsenic concentration, equal to 83.1 ± 5.9 μg L(-1), was found in a snow sample collected in Legnica. As(V) was present in all of the investigated samples, and in most of them, it was the sole species observed. However, in snow sample collected in Legnica, more than 97 % of the determined concentration, amounting to 81 ± 11 μg L(-1), was in the form of As(III), the most toxic arsenic species.

Chromosome Territory Modeller and Viewer

This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi–a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters. ChroTeMo has been developed as a fully probabilistic modeller. Due to this feature, the comparison between the experimental data on the structure of a nucleus and the results obtained from ChroTeMo can indicate whether the distribution of chromosomes inside a nucleus is also fully probabilistic or is subjected to certain non-random patterns. The presented tools have been written in Python, so they are multiplatform, portable and easy to read. Moreover, if necessary they can be further developed by users writing their portions of code. The source code, documentation, and wiki, as well as the issue tracker and the list of related articles that use ChroTeMo and ChroTeVi, are accessible in a public repository at Github under GPL 3.0 license.

Chromium Speciation in Wastewater and Sewage by Solid-Phase Extraction Using a New Diphenylcarbazone-Incorporated Resin

A new procedure for the determination of chromium species in polluted environmental samples by flame atomic absorption spectrometry was developed in this work. A new material containing 1,5-diphenylcarbazone included in a polymeric matrix was prepared and employed as a solid-phase extraction material for selective separation of Cr(III) ions under dynamic conditions. Chromium(III) ions were retained on this sorbent with high efficiency and repeatability (95 %, RSD = 1 %) from solutions with pH 9.0. The quantitative recovery of analyte was obtained with 0.1 mol L-1 EDTA. The concentration of Cr(VI) ions was calculated from the difference between the concentration of total chromium and Cr(III) ions. The prepared sorbent exhibits good chemical and mechanical stability, sorption capacity and selectivity towards Cr(III) ions in the presence of Cu(II), Ni(II), Mn(II) and Ca(II) ions. The accuracy of the separation method was proved by analysis of reference material of wastewater RES 10.2. The developed procedure was applied for chromium speciation analysis in municipal sewage samples.

Do Dynamic Compared to Static Facial Expressions of Happiness and Anger Reveal Enhanced Facial Mimicry?

Facial mimicry is the spontaneous response to others’ facial expressions by mirroring or matching the interaction partner. Recent evidence suggested that mimicry may not be only an automatic reaction but could be dependent on many factors, including social context, type of task in which the participant is engaged, or stimulus properties (dynamic vs static presentation). In the present study, we investigated the impact of dynamic facial expression and sex differences on facial mimicry and judgment of emotional intensity. Electromyography recordings were recorded from the corrugator supercilii, zygomaticus major, and orbicularis oculi muscles during passive observation of static and dynamic images of happiness and anger. The ratings of the emotional intensity of facial expressions were also analysed. As predicted, dynamic expressions were rated as more intense than static ones. Compared to static images, dynamic displays of happiness also evoked stronger activity in the zygomaticus major and orbicularis oculi, suggesting that subjects experienced positive emotion. No muscles showed mimicry activity in response to angry faces. Moreover, we found that women exhibited greater zygomaticus major muscle activity in response to dynamic happiness stimuli than static stimuli. Our data support the hypothesis that people mimic positive emotions and confirm the importance of dynamic stimuli in some emotional processing.

Reconstruction of the pollution history of alkylphenols (4-tert-octylphenol, 4-nonylphenol) in the Baltic Sea

This paper reports the reconstruction of the pollution history of 4-tert-octylphenol (OP) and 4-nonylphenol (NP) in the Baltic Sea. Alkylphenols are endocrine-disrupting compound and therefore toxic to aquatic organisms. Sediment cores were collected from regions with relatively stable sedimentation conditions. The cores were dated by the (210)Pb method. The OP and NP were determined using HPLC-FL. The highest inventory of these compounds was observed in the Gotland Deep (610 μg m(2) of NP and 47 μg m(2) of OP) and the lowest-on the slope of the Gdansk Deep (24 μg m(2) of NP and 16 μg m(2) of OP). Such spatial distribution was probably, among other factors, the result of the uplift of the sea floor. The pollution trends of OP and NP in sediments coincided with the following: (1) the beginnings of eutrophication (1960s/1970s of the twentieth century) and (2) strong increase in the areal extent and volume of hypoxia and anoxia in the Baltic (present century).

Evolutionary interaction between W/Y chromosome and transposable elements

The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.

Molecular anatomy of the thalamic complex and the underlying transcription factors

Thalamocortical loops have been implicated in the control of higher-order cognitive functions, but advances in our understanding of the molecular underpinnings of neocortical organization have not been accompanied by similar analyses in the thalamus. Using expression-based correlation maps and the manual mapping of mouse and human datasets available in the Allen Brain Atlas, we identified a few individual regions and several sets of molecularly related nuclei that partially overlap with the classic grouping that is based on topographical localization and thalamocortical connections. These new molecular divisions of the adult thalamic complex are defined by the combinatorial expression of Tcf7l2, Lef1, Gbx2, Prox1, Pou4f1, Esrrg, and Six3 transcription factor genes. Further in silico and experimental analyses provided the evidence that TCF7L2 might be a pan-thalamic specifier. These results provide substantial insights into the "molecular logic" that underlies organization of the thalamic complex.

Helicobacter pylori HP0231 Influences Bacterial Virulence and Is Essential for Gastric Colonization

The Dsb protein family is responsible for introducing disulfide bonds into nascent proteins in prokaryotes, stabilizing the structure of many proteins. Helicobacter pylori HP0231 is a Dsb-like protein, shown to catalyze disulfide bond formation and to participate in redox homeostasis. Notably, many H. pylori virulence factors are stabilized by the formation of disulfide bonds. By employing H. pylori HP0231 deficient strains we analyzed the effect of lack of this bacterial protein on the functionality of virulence factors containing putative disulfide bonds. The lack of H. pylori HP0231 impaired CagA translocation into gastric epithelial cells and reduced VacA-induced cellular vacuolation. Moreover, H. pylori HP0231 deficient bacteria were not able to colonize the gastric mucosa of mice, probably due to compromised motility. Together, our data demonstrate an essential function for H. pylori HP0231 in gastric colonization and proper function of bacterial virulence factors related to gastric pathology.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

Health-related quality of life and mental distress in patients with partial deafness: preliminary findings

The aim of the study was to evaluate mental distress and health-related quality of life in patients with bilateral partial deafness (high-frequency sensorineural hearing loss) before cochlear implantation, with respect to their audiological performance and time of onset of the hearing impairment. Thirty-one patients and 31 normal-hearing individuals were administered the Beck Depression Inventory (BDI), the State-Trait-Anxiety-Inventory (STAI) and the World Health Organization Quality of Life-BREF questionnaire (WHOQOL-BREF). Patients also completed the Nijmegen-Cochlear-Implant-Questionnaire (NCIQ), a tool for evaluation of quality of life related to hearing loss. Patients revealed increased depressive and anxiety symptoms, as well as decreased health-related quality of life (psychological health, physical health), in comparison with their healthy counterparts (t tests, p < 0.05). Furthermore, a General Linear Model demonstrated in patients with a prelingual onset of hearing loss enhanced self-evaluated social interactions and activity (NCIQ), when their outcomes were contrasted with those obtained in individuals with postlingual partial deafness (p < 0.05). The study failed to show any effect of collateral tinnitus. Patients not using hearing aids had better audiological performance and, therefore, better sound perception and speech production, as measured with NCIQ. There was no effect of hearing aid use with respect to mental distress. Additional statistically significant correlations seen in patients included those between a steeper slope hearing loss configuration (averaged pure-tone thresholds at 1 and 2 kHz with subtracted threshold at 0.5 kHz) and better audiometric speech detection, between audiometric thresholds and the subjectively rated sound perception (NCIQ), as well as left-ear audiometric word recognition scores and the subjectively perceived ability to recognize advanced sounds (NCIQ). In addition, a longer duration of postlingual deafness, as well as a younger age at the onset were both related to worse speech detection thresholds. The results of the study provide evidence that successful rehabilitation in patients with partial deafness might have to go beyond the standard speech therapy. Enhancement of the regular diagnostic assessment with additional psychological tools is highly recommended. Further investigation is required as to the role of functional residual hearing, hearing aid use and tinnitus, in relation to future outcomes of cochlear implantation.

Injectable gellan gum-based nanoparticles-loaded system for the local delivery of vancomycin in osteomyelitis treatment

Infection spreading in the skeletal system leading to osteomyelitis can be prevented by the prolonged administration of antibiotics in high doses. However systemic antibiotherapy, besides its inconvenience and often low efficacy, provokes numerous side effects. Thus, we formulated a new injectable nanoparticle-loaded system for the local delivery of vancomycin (Vanc) applied in a minimally-invasive way. Vanc was encapsulated in poly(L-lactide-co-glycolide) nanoparticles (NPs) by double-emulsification. The size (258 ± 11 nm), polydispersity index (0.240 ± 0.003) and surface potential (-25.9 ± 0.2 mV) of NPs were determined by dynamic light scattering and capillary electrophoresis measurements. They have a spherical morphology and a smooth topography as observed using atomic force microscopy. Vanc loading and encapsulation efficiencies were 8.8 ± 0.1 and 55.2 ± 0.5 %, respectively, based on fluorescence spectroscopy assays. In order to ensure injectability, NPs were suspended in gellan gum and cross-linked with Ca(2+); also a portion of dissolved antibiotic was added to the system. The resulting system was found to be injectable (extrusion force 11.3 ± 1.1 N), reassembled its structure after breaking as shown by rheology tests and ensured required burst release followed by sustained Vanc delivery. The system was cytocompatible with osteoblast-like MG-63 cells (no significant impact on cells' viability was detected). Growth of Staphylococcus spp. reference strains and also those isolated from osteomyelitic joints was inhibited in contact with the injectable system. As a result we obtained a biocompatible system displaying ease of application (low extrusion force), self-healing ability after disruption, adjustable drug release and antimicrobial properties.