Reconstruction of an Integrated Genome-Scale Co-Expression Network Reveals Key Modules Involved in Lung Adenocarcinoma

Our goal of this study was to reconstruct a “genome-scale co-expression network” and find important modules in lung adenocarcinoma so that we could identify the genes involved in lung adenocarcinoma. We integrated gene mutation, GWAS, CGH, array-CGH and SNP array data in order to identify important genes and loci in genome-scale. Afterwards, on the basis of the identified genes a co-expression network was reconstructed from the co-expression data. The reconstructed network was named “genome-scale co-expression network”. As the next step, 23 key modules were disclosed through clustering. In this study a number of genes have been identified for the first time to be implicated in lung adenocarcinoma by analyzing the modules. The genes EGFR, PIK3CA, TAF15, XIAP, VAPB, Appl1, Rab5a, ARF4, CLPTM1L, SP4, ZNF124, LPP, FOXP1, SOX18, MSX2, NFE2L2, SMARCC1, TRA2B, CBX3, PRPF6, ATP6V1C1, MYBBP1A, MACF1, GRM2, TBXA2R, PRKAR2A, PTK2, PGF and MYO10 are among the genes that belong to modules 1 and 22. All these genes, being implicated in at least one of the phenomena, namely cell survival, proliferation and metastasis, have an over-expression pattern similar to that of EGFR. In few modules, the genes such as CCNA2 (Cyclin A2), CCNB2 (Cyclin B2), CDK1, CDK5, CDC27, CDCA5, CDCA8, ASPM, BUB1, KIF15, KIF2C, NEK2, NUSAP1, PRC1, SMC4, SYCE2, TFDP1, CDC42 and ARHGEF9 are present that play a crucial role in cell cycle progression. In addition to the mentioned genes, there are some other genes (i.e. DLGAP5, BIRC5, PSMD2, Src, TTK, SENP2, PSMD2, DOK2, FUS and etc.) in the modules.     

Water‐miscible ionic liquids as novel effectors for the firefly luciferase reaction

Ionic liquids (IL) are used as a new class of solvents for various reactions. Especially using IL in biocatalysis in an aqueous milieu has attracted considerable attention because enzymes show remarkable differences in their catalytic features in IL‐containing reaction media. Firefly luciferase is widely used in many analytical techniques, because light production of firefly luciferase is one of the most sensitive analytical measures in the ultrasensitive detection of adenosine‐5′‐triphosphate, e.g. for measuring microbial contamination and monitoring gene expression, as well as for monitoring tumor growth and metastasis in whole animals. Firefly luciferase is an unstable enzyme and its inactivation can lead to low sensitivity in the above‐mentioned assays. The present study addresses the comparative influence of six different water‐immiscible IL, the 3‐methylimidazolium derivatives [BMIM]Cl, [HMIM]Cl, [BMIM]Br, [EMIM]Br, [HMIM]Br, and [BMIM]BF₄, on the kinetic properties, structural stability, and function of firefly luciferase from Photinus pyralis using circular dichroism, fluorescence spectroscopy, and a bioluminescence assay. The incubation of luciferase with various IL showed that, with the exception of [BMIM]BF₄, the activity and stability of luciferase was considerably increased in the presence of IL, compared to luciferase in aqueous medium. Moreover, K_m for the substrate adenosine‐5′‐triphosphate in the presence of IL (except for [BMIM]BF₄) decreased while K_m for luciferin remained constant.     

Effects of different processing methods of flaxseed on ruminal degradability and in vitro post-ruminal nutrient disappearance

The aim of the study was to determine the effects of different heat-processing methods of flaxseed on the in situ effective dry matter degradability (EDMD) and the in situ effective crude protein degradability (ECPD). The treatments included roasting, steep roasting, rolled roasting, rolled steep roasting, microwave irradiation and extrusion. Three rumen-fistulated sheep were used for in situ incubations. Furthermore, the effects of heat-processing methods on post-ruminal in vitro nutrient disappearance and total tract disappearance were measured by a three-step in vitro technique. The seeds were roasted and extruded at 140°C to 145°C. One lot of roasted seeds was gradually cooled for about 1 h (roasting) and another lot was held in temperature isolated barrels for 45 min (steep roasting). Moreover, roasted and steep roasted flaxseed was rolled in a roller mill. The lowest and highest EDMD was observed for unheated and extruded flaxseed, respectively (p < 0.05). The highest ECPD was observed for extruded flaxseed (p < 0.05). Roasting and microwave irradiation reduced ECPD of flaxseed (p < 0.05). In vitro post-ruminal disappearance of crude nutrients including fibre fractions was highest for rolled-roasted and rolled steep-roasted flaxseed (p < 0.05). The lowest and highest total tract disappearance rates of crude nutrients and fibre fractions were estimated for unheated and extruded flaxseed, respectively (p < 0.05). The post-ruminal disappearance of crude nutrients was also increased by roasting, in which rolling enhanced this effect. In conclusion, all investigated heat treatments had significant effects on in situ and in vitro degradability of nutrients. As well, rolling of roasted flaxseed enhanced the respective effects. Therefore, different methods of heat processing can be used to modify the feed value of flaxseed for specific purposes.     

Association of IL-6 promoter and IFN-γ gene polymorphisms with acute rejection of liver transplantation

Liver transplantation is one of the most important therapies for end-stage liver diseases and is associated with major problems including infections and acute rejection. The outcome of transplantation can be determined by immune responses as a key role in response to the graft. Inflammatory and anti-inflammatory mediators especially cytokines influence the graft microenvironment. Th1 and Th2 immune responses in contrast to regulatory responses cause acute rejection or help graft survival. In this study, we evaluated the gene polymorphisms of IL-6 G-174C, TGF-β T + 869C, IL-4 C-590T, and IFN-γ T + 874A cytokines in liver transplant patients. ARMS-PCR method was used to characterize IL-6 G-174C, TGF-β T + 869C and IFN-γ T + 874A polymorphisms and PCR-RFLP using AvaII restriction enzyme was done for IL-4 C-590T characterization in 70 liver transplant patients. Acute rejection episodes were diagnosed according to standard criteria. The analysis of the results showed that IL-6-174 GG genotype ( P = 0.009, OR = 4.333, 95% CI = 1.043–18.000), IL-6-174G allele (P = 0.011, OR = 5.273, 95% CI = 1.454–19.127) was more frequent and IFN-γ +874 TT genotype was less frequent (P = 0.043, OR = 0.143, 95% CI = 0.0118–1.190) in acute rejection than in non-rejection patients. TGF-β T + 869C and IL-4 C-590T frequencies were not significantly different (P > 0.05). According to the results, it can be conclude that IL-6 G-174C and IFN-γ T + 874A gene polymorphisms have predictive values for acute rejection after liver transplantation. High producer genotype of IL-6 is a genetic risk factor and IFN-γ is a protective factor for acute rejection development.     

Deletion of extra C-terminal segment and its effect on the function and structure of artemin

Artemin acts as a molecular chaperone by protecting Artemia embryos undergoing encystment from damage, caused by heat or other forms of stress. According to the amino acid sequence alignment, although artemin shows a fair amount of homology with ferritin, it also contains an extra C-terminal. Analysis of the C-terminal extension of artemin model in previous studies has shown that there are some favorable interactions between this region and its surrounding cleft. In the current study we tried to investigate the role of this C-terminal in chaperone activity of artemin. This extra C-terminal (39 residues) was deleted and the truncated gene was cloned and expressed in Escherichia coli. According to in vivo chaperone-like activity studies, both full-length and C-terminal truncated artemin conferred thermotolerance on transfected E. coli cells. However, bacteria expressing truncated derivative of artemin was less resistant than those producing native artemin against heat. Moreover, the activity recovery on carbonic anhydrase (CA), as protein substrate, was less in the presence of truncated artemin than that of full-length artemin. The results demonstrated that C-terminal deletion decreases the ability of artemin for chaperone-like activity. Theoretical investigations showed that deletion of artemin C-terminal extension makes substantial structural alterations in a way that structural stability and overall integrity of artemin decrease.     

Physicochemical studies on glycation-induced structural changes in human IgG

Glycation of biomolecules leads to the formation of advanced glycation end products (AGEs). Glycation of immunoglobulin G (IgG) has been implicated in autoimmune diseases such as rheumatoid arthritis (RA). In this study, human IgG was glycated with physiological concentration of glucose. The changes induced in IgG were analyzed by UV, fluorescence, circular dichroism, and Fourier transform infrared (FTIR) spectroscopy; thermal denaturation studies, native, and Sodium dodecyl sulphate (SDS)-polyacrylamide gel electrophoresis. The ketoamine moieties and carbonyl content were also quantitated in glycated IgG. We report structural perturbations, increased carbonyl content, and ketoamine moieties in the glycated IgG. This may interfere with the normal function of IgG and may contribute to initiation of arthritic complications. AGEs damaged IgG may be used as a biomarker for early detection of RA and the associated secondary complications.     

Immunological studies on glycated human IgG

AimsTo study the immunogenicity of advanced glycation end product (AGE) modified IgG (AGE-IgG) in experimental animals.Main methodsHuman IgG was subjected to in vitro glycation with glucose and the formation of N^ε-(carboxymethyl)lysine (CML) was evaluated by high performance liquid chromatography (HPLC). The immunogenicity of native and AGE-IgG was investigated by raising polyclonal antibodies against them in rabbits. The induced antibodies were purified on a Protein-A agarose affinity column. Specific binding of antibodies was screened by competitive inhibition assay and band shift assay. Cross reactions of induced antibodies with various proteins or amino acids and their glycated conformers were ascertained by competitive inhibition ELISA.Key findingsWe detected the CML formation in AGE-IgG. The AGE-IgG was found to be highly immunogenic due to the generation of neo-epitopes on it. Affinity purified antibodies exhibited high degree of specific binding with AGE-IgG in comparison to the native IgG. Antibodies against AGE-IgG exhibited diverse antigen binding characteristics and the glycated conformers of various proteins and amino acids were found to be effective inhibitors of antibody-immunogen interaction in cross reaction studies. Band shift assay reiterated the results obtained by direct binding and competitive inhibition assay.SignificanceThe induced antibodies against AGE-IgG resembled the diverse antigen binding characteristics of autoantibodies found in rheumatoid arthritis (RA). IgG modified by AGEs under oxidative stress presents unique neo-epitopes which may be one of the factors for the induction of autoantibodies in RA patients.     

Fatty acid esters of juvenoid alcohols as insect hormonogen agents (juvenogens)

A series of 8 new juvenogens (3--10) was prepared starting from a pair of isomeric insect juvenile hormone bioanalogues ( and ). The biological activity of the juvenogens -- was tested for their effect on reproduction of the blowfly Neobellieria (Sarcophaga) bullata and for the juvenilizing activity on the termite Prorhinotermes simplex. Results of biological screening are important in structure--activity studies and promising for potential practical application of some of the juvenogens studied, especially against termites.     

Detection and classification of neurotoxins using a novel short-term plasticity quantification method

A tissue-based biosensor is described for screening chemical compounds that rapidly affect the nervous system. The proposed sensor is an extension of a previous work on cultured hippocampal slices [Biosens. Bioelectron. 16 (2001) 491]. The detection of the chemical compounds is based on a novel quantification method of short-term plasticity (STP) of the CA1 system in acute hippocampal slices, using random electrical impulse sequences as inputs and population spike (PS) amplitudes as outputs. STP is quantified by the first and the second order kernels using a variant of the Volterra modeling approach. This approach is more specific and time-efficient than the conventional paired pulse and fixed frequency train methods [J. Neurosci. Methods 2 (2002) 111]. Describing the functional state of the biosensor, the kernels changed accordingly as chemical compounds were added. The second order kernel was decomposed into nine Laguerre functions. The corresponding Laguerre coefficients along with the first order kernel were used as features for classification purposes. The biosensor was tested using picrotoxin (100 μM), trimethylopropane phosphate (10 μM), tetraethylammonium (4 mM), valproate (5 mM), carbachol (5 mM), DAP5 (25 μM), CNQX (3 μM), and DNQX (0.15, 1.5, 3, 5 and 10 μM). Each chemical compound gave a different feature profile corresponding to its pharmacological class. The first order kernel and the Laguerre coefficients formed the input to an artificial neural network (ANN) comprised of a single layer of perceptrons. The ANN was able to classify each tested compound into its respective class.