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Limited evidence for parent-of-origin effects in inflammatory bowel disease associated loci
Karin Fransen, Mitja Mitrovič, Uroš Potočnik, 2012, izvirni znanstveni članek

Opis: Background Genome-wide association studies of two main forms of inflammatory bowel diseases (IBD), Crohnʼs disease (CD) and ulcerative colitis (UC), have identified 99 susceptibility loci, but these explain only ~23% of the genetic risk. Part of the Žhidden heritabilityʼ could be in transmissible genetic effects in which mRNA expression in the offspring depends on the parental origin of the allele (genomic imprinting), since children whose mothers have CD are more often affected than children with affected fathers. We analyzed parent-of-origin (POO) effects in Dutch and Indian cohorts of IBD patients. Methods We selected 28 genetic loci associated with both CD and UC, and testedthem for POO effects in 181 Dutch IBD case-parent trios. Three susceptibility variants in NOD2 were tested in 111 CD trios and a significant finding was re-evaluated in 598 German trios. The UC-associated gene, BTNL2, reportedly imprinted, was tested in 70 Dutch UC trios. Finally, we used 62 independent Indian UC trios to test POO effects of five established Indian UC risk loci. Results We identified POO effects for NOD2 (L1007fs; OR = 21.0, P-value = 0.013) for CD; these results could not be replicated in an independent cohort (OR = 0.97, P-value = 0.95). A POO effect in IBD was observed for IL12B (OR = 3.2, P-value = 0.019) and PRDM1 (OR = 5.6, P-value = 0.04). In the Indian trios the IL10 locus showed a POO effect (OR = 0.2, P-value = 0.03). Conclusions Little is known about the effect of genomic imprinting in complex diseases such as IBD. We present limited evidence for POO effects for the tested IBD loci. POO effects explain part of the hidden heritability for complex genetic diseases but need to be investigated further.
Ključne besede: inflammatory bowel diseases, IBD, genetic locus, genetics
Objavljeno: 10.07.2015; Ogledov: 559; Prenosov: 157
.pdf Celotno besedilo (495,25 KB)
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3.
Uporaba primerjalne genomske hibridizacije kot diagnostične metode v medicinskem genetskem laboratoriju
Alenka Erjavec Škerget, Špela Stangler Herodež, Andreja Zagorac, Boris Zagradišnik, Nadja Kokalj-Vokač, 2011, izvirni znanstveni članek

Opis: Namen: Primerjalna genomska hibridizacija (PGH) je molekularno citogenetska tehnika za identifikacijo kromosomskih neravnovesij po celotnem genomu. Zaradi njene kompleksnosti jo kot rutinsko diagnostično metodo uporablja samo nekaj laboratorijev po svetu. Predstaviti želimo svoje izkušnje pri delu s tehniko PGH in njeno diagnostično uporabnost pri post-natalnih kliničnih vzorcih. Metode: Validacijo PGH tehnike smo opravili na vzorcu 10 preiskovancev z diagnozo nepojasnjena mentalna retardacija in s predhodno določenimi subtelomernimi kromosomskimi spremembami v velikostnem razredu 3,9 do 37 Mbp. Kot potrditveno metodo za določitev kromosomske aneuploidije smo PGH uporabili pri petih vzorcih embrionalnega tkiva po spontanih splavih. Pri enajstih hematoloških onkoloških vzorcih smo PGH uporabili pri razreševanju kompleksno preurejenih kariotipov. Rezultati: S PGH smo našli subtelomerne kromosomske spremembe, večje od 8 Mbp. Z metodo PGH smo potrdili vse z molekularno kariotipizacijo predhodno najdene kromosomske aneuploidije v embrionalnih tkivih po spontanih abortusih, kjer celice niso bile več mitotsko aktivne. Največja uporabnost PGH se je pokazala pri pojasnjevanju kompleksnih kromosomskih preureditev v primerih hematoloških malignih obolenj. Zaključek: Čeprav je PGH tehnično zahtevna in zamudna tehnika in kot taka neprimerna za rutinsko diagnostično delo, je po naših izkušnjah nepogrešljiva v posameznih primerih, v katerih druge genetske analize niso uporabne, npr. pri mitotsko neaktivnem celičnem materialu ali pri kompleksno preurejenih kariotipih. Naše izkušnje in rezultati potrjujejo njeno uporabnost predvsem v tistih genetskih laboratorijih, kjer zaradi ekonomskih razlogov še niso uspeli vpeljati pregledovanja genoma na osnovi t.i. micro-array tehnologije.
Ključne besede: comaprative geonimc hybridization, medical genetics, diagnostic method
Objavljeno: 10.07.2015; Ogledov: 531; Prenosov: 13
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4.
Effect of base sequence on G-wire formation in solution
Lea Spindler, Martin Rigler, Irena Drevenšek Olenik, Mateus Webba da Silva, Nason Ma'ani Hessari, 2010, izvirni znanstveni članek

Opis: The formation and dimensions of G-wires by different short G-rich DNA sequences in solution were investigated by dynamic light scattering (DLS) and polyacrilamide gel electrophoresis (PAGE). To explore the basic principles of wire formation, we studied the effects of base sequence, method of preparation, temperature, and oligonucleotide concentration. Both DLS and PAGE show that thermal annealing induces much less macromolecular self-assembly than dialysis. The degree of assembly and consequently length of G-wires (5-6 nm) are well resolved by both methods for DNA sequences with intermediate length, while some discrepancies appear for the shortest and longest sequences. As expected, the longest DNA sequence gives the longest macromolecular aggregates with a length of about 11 nm as estimated by DLS. The quadruplex topologies show no concentration dependence in the investigated DNA concentration range (0.1 mM–0.4 mM) and no structural change upon heating.
Ključne besede: DNA, dynamic light scattering, DLS, polyacrylamide gel electrophoresis, PAGE, genetics
Objavljeno: 14.06.2017; Ogledov: 347; Prenosov: 180
.pdf Celotno besedilo (3,34 MB)
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5.
Detection of mutations in the CYP21A2 gene
Špela Stangler Herodež, Lusien Fijavž, Boris Zagradišnik, Nadja Kokalj-Vokač, 2015, izvirni znanstveni članek

Opis: The objective of this study was to compare the CYP 21A2 genetic profiles of couples with unexplained fertility problems (UFP) with genetic profiles of healthy controls (HCs). Furthermore, we analyzed associations between mutations in the CYP21A2 gene and various clinical and laboratory parameters. Allele-specific polymerase chain reaction (PCR) was used in 638 probands with UFP and 200 HCs. Statistic analysis with χ2 was used to study the association of mutations with infertility. The effect of mutations on particular clinical and laboratory parameters was assessed with the analysis of variance (ANOVA) test. With regard to the CYP21A2 gene, 0.6% of probands with UFP and 0.5% of HCs were positive for the c.290-13A/C>G mutation; 0.6% of probands with UFP and 1.5% of HCs were positive for the p.I172N mutation; there were no probands with UFP positive for the p.P30L mutation, whereas 0.5% of HCs were; and 0.2% of probands with UFP and 0.5% of HCs were found to have the p.V281L mutation. We found a significant association between c.290-13A/C>G mutation and the frequency of significant hormone deviations (χ2 = 6.997, p = 0.008). Similar association was also observed between the c.29013A/C>G mutation and the frequency of polycystic ovary syndrome (PCOS) (χ2 = 16.775, p = 0.000). Our findings indicate that no significant difference in the prevalence of CYP 21A2 mutations can be found in probands with UFP when compared with HCs without infertility history. The results also imply the significant association of the c.290-13A/ C>G mutation in the CYP21A2 gene, not only with the frequency of PCOS, but also with the frequency of significant hormone deviations.
Ključne besede: CYP21A2 gene, genetics, infertility, mutations, unexplained infertility problems (UFP), healthy controls (HCs)
Objavljeno: 30.03.2017; Ogledov: 338; Prenosov: 47
.pdf Celotno besedilo (249,68 KB)
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6.
Family physicians' management of genetic aspects of a cardiac disease
Zalika Klemenc-Ketiš, Borut Peterlin, 2014, izvirni znanstveni članek

Opis: The aim of this study was to find out how Slovenian family physicians (FPs) would manage a hypothetical clinical case, to explore their views about possible ethical dilemmas associated with this clinical case and to determine possible associations with demographic and other characteristics of FPs. This was an observational cross-sectional postal study in the Slovenian FPs’ surgeries. The study population consisted of the whole population of Slovenian FPs (n = 950). The main outcome measures were the percentages of the answers of FPs on different questions about the clinical case on the management of patient and his relative with hereditary cardiomyopathy. There were 271 FPs who answered the questionnaire (response rate was 27.1%). A sample included 66 (24.4%) men and the mean age of all respondents was 45.5 ± 10.6 years. When dealing with the clinical case, most FPs expressed willingness to take the patient’s family history. Only 34.2% FPs did not believe that ordering genetic tests was part of their job. Additionally, only 50.0% of them felt competent to interpret the genetic risk, 25.0% of them would give information about genetic testing and only 6.0% would interpret the results of the genetic testing. Family physicians in Slovenia were willing to include genetic tasks into routine management of their patients, but they do not feel competent enough to interpret the genetic risks and the results of genetic testing. However, an important part of FPs would not refer patients at risk to genetic counseling. The inclusion of genetic topics to family medicine specialization curriculum is needed.
Ključne besede: case management, family medicine, genetics
Objavljeno: 30.03.2017; Ogledov: 411; Prenosov: 43
.pdf Celotno besedilo (246,39 KB)
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7.
Novel insights into the downstream pathways and targets controlled by transcription factors CREM in the testis
Rok Košir, Peter Juvan, Martina Perše, Tomaž Büdefeld, Gregor Majdič, Martina Fink, Paolo Sassone-Corsi, Damjana Rozman, 2012, izvirni znanstveni članek

Opis: The essential role of the Crem gene in normal sperm development is widely accepted and is confirmed by azoospermia in male mice lacking the Crem gene. The exact number of genes affected by Crem absence is not known, however a large difference has been observed recently between the estimated number of differentially expressed genes found in Crem knock-out (KO) mice compared to the number of gene loci bound by CREM. We therefore re-examined global gene expression in male mice lacking the Crem gene using whole genome transcriptomeanalysis with Affymetrix microarrays and compared the lists of differentially expressed genes from Crem-/- mice to a dataset of genes where binding of CREM was determined by Chip-seq. We determined the global effect ofCREM on spermatogenesis as well as distinguished between primary and secondary effects of the CREM absence. We demonstrated that the absence of Crem deregulates over 4700 genes in KO testis. Among them are 101 genes associated with spermatogenesis 41 of which are bound by CREM and are deregulated in Crem KO testis. Absence of several of these genes in mouse models has proven their importance for normal spermatogenesis and male fertility. Our study showed that the absence of Crem plays a more important role on different aspects of spermatogenesis as estimated previously, with itsimpact ranging from apoptosis induction to deregulation of major circadian clock genes, steroidogenesis and the cell-cell junction dynamics. Several new genes important for normal spermatogenesis and fertility are down-regulated inKO testis and are therefore possible novel targets of CREM.
Ključne besede: spermatogenesis, genetics, Crem, mice
Objavljeno: 19.06.2017; Ogledov: 222; Prenosov: 151
.pdf Celotno besedilo (1,77 MB)
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8.
Genetic etiology of primary premature ovarian insuffiency
Maja Franic Ivanisevic, Damir Franić, Miomira Ivovic, Milina Tancic Gajic, Ljiljana Marina, Marija Barac, Svetlana Vujovic, 2016, pregledni znanstveni članek

Opis: Primary premature ovarian insufficiency (PPOI) is characterized by hypergonadotropic amenorrhea and hypoestrogenism in women under 40 years of age. PPOI incidence is 1:10,000 in women aged 18-25, 1:1000 in women aged 25-30 and 1:100 in women aged 35-40. In 10%-28% of cases, PPOI causes primary and in 4%-18% secondary amenorrhea. The process is a consequence of accelerated oocyte atresia, diminished number of germinated cells, and central nervous system aging. Specific genes are responsible for the control of oocyte number undergoing the ovulation process and the time to cessation of the reproductive function. A positive family history of PPOI is found in 15% of women with PPOI, indicating the existing genetic etiology. Primary POI comprises genetic aberrations linked to chromosome X (monosomy, trisomy, translocation, deletion) or to autosomal chromosome. Secondary POI implies surgical removal of ovaries, chemotherapy and radiotherapy, and infections. Diagnostic criteria include follicle stimulating hormone level >40 IU/L and estradiol level <50 pmol/L.
Ključne besede: primary ovarian insufficiency, etiology, genetics
Objavljeno: 08.05.2018; Ogledov: 225; Prenosov: 26
.pdf Celotno besedilo (85,20 KB)
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