Browsing by Subject "metabolism"

Now showing 1 - 7 of 7

Open Access
Differences in the accumulation and distribution profile of heavy metals and metalloid between male and female crayfish (Astacus leptodactylus)
(2013) Tunca, E.; Ucuncu, E.; Ozkan, A.D.; Ulger, Z.E.; Cansizoǧlu, A.E.; Tekinay, T.
Concentrations of selected heavy metals and a metalloid were measured by ICP-MS in crayfish (Astacus leptodactylus) collected from Lake Hirfanli, Turkey. Aluminum (Al), chromium (52Cr, 53Cr), copper ( 63Cu, 65Cu), manganese (Mn), nickel (Ni) and arsenic (As) were measured in the exoskeleton, gills, hepatopancreas and abdominal muscle tissues of 60 crayfish of both genders. With the exception of Al, differences were determined between male and female cohorts for the accumulation trends of the above-mentioned elements in the four tissues. It was also noted that the accumulation rates of Ni and As were significantly lower in gill tissue of females compared to males and no significant difference was observed for Cu isotopes in female crayfish. Cluster Analysis (CA) recovered similar results for both genders, with links between accumulations of Ni and As being notable. Accumulation models were described separately for male and female crayfish using regression analysis, and are presented for models where R2 > 0.85. © 2013 Springer Science+Business Media New York.
Open Access
GOPred: GO molecular function prediction by combined classifiers
(2010) Saraç Ö.S.; Atalay V.; Cetin-Atalay, R.
Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred). © 2010 Saraç et al.
Open Access
Mutation in TOR1AIP1 encoding LAP1B in a form of muscular dystrophy: A novel gene related to nuclear envelopathies
(Elsevier Ltd, 2014) Kayman-Kurekci G.; Talim, B.; Korkusuz P.; Sayar, N.; Sarioglu, T.; Oncel I.; Sharafi P.; Gundesli H.; Balci-Hayta, B.; Purali, N.; Serdaroglu-Oflazer P.; Topaloglu H.; Dincer P.
We performed genome-wide homozygosity mapping and mapped a novel myopathic phenotype to chromosomal region 1q25 in a consanguineous family with three affected individuals manifesting proximal and distal weakness and atrophy, rigid spine and contractures of the proximal and distal interphalangeal hand joints. Additionally, cardiomyopathy and respiratory involvement were noted. DNA sequencing of torsinA-interacting protein 1 (TOR1AIP1) gene encoding lamina-associated polypeptide 1B (LAP1B), showed a homozygous c.186delG mutation that causes a frameshift resulting in a premature stop codon (p.E62fsTer25). We observed that expression of LAP1B was absent in the patient skeletal muscle fibres. Ultrastructural examination showed intact sarcomeric organization but alterations of the nuclear envelope including nuclear fragmentation, chromatin bleb formation and naked chromatin. LAP1B is a type-2 integral membrane protein localized in the inner nuclear membrane that binds to both A- and B-type lamins, and is involved in the regulation of torsinA ATPase. Interestingly, luminal domain-like LAP1 (LULL1)-an endoplasmic reticulum-localized partner of torsinA-was overexpressed in the patient's muscle in the absence of LAP1B. Therefore, the findings suggest that LAP1 and LULL1 might have a compensatory effect on each other. This study expands the spectrum of genes associated with nuclear envelopathies and highlights the critical function for LAP1B in striated muscle. © 2014 Elsevier B.V.
Open Access
Perisylvian GABA levels in schizophrenia and bipolar disorder
(Elsevier Ireland Ltd, 2017) Atagün, M. İ.; Şıkoglu, M. E.; Soykan, Ç.; Can, S. S.; Ulusoy-Kaymak S.; Çayköylü, A.; Algın O.; Phillips, M. L.; Öngür, D.; Moore, C. M.
The aim of this study is to measure GABA levels of perisylvian cortices in schizophrenia and bipolar disorder patients, using proton magnetic resonance spectroscopy (1H-MRS). Patients with schizophrenia (n = 25), bipolar I disorder (BD-I; n = 28) and bipolar II disorder (BD-II; n = 20) were compared with healthy controls (n = 30).1H-MRS data was acquired using a Siemens 3 T whole body scanner to quantify right and left perisylvian structures’ (including superior temporal lobes) GABA levels. Right perisylvian GABA values differed significantly between groups [χ2= 9.62, df: 3, p = 0.022]. GABA levels were significantly higher in the schizophrenia group compared with the healthy control group (p = 0.002). Furthermore, Chlorpromazine equivalent doses of antipsychotics correlated with right hemisphere GABA levels (r2= 0.68, p = 0.006, n = 33). GABA levels are elevated in the right hemisphere in patients with schizophrenia in comparison to bipolar disorder and healthy controls. The balance between excitatory and inhibitory controls over the cortical circuits may have direct relationship with GABAergic functions in auditory cortices. In addition, GABA levels may be altered by brain regions of interest, psychotropic medications, and clinical stage in schizophrenia and bipolar disorder. ï¿½ 2016 Elsevier Ireland Ltd
Open Access
Phytoremediation of Cu, Cr and Pb mixtures by lemna minor
(2013) Üçüncü, E.; Tunca, E.; Fikirdeşici, S.; Özkan, A.D.; Altindaǧ, A.
The present study reports the capacity of the aquatic macrophyte Lemna minor to remediate combinations of Cu(II), Pb(II) and Cr(III) from a simulated natural environment. The effect of these metal mixtures on the growth of L. minor was also investigated using growth rate and biomass inhibition calculations. L. minor was successful in removing Cr and Pb from the water, and it remained an effective remediation agent when both metals were present in the environment. However, a relatively low absorption capacity was observed for Cu, increasing concentrations of which were associated with significant decreases in growth rate. No statistically significant difference was found between the 24 h and 7 days absorption rates of Cu, Pb and Cr, suggesting that, at the concentrations tested, equilibrium occurs within 24 h of metal exposure. © 2013 Springer Science+Business Media New York.
Open Access
SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation
(2011) Acun, T.; Oztas, E.; Yagci, T.; Yakicier, M.C.
Background: Smad interacting protein-1 is a transcription factor that is implicated in transforming growth factor-β/bone morphogenetic protein signaling and a repressor of E-cadherin and human telomerase reverse transcriptase. It is also involved in epithelial-mesenchymal transition and tumorigenesis. However, genetic and epigenetic alterations of SIP1 have not been fully elucidated in cancers. In this study, we investigated mutations and promoter hypermethylation of the SIP1 gene in human hepatocellular carcinomas.Methods: SIP1 expression was analyzed in HCC cell lines and primary tumors in comparison to normal and non-tumor liver tissues by using semi-quantitative RT-PCR, quantitative real-time RT-PCR and immunohistochemistry. Mutation and deletion screening of the SIP1 gene were performed by direct sequencing in HCC-derived cells. Restoration of SIP1 expression was sought by treating HCC cell lines with the DNA methyl transferase inhibitor, 5-AzaC, and the histone deacetylase inhibitor, TSA. SIP1 promoter methylation was analyzed by the combined bisulfite restriction analysis assay in in silico-predicted putative promoter and CpG island regions.Results: We found that the expression of SIP1 was completely lost or reduced in five of 14 (36%) HCC cell lines and 17 of 23 (74%) primary HCC tumors. Immunohistochemical analysis confirmed that SIP1 mRNA downregulation was associated with decreased expression of the SIP1 protein in HCC tissues (82.8%). No somatic mutation was observed in SIP1 exons in any of the 14 HCC cell lines. Combined treatment with DNA methyl transferase and histone deacetylase inhibitors synergistically restored SIP1 expression in SIP1-negative cell lines. Analysis of three putative gene regulatory regions revealed tumor-specific methylation in more than half of the HCC cases.Conclusions: Epigenetic mechanisms contribute significantly to the downregulation of SIP1 expression in HCC. This finding adds a new level of complexity to the role of SIP1 in hepatocarcinogenesis. © 2011 Acun et al; licensee BioMed Central Ltd.
Open Access
Systematic discovery of Rab GTPases with synaptic functions in Drosophila
(2011) Chan, C.-C.; Scoggin, S.; Wang, D.; Cherry, S.; Dembo, T.; Greenberg, B.; Jin, E.J.; Kuey, C.; Lopez, A.; Mehta, S.Q.; Perkins, T.J.; Brankatschk, M.; Rothenfluh, A.; Buszczak, M.; Hiesinger P.R.
Background: Neurons require highly specialized intracellular membrane trafficking, especially at synapses. Rab GTPases are considered master regulators of membrane trafficking in all cells, and only very few Rabs have known neuron-specific functions. Here, we present the first systematic characterization of neuronal expression, subcellular localization, and function of Rab GTPases in an organism with a brain. Results: We report the surprising discovery that half of all Drosophila Rabs function specifically or predominantly in distinct subsets of neurons in the brain. Furthermore, functional profiling of the GTP/GDP-bound states reveals that these neuronal Rabs are almost exclusively active at synapses and the majority of these synaptic Rabs specifically mark synaptic recycling endosomal compartments. Our profiling strategy is based on Gal4 knockins in large genomic fragments that are additionally designed to generate mutants by ends-out homologous recombination. We generated 36 large genomic targeting vectors and transgenic rab-Gal4 fly strains for 25 rab genes. Proof-of-principle knockout of the synaptic rab27 reveals a sleep phenotype that matches its cell-specific expression. Conclusions: Our findings suggest that up to half of all Drosophila Rabs exert specialized synaptic functions. The tools presented here allow systematic functional studies of these Rabs and provide a method that is applicable to any large gene family in Drosophila. © 2011 Elsevier Ltd. All rights reserved.