До історії музею історико-краєзнавчих досліджень СумДУ

Наук. кер.: С.І. Дегтярьо

Assessment of the use of partitioning and interfacial tracers to determine the content and mass removal rates of nonaqueous phase liquids

It was assessed whether partitioning and interfacial tracers can be used to determine the content and mass removal rate of nonaqueous phase liquid (NAPL) in porous media. Retardation factors for these tracers were determined for five different model matrices contaminated with hexadecane as NAPL. The retardation of the partitioning tracer 2,4-dimethyl-3-pentanol was correlated with the degree of NAPL saturation for four of the five matrices (r(2) = 0.93, n = 8), The observed retardation factors matched the retardation factors predicted with the independently determined hexadecane-water partitioning constant and the degree of NAPL saturation, indicating that this tracer may be used to estimate the degree of NAPL saturation of porous media. The mass removal rates of NAPL from columns packed with different matrices were determined by measuring the amount of hexadecane in the column effluent during elution with electrolyte solution. These removal rates differed over 3 orders of magnitude, dependent on the matrix used. The retardation of the interfacial tracer alkylbenzenesulfonate was higher for matrices with higher NAPL mass removal rates but was not correlated to the degree of NAPL saturation. This indicates that the retardation factors of alkylbenzenesulfonates in NAPL-contaminated media contain information related to the NAPL mass removal rates

Implementing structured, multiprofessional medical ethical decision-making in a neonatal intensive care unit

Background In neonatal intensive care, a child’s death is often preceded by a medical decision. Nurses, social workers and pastors, however, are often excluded from ethical case deliberation. If multiprofessional ethical case deliberations do take place, participants may not always know how to perform to the fullest. Setting A level-IIID neonatal intensive care unit of a paediatric teaching hospital in the Netherlands. Methods Structured multiprofessional medical ethical decision-making (MEDM) was implemented to help overcome problems experienced. Important features were: all professionals who are directly involved with the patient contribute to MEDM; a five-step procedure is used: exploration, agreement on the ethical dilemma/ investigation of solutions, analysis of solutions, decision-making, planning actions; meetings are chaired by an impartial ethicist. A 15-item questionnaire to survey staff perceptions on this intervention just before and 8 months after implementation was developed. Results Before and after response rates were 91/105 (87%) and 85/113 (75%). Factor analysis on the questionnaire suggested a four-factor structure: participants’ role; structure of MEDM; content of ethical deliberation; and documentation of decisions/ conclusions. Effect sizes were 1.67 (p<0.001), 0.69 (p<0.001) and 0.40 (p<0.01) for the first three factors respectively, but only 0.07 (p¼0.65) for the fourth factor. Nurses’ perceptions of improvement did not significantly exceed those of physicians. Conclusion Professionals involved in ethical case deliberation perceived that the process of decisionmaking had improved; they we

Mouse model for the DNA repair/basal transcription disorder Trichothiodystrophy reveals cancer predisposition.

Patients with the nucleotide excision repair (NER) disorder xeroderma pigmentosum (XP) are highly predisposed to develop sunlight-induced skin cancer, in remarkable contrast to photosensitive NER-deficient trichothiodystrophy (TTD) patients carrying mutations in the same XPD gene. XPD encodes a helicase subunit of the dually functional DNA repair/basal transcription complex TFIIH. The pleiotropic disease phenotype is hypothesized to be, in part, derived from a repair defect causing UV sensitivity and, in part, from a subtle, viable basal transcription deficiency accounting for the cutaneous, developmental, and the typical brittle hair features of TTD. To understand the relationship between deficient NER and tumor susceptibility, we used a mouse model for TTD that mimics an XPD point mutation of a TTD patient in the mouse germline. Like the fibroblasts from the patient, mouse cells exhibit a partial NER defect, evident from the reduced UV-induced DNA repair synthesis (residual repair capacity approximately 25%), limited recovery of RNA synthesis after UV exposure, and a relatively mild hypersensitivity to cell killing by UV or 7,12-dimethylbenz[a]anthracene. In accordance with the cellular studies, TTD mice exhibit a modestly increased sensitivity to UV-induced inflammation and hyperplasia of the skin. In striking contrast to the human syndrome, TTD mice manifest a dear susceptibility to UV- and 7,12-dimethylbenz[a]anthracene-induced skin carcinogenesis, albeit not as pronounced as the totally NER-deficient XPA mice. These findings open up the possibility that TTD is associated with a so far unnoticed cancer predisposition and support the notion that a NER deficiency enhances cancer susceptibility. These findings have important implications for the etiology of the human disorder and for the impact of NER on carcinogenesis

Can subtle changes in gene expression be consistently detected with different microarray platforms?

Background: The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results: Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. Conclusion: The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression

Transcription-coupled and global genome repair differentially influence UV-B-induced acute skin effects and syste

Exposure to UV-B radiation impairs immune responses in mammals by inhibiting especially Th1-mediated contact hypersensitivity and delayed-type hypersensitivity. Immunomodulation is not restricted to the exposed skin, but is also observed at distant sites, indicating the existence of mediating factors such as products from exposed skin cells or photoactivated factors present in the superficial layers. DNA damage appears to play a key role, because enhanced nucleotide excision repair (NER) strongly counteracts immunosuppression. To determine the effects of the type and genomic location of UV-induced DNA damage on immunosuppression and acute skin reactions (edema and erythema) four congenic mouse strains carrying different defects in NER were compared: CSB and XPC mice lacking transcription-coupled or global genome NER, respectively, as well as XPA and TTD/XPD mice carrying complete or partial defects in both NER subpathways, respectively. The major conclusions are that 1) transcription-coupled DNA repair is the dominant determinant in protection against acute skin effects; 2) systemic immunomodulation is only affected when both NER subpathways are compromised; and 3) sunburn is not related to UV-B-induced immunosuppression

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

p53 binds enhancers to regulate key target genes. Here, we globally mapped p53-regulated enhancers by looking at enhancer RNA (eRNA) production. Intriguingly, while many p53-induced enhancers contained p53-binding sites, most did not. As long non-coding RNAs(lncRNAs) are prominent regulators of chromatin dynamics, we hypothesized that p53-induced lncRNAs contribute to the activation of enhancers by p53. Among p53-induced lncRNAs, we identified LED and demonstrate that its suppression attenuates p53 function. Chromatin-binding and eRNA expression analyses show that LED associates with and activates strong enhancers. One prominent target of LED was located at an enhancer region within CDKN1A gene, a potent p53-responsive cell cycle inhibitor. LED knockdown reduces CDKN1A enhancer induction and activity, and cell cycle arrest following p53 activation. Finally, promoter-associated hypermethylation analysis shows silencing of LED in human tumours. Thus, our study identifies a new layer of complexity in the p53 pathway and suggests its dysregulation in cancer