Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays

<p>Abstract</p> <p>Background</p> <p>Tumor-predominant splice isoforms were identified during comparative <it>in silico </it>sequence analysis of EST clones, suggesting that global aberrant alternative pre-mRNA splicing may be an epigenetic phenomenon in cancer. We used an exon expression array to perform an objective, genome-wide survey of glioma-specific splicing in 24 GBM and 12 nontumor brain samples. Validation studies were performed using RT-PCR on glioma cell lines, patient tumor and nontumor brain samples.</p> <p>Results</p> <p>In total, we confirmed 14 genes with glioma-specific splicing; seven were novel events identified by the exon expression array (<it>A2BP1, BCAS1, CACNA1G, CLTA, KCNC2, SNCB</it>, and <it>TPD52L2</it>). Our data indicate that large changes (> 5-fold) in alternative splicing are infrequent in gliomagenesis (< 3% of interrogated RefSeq entries). The lack of splicing changes may derive from the small number of splicing factors observed to be aberrantly expressed.</p> <p>Conclusion</p> <p>While we observed some tumor-specific alternative splicing, the number of genes showing exclusive tumor-specific isoforms was on the order of tens, rather than the hundreds suggested previously by <it>in silico </it>mining. Given the important role of alternative splicing in neural differentiation, there may be selective pressure to maintain a majority of splicing events in order to retain glial-like characteristics of the tumor cells.</p

Methylation of the candidate biomarker TCF21 is very frequent across a spectrum of early-stage nonsmall cell lung cancers

The transcription factor TCF21 is involved in mesenchymal-to-epithelial differentiation and was shown to be aberrantly hypermethylated in lung and head and neck cancers. Because of its reported high frequency of hypermethylation in lung cancer, we sought to characterize the stages and types of non-small cell lung cancer (NSCLC) that are hypermethylated and to define the frequency of hypermethylation and associated “second hits”

Chemical and biological study of essential oils from <i>Eugenia pruniformis</i> Cambess., an endemic species from Brazilian Atlantic Forest

Eugenia pruniformis Cambess. is an endemic species from Brazilian Atlantic Forest. Essential oils from leaves and fruits from this species were obtained by hydrodistillation and analyzed by GCMS/CG-FID. In all, 25 compounds were identified, with predominance of sesquiterpene hydrocarbons in both plant parts. The major compounds were β-caryophyllene, bicyclogermacrene, germacrene D, δ- cadinene and α-copaene. Antioxidant activity was performed for essential oil from leaves using ORAC method, showing value of 0.30 ± 0.06 mmol TE/g. Anticholinesterasic evaluation was also performed for this oil, indicating that it inhibited acetylcholinesterase, showing an IC50 of 1798 μg/mL. These results indicate that this essential oil may be considered as a potential source of substances for Alzheimer’s disease Treatment. To our knowledge, these are the first contributions to biological and phytochemical characterization of E. pruniformis, an almost unexplored species from Brazilian Atlantic Forest.Colegio de Farmacéuticos de la Provincia de Buenos Aire

Effects of MDM2, MDM4 and TP53 Codon 72 Polymorphisms on Cancer Risk in a Cohort Study of Carriers of TP53 Germline Mutations

Previous studies have shown that MDM2 SNP309 and p53 codon 72 have modifier effects on germline P53 mutations, but those studies relied on case-only studies with small sample sizes. The impact of MDM4 polymorphism on tumor onset in germline mutation carriers has not previously been studied.We analyzed 213 p53 germline mutation carriers including 168(78.9%) affected with cancer and 174 who had genotypic data. We analyzed time to first cancer using Kaplan-Meier and Cox proportional hazards methods, comparing risks according to polymorphism genotypes. For MDM2 SNP309, a significant difference of 9.0 years in the average age of cancer diagnosis was observed between GG/GT and TT carriers (18.6 versus 27.6 years, P = 0.0087). The hazards ratio was 1.58 (P = 0.03) comparing risks among individuals with GG/GT to risk among TT, but this effect was only significant in females (HR = 1.60, P = 0.02). Compared to other genotypes, P53 codon 72 PP homozygotes had a 2.24 times (P = 0.03) higher rate for time to develop cancer. We observed a multiplicative joint effect of MDM2 and p53 codon72 polymorphism on risk. The MDM4 polymorphism had no significant effects.Our results suggest that the MDM2 SNP309 G allele is associated with cancer risk in p53 germline mutation carriers and accelerates time to cancer onset with a pronounced effect in females. A multiplicative joint effect exists between the MDM2 SNP309 G allele and the p53 codon 72 G allele in the risk of cancer development. Our results further define cancer risk in carriers of germline p53 mutations

Potencijalna upotreba izotopa važnih za okoliš u ispitivanju migracije onečišćujućih tvari

This article presents the use of natural abundance stable isotope (hydrogen, carbon, nitrogen, oxygen, chlorine) analysis data as a tool for providing important information about the origin of contaminants, the contribution of different sources to a multi-source plume, characterisation of their complex transport (rate and mechanisms) and for evaluating the success of contaminated site remediation. Isotopic signatures of contaminants are useful tracers of their sources, while isotopic fractionation can be used to quantitatively assess the progress of an environmental process such as biodegradation. This new isotopic approach is reliable and can offer more information than traditional techniques in pollutant migration studies, particularly after waste disposal. During biological degradation of any organic compound, molecules containing lighter isotopes are degraded, and the portion of heavier isotopes in the substrate is increased, identifying specific microbial roles in biogeochemical cycling. Since isotopic fractionation is proportional to degradation, depending on the type of contamination, a microbial degradation of 50 % to 99 % of the initial concentration can be quantified using isotope ratio measurements.Cilj ovog rada je da se prikaže korištenje podataka analize prirodne obilnosti stabilnih izotopa (vodika, ugljika, dušika, kisika i klora) kao alata za dobivanje važnih informacija o porijeklu onečišćujućih tvari, doprinosu različitih multikomponentnih onečišćivača, karakterizaciji njihova kompleksnog transporta (brzine i mehanizma) i praćenja uspjeha remedijacije onečišćenih mjesta. Izotopski sadržaji onečišćujućih tvari koriste se kao traseri za određivanje njihovih izvora, dok se izotopsko frakcioniranje može iskoristiti za kvantitativnu procjenu toka procesa kao što je biodegradacija. Takav nov izotopski pristup je pouzdan i nudi više informacija od tradicionalnih tehnika kontrole putovanja onečišćivala, napose nakon odlaganja opasnog otpada na zemljištu. Za vrijeme biodegradacije nekog organskog spoje molekule koje sadržavaju lake izotope lakše se degradiraju, a dio težih izotopa u supstratu se povećava, što upućuje na mikrobiološku ulogu u biokemijskom ciklusu. Kako je izotopsko frakcioniranje proporcionalno degradaciji zavisno od tipa onečišćenja, korištenjem podataka mjerenja izotopskih odnosa može se procijeniti mikrobiološka degradacija od 50 % do 99 % od početne koncentracije