The role of NF-κB transcription factor in cellular response to ionizing radiation

The NF-κB transcription factor is involved in different aspects of the cellular response to stress, including atypical NF-κB pathway activated by damage induced by ionizing radiation. Moreover, NF-κB could be involved in the regulation of genes activated by other stress-responsive factors. Here we aimed to perform the integrative genomics screening to compare subsets of NF-κB-dependent genes induced by a pro-inflammatory stimulus and a high dose of ionizing radiation and also to identify new genes potentially co-regulated by NF-κB and p53 transcription factors in irradiated cells. Methods. The RelA-containing NF-κB dimers were activated by TNFα cytokine (classical proinflammatory pathway) and a single 4 or 10 Gy dose (atypical radiation-induced pathway) in human osteosarcoma cells. NF-κB-dependent and p53-dependent genes were identified using the gene expression profiling (by RNA-Seq) in cells with downregulated RELA or TP53 combined with the global profiling of RelA and p53 binding sites (by ChIP-Seq). Candidate genes were subsequently validated by quantitative PCR. Results: There were 37 NF-κB-dependent protein-coding genes identified: in all cases RelA bound in their regulatory regions upon activation while downregulation of RELA suppressed their stimulus-induced upregulation, which apparently indicated the positive regulation mode (this set of genes included a few “novel” NF-κB-dependent species). The kinetics of the NF-κB activation was slower in cells exposed to radiation than in cytokine-stimulated ones. However, subsets of NF-κB-dependent genes upregulated by both types of stimuli were essentially the same. Moreover, we identified a subset of radiation-modulated genes whose expression was affected by silencing of both TP53 and RELA, and a subset of radiation-upregulated genes where radiation stimulated binding of both p53 and RelA. For three genes an antagonistic effect of both transcription factors was observed: IL4I1 was activated by NF-κB and inhibited by p53, while CDKN1A and SERPINE1 were activated by p53 and inhibited by NF-κB. Moreover, RRAD was putatively co-activated by both factors. Conclusions: One could expect that similar cellular processes resulting from activation of the NF-κB pathway could be induced in cells responding to pro-inflammatory cytokines and in cells where so-called “sterile inflammation” response was initiated by radiation-induced damage. Moreover, certain stress-responsive genes induced by ionizing radiation could be co-regulated by NF-κB and p53.publishedVersio

Use of the far infrared spectroscopy for NaCl and KCl minerals characterization : a case study of halides from Kłodawa in Poland

The paper presents research on chloride minerals of natural origin from Kłodawa (Poland), i.e., colorless, blue and purple halite as well as colorless sylvite. Selected samples of minerals were studied by chemical analysis (ICP-OES, ICP-MS, titration methods) and crystallographic measurements. Then, for the tested halides, research was carried out using far-infrared spectroscopy. Spectroscopic studies confirmed the simple way of distinguishing NaCl and KCl minerals using far-infrared spectroscopy, known in the literature. The novelty is that the article presents for the first time the experimental far infrared spectra of natural blue and purple halite. It was observed that the blue (178 cm−1) and purple (176 cm−1) halites have the strongest infrared band slightly shifted towards higher wavenumbers compared to colorless halite (174 cm−1). As part of the work, the infrared spectra of the crystal structure models of sodium and potassium chloride were calculated for the first time using the density functional theory (with the B3LYP functional and the 6-31G* basis set, 125-atom model). The proposed approach can be used not only as a powerful method differentiating NaCl and KCl minerals, but it can also help with understanding of different defects in crystal lattices for naturally occurring halides and crystals of other minerals

Platelets augment respiratory burst in neutrophils activated by selected species of gram-positive or gram-negative bacteria.

Neutrophils and platelets circulate in blood system and play important physiological roles as part of immunological system. Neutrophils are the first line of host defense against various intruders, and platelets are satellite cells cooperating with other components of defense system. Recent studies report about the cooperation among these types of cells. We analyzed the effect of platelets on oxygen burst in neutrophils triggered by Staphylococcus aureus and Escherichia coli bacteria in vitro. The effect of platelets on oxygen burst in neutrophils was measured by luminol enhanced chemiluminescence. Opsonized and non-opsonized bacteria were used as activators. Activation of neutrophils with live non-opsonized and opsonized bacteria in the presence of platelets increased the oxygen burst as compared to the same system without platelets. The gram-positive bacteria (Staphylococcus aureus) were causing higher activation than gram-negative bacteria (Escherichia coli). This work demonstrate that platelets potentate the response of neutrophils augmenting their respiratory burst in vitro when triggered by bacteria

Expression of matrix metalloproteinase-9 in the neoplastic and interstitial inflammatory infiltrate cells in gastric cancer.

Matrix metalloproteinases (MMPs) play an important role in the extracellular matrix degradation, that is an essential step in tumor invasion and metastases. The current study objective was to evaluate the expression of MMP-9 in the neoplastic and in the interstitial inflammatory infiltrate cells in gastric cancer (GC). Moreover, the relationship between expression of this enzyme and clinicopathological features of GC, such as TNM stage, the depth of tumor invasion, lymph node and distant metastases were assessed. The study comprised 54 patients with gastric cancer. Immunohistochemistry was used to determine the expression of MMP-9 in gastric cancer cells. The semi-quantitative scale was applied to evaluate the expression of metalloproteinase-9. Immunohistochemical testing revealed a positive reaction of MMP-9 in 98% of all cancer tissue specimens and in 93% of inflammatory cells. The expression of MMP-9 in the neoplastic and inflammatory cells increased with more advance tumor stage, depth of tumor invasion and presence of lymph node as well as distant metastases. These findings indicate the significance of interstitial inflammatory infiltrate cells in the MMP-9 synthesis and the role of this enzyme in the invasiveness and metastatic potential of GC

Expression of tissue inhibitors of metalloproteinase 1 (TIMP-1) in gastric cancer tissue.

Degradation of extracellular matrix (ECM) is an essential step of invasion and metastasis of gastric cancer. The proteolysis of basement membranes depends on the balance between activities of matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs). The aim of the study was to assess the expression of TIMP-1 in gastric cancer (GC) and interstitial inflammatory infiltrate cells within GC tissue in relation to clinico-pathological features of tumor and to estimate the prognostic significance of TIMP-1 expression for patients' survival. The presence of TIMP-1 in 54 cases of gastric cancer samples was investigated by immunohistochemistry. The expression of TIMP-1 in cancer and interstitial inflammatory infiltrate cells was evaluated in semi-quantitative scale. The immunoreactivity of TIMP-1 in cancer and inflammatory cells was positive in 100% of cases and varied from weak to intense reaction. The intensity of TIMP-1 expression increased with more advanced tumor stages and in patients who died of cancer during 2-year observation. TIMP-1 expression in interstitial inflammatory infiltrate cells was the independent prognostic factor for patients' survival. The results suggest the role of TIMP-1 in gastric tumorigenesis, although this issue requires further investigtions

Generation of specific inhibitors of SUMO-1– and SUMO-2/3–mediated protein-protein interactions using Affimer (Adhiron) technology

Because protein-protein interactions underpin most biological processes, developing tools that target them to understand their function or to inform the development of therapeutics is an important task. SUMOylation is the posttranslational covalent attachment of proteins in the SUMO family (SUMO-1, SUMO-2, or SUMO-3), and it regulates numerous cellular pathways. SUMOylated proteins are recognized by proteins with SUMO-interaction motifs (SIMs) that facilitate noncovalent interactions with SUMO. We describe the use of the Affimer system of peptide display for the rapid isolation of synthetic binding proteins that inhibit SUMO-dependent protein-protein interactions mediated by SIMs both in vitro and in cells. Crucially, these synthetic proteins did not prevent SUMO conjugation either in vitro or in cell-based systems, enabling the specific analysis of SUMO-mediated protein-protein interactions. Furthermore, through structural analysis and molecular modeling, we explored the molecular mechanisms that may underlie their specificity in interfering with either SUMO-1–mediated interactions or interactions mediated by either SUMO-2 or SUMO-3. Not only will these reagents enable investigation of the biological roles of SUMOylation, but the Affimer technology used to generate these synthetic binding proteins could also be exploited to design or validate reagents or therapeutics that target other protein-protein interactions

(Photo)physical properties of new molecular glasses end-capped with thiophene rings composed of diimide and imine units

New symmetrical arylene bisimide derivatives formed by using electron-donating-electron-accepting systems were synthesized. They consist of a phthalic diimide or naphthalenediimide core and imine linkages and are end-capped with thiophene, bithiophene, and (ethylenedioxy)thiophene units. Moreover, polymers were obtained from a new diamine, N,N′-bis(5- aminonaphthalenyl)naphthalene-1,4,5,8-dicarboximide and 2,5- thiophenedicarboxaldehyde or 2,2′-bithiophene-5,5′-dicarboxaldehyde. The prepared azomethine diimides exhibited glass-forming properties. The obtained compounds emitted blue light with the emission maximum at 470 nm. The value of the absorption coefficient was determined as a function of the photon energy using spectroscopic ellipsometry. All compounds are electrochemically active and undergo reversible electrochemical reduction and irreversible oxidation processes as was found in cyclic voltammetry and differential pulse voltammetry (DPV) studies. They exhibited a low electrochemically (DPV) calculated energy band gap (Eg) from 1.14 to 1.70 eV. The highest occupied molecular orbital and lowest unoccupied molecular orbital levels and Eg were additionally calculated theoretically by density functional theory at the B3LYP/6-31G(d,p) level. The photovoltaic properties of two model compounds as the active layer in organic solar cells in the configuration indium tin oxide/poly(3,4-(ethylenedioxy)thiophene):poly(styrenesulfonate)/active layer/Al under an illumination of 1.3 mW/cm2 were studied. The device comprising poly(3-hexylthiophene) with the compound end-capped with bithiophene rings showed the highest value of Voc (above 1 V). The conversion efficiency of the fabricated solar cell was in the range of 0.69-0.90%

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

Tobacco and alcohol use are leading causes of mortality that influence risk for many complex diseases and disorders 1 . They are heritable 2,3 and etiologically related 4,5 behaviors that have been resistant to gene discovery efforts 6–11 . In sample sizes up to 1.2 million individuals, we discovered 566 genetic variants in 406 loci associated with multiple stages of tobacco use (initiation, cessation, and heaviness) as well as alcohol use, with 150 loci evidencing pleiotropic association. Smoking phenotypes were positively genetically correlated with many health conditions, whereas alcohol use was negatively correlated with these conditions, such that increased genetic risk for alcohol use is associated with lower disease risk. We report evidence for the involvement of many systems in tobacco and alcohol use, including genes involved in nicotinic, dopaminergic, and glutamatergic neurotransmission. The results provide a solid starting point to evaluate the effects of these loci in model organisms and more precise substance use measures