“Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids

The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The experimentally observed distribution of hydrophobicity in the protein body is compared to the idealized one expressed by a three-dimensional Gauss function. The differences between these two distributions reveal the specificity of structural/functional characteristics of the protein. The residues of hydrophobicity deficiency versus the idealized distribution are assumed to indicate cavities with the potential to bind ligands, while the residues of hydrophobicity excess are interpreted as potentially participating in protein-protein complexation. The distribution of hydrophobicity irregularity seems to be specific for particular structures and functions of proteins. A comparative analysis of such profiles is carried out to identify the potential biological activity of proteins of unknown function.     

Development of mechanical papillae of the tongue in the domestic goose (<Emphasis Type="Italic">Anser anser f. domestica</Emphasis>) during the embryonic period

Three types of mechanical papillae, i.e., conical, filiform, and hair-like papillae, are present on the tongue in the domestic goose. Within conical papillae, we distinguish three categories: large and small conical papillae on the body and conical papillae on the lingual prominence. The arrangement of mechanical papillae on the tongue in Anseriformes is connected functionally with different feeding mechanisms such as grazing and filter-feeding. The present work aims to determine whether morphology of three types of mechanical papillae in goose at the time of hatching is the same as in an adult bird and if the tongue is prepared to fulfill feeding function. Our results revealed that the primordia of the large conical papillae start to develop during the differentiation stage. The primordia of the small conical papillae and conical papillae of the lingual papillae start to develop during the growth stage. At the end of the growth stage, only large conical papillae, three pairs of small conical papillae, and conical papillae of the lingual prominence have similar arrangement as in an adult bird. The shape and arrangement of the remaining small conical papillae probably will be changed after hatching. During embryonic period, the filiform papillae and hair-like papillae are not formed. The embryonic epithelium that covered the mechanical papillae undergoes transformation leading to the formation of multilayered epithelium. During prehatching stage, epithelium becomes orthokeratinized epithelium. In conclusion, the tongue of the domestic goose after hatching is well prepared only for grazing. The filtration of food from water is limited due to the lack of filiform papillae.     

Resolving the naturalization strategy of <Emphasis Type="Italic">Solidago</Emphasis> × <Emphasis Type="Italic">niederederi</Emphasis> (Asteraceae) by the production of sexual ramets and seedlings

In this study, the authors aimed to revise the ability of Solidago × niederederi, a hybrid between S. canadensis and S. virgaurea, to produce sexual ramets and seedlings as a part of its naturalization strategy. Based on a two-season garden cultivation experiment, we showed that the hybrid produces more generative ramets than vegetative ones and the number of generative ramets increases from one season to another with an increasing number of stem buds located on the caudices. We also revealed a spontaneous seedling recruitment by the hybrid during cultivation in the garden. Based on the seed germination test under laboratory conditions, we evidenced that the hybrid can reach a higher final germination percentage than S. canadensis but a lower one than S. virgaurea. Based on field studies conducted in 35 populations in Poland, the hybrid formed the largest populations in tree plantations and on abandoned fields, reaching 16.5 and 15.7 ramet clusters on average, respectively. The most abundant populations were found on abandoned fields; however, the mean number of ramets per cluster did not differ remarkably among habitats (H = 6.5, p = 0.163). In all populations, the mean number of vegetative ramets per cluster reached 0.85, while the generative ones achieved 6.43 on average. The statistical analysis proved that the aforementioned differences are significant (t = ?12.6, p = 0.0002). Our results suggest that S. × niederederi is able to generate its own offspring by sexual reproduction and that abandoned fields seem to be the most suitable habitats for its establishment.     

Long-Term Consumption of High-Fat Diet in Rats: Effects on Microglial and Astrocytic Morphology and Neuronal Nitric Oxide Synthase Expression

Obesity in humans is associated with cognitive decline and elevated risk of neurodegenerative diseases of old age. Variations of high-fat diet are often used to model these effects in animal studies. However, we previously reported improvements in markers of memory and learning, as well as larger hippocampi and higher metabolite concentrations in Wistar rats fed high-fat, high-carbohydrate diet (HFCD, 60 % energy from fat, 28 % from carbohydrates) for 1 year; this diet leads to mild ketonemia (Setkowicz et al. in PLoS One 10:e0139987, 2015). In the present study, we follow up on this cohort to assess glial morphology and expression of markers related to gliosis. Twenty-five male Wistar rats were kept on HFCD and twenty-five on normal chow. At 12 months of age, the animals were sacrificed and processed for immunohistochemical staining for astrocytic (glial fibrillary acidic protein), microglial (Iba1), and neuronal (neuronal nitric oxide synthetase, nNOS) markers in the hippocampus. We have found changes in immunopositive area fraction and cellular complexity, as studied by a simplified Sholl procedure. To our knowledge, this study is the first to apply this methodology to the study of glial cells in HFCD animals. GFAP and Iba1 immunoreactive area fraction in the hippocampi of HFCD-fed rats were decreased, while the mean number of intersections (an indirect measure of cell complexity) was decreased in GFAP-positive astrocytes, but not in Iba1-expressing microglia. At the same time, nNOS expression was lowered after HFCD in both the cortex and the hippocampus.     

MicroRNA-deficient NK cells exhibit decreased survival but enhanced function

NK cells are innate immune lymphocytes important for early host defense against infectious pathogens and malignant transformation. MicroRNAs (miRNAs) are small RNA molecules that regulate a wide variety of cellular processes, typically by specific complementary targeting of the 3'UTR of mRNAs. The Dicer1 gene encodes a conserved enzyme essential for miRNA processing, and Dicer1 deficiency leads to a global defect in miRNA biogenesis. In this study, we report a mouse model of lymphocyte-restricted Dicer1 disruption to evaluate the role of Dicer1-dependent miRNAs in the development and function of NK cells. As expected, Dicer1-deficient NK cells had decreased total miRNA content. Furthermore, miRNA-deficient NK cells exhibited reduced survival and impaired maturation defined by cell surface phenotypic markers. However, Dicer1-deficient NK cells exhibited enhanced degranulation and IFN-γ production in vitro in response to cytokines, tumor target cells, and activating NK cell receptor ligation. Moreover, a similar phenotype of increased IFN-γ was evident during acute MCMV infection in vivo. miRs-15a/15b/16 were identified as abundant miRNAs in NK cells that directly target the murine IFN-γ 3'UTR, thereby providing a potential mechanism for enhanced IFN-γ production. These data suggest that the function of miRNAs in NK cell biology is complex, with an important role in NK cell development, survival, or homeostasis, while tempering peripheral NK cell activation. Further study of individual miRNAs in an NK cell specific fashion will provide insight into these complex miRNA regulatory effects in NK cell biology.     

Colorectal adenoma and cancer detection based on altered methylation pattern of SFRP1, SFRP2, SDC2, and PRIMA1 in plasma samples

Aberrant methylation is one of the most frequent epigenetic alterations that can contribute to tumor formation. Cell-free DNA can originate from tumor tissue; therefore, the evaluation of methylation markers in cell-free DNA can be a promising method for cancer screening. Our aim was to develop a panel of biomarkers with altered methylation along the colorectal adenoma-carcinoma sequence in both colonic tissue and plasma. Methylation of selected CpG sites in healthy colonic (n = 15), adenoma (n = 15), and colorectal cancer (n = 15) tissues was analyzed by pyrosequencing. MethyLight PCR was applied to study the DNA methylation of SFRP1, SFRP2, SDC2, and PRIMA1 gene promoters in 121 plasma and 32 biopsy samples. The effect of altered promoter methylation on protein expression was examined by immunohistochemistry. Significantly higher (P < 0.05) DNA methylation levels were detected in the promoter regions of all 4 markers, both in CRC and adenoma tissues compared with healthy controls. Methylation of SFRP1, SFRP2, SDC2, and PRIMA1 promoter sequences was observed in 85.1%, 72.3%, 89.4%, and 80.9% of plasma samples from patients with CRC and 89.2%, 83.8%, 81.1% and 70.3% from adenoma patients, respectively. When applied as a panel, CRC patients could be distinguished from controls with 91.5% sensitivity and 97.3% specificity [area under the curve (AUC) = 0.978], while adenoma samples could be differentiated with 89.2% sensitivity and 86.5% specificity (AUC = 0.937). Immunohistochemical analysis indicated decreasing protein levels of all 4 markers along the colorectal adenoma-carcinoma sequence. Our findings suggest that this methylation biomarker panel allows non-invasive detection of colorectal adenoma and cancer from plasma samples.     

Oxidative stress reprograms lipopolysaccharide signaling via Src kinase-dependent pathway in RAW 264.7 macrophage cell line

Oxidative stress generated during ischemia/reperfusion injury has been shown to augment cellular responsiveness. Whereas oxidants are themselves known to induce several intracellular signaling cascades, their effect on signaling pathways initiated by other inflammatory stimuli remains poorly elucidated. Previous work has suggested that oxidants are able to prime alveolar macrophages for increased NF-kappa B translocation in response to treatment with lipopolysaccharide (LPS). Because oxidants are known to stimulate the Src family of tyrosine kinases, we hypothesized that the oxidants might contribute to augmented NF-kappa B translocation by LPS via the involvement of Src family kinases. To model macrophage priming in vitro, the murine macrophage cell line, RAW 264.7, was first incubated with various oxidants and then exposed to low dose LPS. These studies show that oxidant stress is able to augment macrophage responsiveness to LPS as evidenced by earlier and increased NF-kappa B translocation. Inhibition of the Src family kinases by either pharmacological inhibition using PP2 or through a molecular approach by cell transfection with Csk was found to prevent the augmented LPS-induced NF-kappa B translocation caused by oxidants. Interestingly, while Src kinase inhibition was able to prevent the LPS-induced NF-kappa B translocation in oxidant-treated macrophages, this strategy had no effect on NF-kappa B translocation caused by LPS in the absence of oxidants. These findings suggested that oxidative stress might divert LPS signaling along an alternative signaling pathway. Further studies demonstrated that the Src-dependent pathway induced by oxidant pretreatment involved the activation of phosphatidylinositol 3-kinase. Involvement of this pathway appeared to be independent of traditional LPS signaling. Together, these studies provide a novel potential mechanism whereby oxidants might prime alveolar macrophages for altered responsiveness to subsequent inflammatory stimuli and suggest different cellular targets for immunomodulation following ischemia/reperfusion.     

Biological diversity of Salix taxa in Cu,Pb and Zn phytoextraction from soil

The aim of the study was to estimate the efficiency of copper (Cu), lead (Pb) and zinc (Zn) phytoextraction by 145 Salix taxa cultivated in an area affected by industrial activity. Survivability and biomass of plants were also analyzed. The highest Cu, Pb and Zn content in shoots was 33.38 ± 2.91 (S. purpurea × viminalis 8), 24.64 ± 1.97 (S. fragilis 1) and 58.99 ± 4.30 (S. eriocephala 7) mg kg^?1 dry weight, respectively. In the case of unwashed leaves, the highest content of these metals was 135.06 ± 8.14 (S. purpurea 26), 67.98 ± 5.27 (S. purpurea 45) and 142.56 ± 12.69 (S. alba × triandra 2) mg kg^?1 dw, while in washed leaves it was 106.02 ± 11.12 (S. purpurea 45), 55.06 ± 5.75 (S. purpurea 45) and 122.87 ± 12.33 (S. alba × triandra 2) mg kg^?1 dw, respectively. The differences between the highest and lowest values for Cu, Pb and Zn were 545%, 20500% and 535% in shoots; 2692%, 2560% and 7500% in unwashed leaves; and 3286%, 2221% and 6950% in washed leaves, respectively. S. acutifolia was able to effectively accumulate all three metals jointly, producing shoots that were well developed in both length and diameter when compared with the other tested willows—an ability that would suggest its high suitability for practical application.