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Gene Level (gene + level)
Selected AbstractsThe role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimesENVIRONMENTAL MICROBIOLOGY, Issue 6 2008Achim Schmalenberger Summary Sulfonates are a key component of the sulfur present in agricultural soils. Their mobilization as part of the soil sulfur cycle is mediated by rhizobacteria, and involves the oxidoreductase AsfA. In this study, the effect of fertilization regime on rhizosphere bacterial asfA distribution was examined at the Broadbalk long-term wheat experiment, Rothamsted, UK, which was established in 1843, and has included a sulfur-free treatment since 2001. Direct isolation of desulfonating rhizobacteria from the wheat rhizospheres led to the identification of several Variovorax and Polaromonas strains, all of which contained the asfA gene. Rhizosphere DNA was isolated from wheat rhizospheres in plots fertilized with inorganic fertilizer with and without sulfur, with farmyard manure or from unfertilized plots. Genetic profiling of 16S rRNA gene fragments [denaturing gradient gel electrophoresis (DGGE)] from the wheat rhizospheres revealed that the level of inorganic sulfate in the inorganic fertilizer was correlated with changes in the general bacterial community structure and the betaproteobacterial community structure in particular. Community analysis at the functional gene level (asfA) showed that 40% of clones in asfAB clone libraries were affiliated to the genus Variovorax. Analysis of asfAB -based terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed considerable differences between sulfate-free treatments and those where sulfate was applied. The results suggest the occurrence of desulfonating bacterial communities that are specific to the fertilization regime chosen and that arylsulfonates play an important role in rhizobacterial sulfur nutrition. [source] Abundance of six tetracycline resistance genes in wastewater lagoons at cattle feedlots with different antibiotic use strategiesENVIRONMENTAL MICROBIOLOGY, Issue 1 2007Nicholas Peak Summary The abundance of six tetracycline resistance genes tet(O), tet(Q), tet(W), tet(M), tet(B) and tet(L), were quantified over time in wastewater lagoons at concentrated animal feeding operations (CAFO) to assess how feedlot operation affects resistance genes in downstream surface waters. Eight lagoons at five cattle feedlots in the Midwestern United States were monitored for 6 months. Resistance and 16S-rRNA gene abundances were quantified using real-time PCR, and physicochemical lagoon conditions, tetracycline levels, and other factors (e.g. feedlot size and weather conditions) were monitored over time. Lagoons were sorted according to antibiotic use practice at each site, and designated as ,no-use', ,mixed-use' or ,high-use' for comparison. High-use lagoons had significantly higher detected resistance gene levels (tetR; 2.8 × 106 copies ml,1) relative to no-use lagoons (5.1 × 103 copies ml,1; P < 0.01) and mixed-use lagoons (7.3 × 105 copies ml,1; P = 0.076). Bivariate correlation analysis on pooled data (n = 54) confirmed that tetR level strongly correlated with feedlot area (r = 0.67, P < 0.01) and ,total' bacterial 16S-rRNA gene level in each lagoon (r = 0.51, P < 0.01), which are both characteristic of large CAFOs. tet(M) was the most commonly detected gene, both in absolute number and normalized to 16S-rRNA gene level, although tet(O), tet(Q) and tet(W) levels were also high in the mixed and high-use lagoons. Finally, resistance gene levels were highly seasonal with abundances being 10,100 times greater in the autumn versus the summer. Results show that antibiotic use strategy strongly affects both the abundance and seasonal distribution of resistance genes in associated lagoons, which has implications on water quality and feedlot management practices. [source] Long-term effects of idiotype vaccination on the specific T-cell response in peripheral blood and bone marrow of multiple myeloma patientsEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 5 2007Amir Osman Abdalla Abstract Objectives:, To elucidate long-term effects of idiotype (Id) vaccination on Id-specific T cells of multiple myeloma (MM) patients and compare Id-specific T-cell responses of peripheral blood with those of bone marrow (BM). Materials and methods:, Id-specific T-cell responses of peripheral blood mononuclear cells (PBMC) were compared with those of BM mononuclear cells (BMMC) in 10 MM patients vaccinated with the Id protein at a median time of 41 months since the last immunization. The PBMC responses at late follow-up were also compared with those during active immunization. The responses were assessed by a proliferation assay, enzyme-linked immunospot (ELISPOT) (,-interferon), cytometric bead array (CBA) for secreted cytokines and quantitative real-time polymerase chain reaction (QRT-PCR) for cytokine gene expression. Results:, At the late testing time, an Id-specific response was detected in PBMC of five patients (ELISPOT, CBA, QRT-PCR) and in BMMC of four patients (CBA, QRT-PCR). A response in both compartments was noted only in three patients. The cytokines gene profile was consistent with a predominance of Th2 cells [interleukin (IL)-4, IL-5, IL-10]. Comparison of the Id-specific responses of PBMC during active immunization with those at the late follow-up showed that the frequency and magnitude of the responses had decreased significantly by time (proliferation/ELISPOT) (P < 0.02) and shifted at the gene level from a Th1 to a Th2 profile (P < 0.05). Conclusion:, Id-specific T cells may decline overtime and shift toward a Th2 response and may be found at a similar frequency of patients in blood and BM. [source] Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiaeFEMS YEAST RESEARCH, Issue 2 2006Akira Ando Abstract Yeasts used in bread making are exposed to high concentrations of sucrose during sweet dough fermentation. Despite its importance, tolerance to high-sucrose stress is poorly understood at the gene level. To clarify the genes required for tolerance to high-sucrose stress, genome-wide screening was undertaken using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 273 deletions that yielded high sucrose sensitivity, approximately 20 of which were previously uncharacterized. These 273 deleted genes were classified based on their cellular function and localization of their gene products. Cross-sensitivity of the high-sucrose-sensitive mutants to high concentrations of NaCl and sorbitol was studied. Among the 273 sucrose-sensitive deletion mutants, 269 showed cross-sensitivities to sorbitol or NaCl, and four (i.e. ade5,7, ade6, ade8, and pde2) were specifically sensitive to high sucrose. The general stress response pathways via high-osmolarity glycerol and stress response element pathways and the function of the invertase in the ade mutants were similar to those in the wild-type strain. In the presence of high-sucrose stress, intracellular contents of ATP in ade mutants were at least twofold lower than that of the wild-type cells, suggesting that depletion of ATP is a factor in sensitivity to high-sucrose stress. The genes identified in this study might be important for tolerance to high-sucrose stress, and therefore should be target genes in future research into molecular modification for breeding of yeast tolerant to high-sucrose stress. [source] Emergence of self-learning fuzzy systems by a new virus DNA,based evolutionary algorithmINTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 3 2003Lihong Ren In this article, we propose a new approach to the virus DNA,based evolutionary algorithm (VDNA-EA) to implement self-learning of a class of Takagi-Sugeno (T-S) fuzzy controllers. The fuzzy controllers use T-S fuzzy rules with linear consequent, the generalized input fuzzy sets, Zadeh fuzzy logic and operators, and the generalized defuzzifier. The fuzzy controllers are proved to be nonlinear proportional-integral (PI) controllers with variable gains. The fuzzy rules are discovered automatically and the design parameters in the input fuzzy sets and the linear rule consequent are optimized simultaneously by the VDNA-EA. The VDNA-EA uses the VDNA encoding method that stemmed from the structure of the VDNA to encode the design parameters of the fuzzy controllers. We use the frameshift decoding method of the VDNA to decode the DNA chromosome into the design parameters of the fuzzy controllers. In addition, the gene transfer operation and bacterial mutation operation inspired by a microbial evolution phenomenon are introduced into the VDNA-EA. Moreover, frameshift mutation operations based on the DNA genetic operations are used in the VDNA-EA to add and delete adaptively fuzzy rules. Our encoding method can significantly shorten the code length of the DNA chromosomes and improve the encoding efficiency. The length of the chromosome is variable and it is easy to insert and delete parts of the chromosome. It is suitable for complex knowledge representation and is easy for the genetic operations at gene level to be introduced into the VDNA-EA. We show how to implement the new method to self-learn a T-S fuzzy controller in the control of a nonlinear system. The fuzzy controller can be constructed automatically by the VDNA-EA. Computer simulation results indicate that the new method is effective and the designed fuzzy controller is satisfactory. © 2003 Wiley Periodicals, Inc. [source] A novel steady-state genetic algorithm approach to the reliability optimization design problem of computer networksINTERNATIONAL JOURNAL OF NETWORK MANAGEMENT, Issue 1 2009A. M. Mutawa This paper introduces the development and implementation of a new methodology for optimizing reliability measures of a computer communication network within specified constraints. A genetic algorithm approach with specialized encoding, crossover, and mutation operators to design a layout topology optimizing source-terminal computer communication network reliability is presented. In this work, we apply crossover at the gene level in conjunction with the regular chromosome-level crossover operators that are usually applied on chromosomes or at boundaries of nodes. This approach provides us with a much better population mixture, and hence faster convergence and better reliability. Applying regular crossover and mutation operators on the population may generate infeasible chromosomes representing a network connection. This complicates fitness and cost calculations, since reliability and cost can only be calculated on links that actually exist. In this paper, a special crossover and mutation operator is applied in a way that will always ensure production of a feasible connected network topology. This results in a simplification of fitness calculations and produces a better population mixture that gives higher reliability rates at shorter convergence times. Copyright © 2008 John Wiley & Sons, Ltd. [source] Species-level selection reduces selfishness through competitive exclusionJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2007D. J. RANKIN Abstract Adaptation does not necessarily lead to traits which are optimal for the population. This is because selection is often the strongest at the individual or gene level. The evolution of selfishness can lead to a ,tragedy of the commons', where traits such as aggression or social cheating reduce population size and may lead to extinction. This suggests that species-level selection will result whenever species differ in the incentive to be selfish. We explore this idea in a simple model that combines individual-level selection with ecology in two interacting species. Our model is not influenced by kin or trait-group selection. We find that individual selection in combination with competitive exclusion greatly increases the likelihood that selfish species go extinct. A simple example of this would be a vertebrate species that invests heavily into squabbles over breeding sites, which is then excluded by a species that invests more into direct reproduction. A multispecies simulation shows that these extinctions result in communities containing species that are much less selfish. Our results suggest that species-level selection and community dynamics play an important role in regulating the intensity of conflicts in natural populations. [source] MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2003L. Bernatchez Abstract Elucidating how natural selection promotes local adaptation in interaction with migration, genetic drift and mutation is a central aim of evolutionary biology. While several conceptual and practical limitations are still restraining our ability to study these processes at the DNA level, genes of the major histocompatibility complex (MHC) offer several assets that make them unique candidates for this purpose. Yet, it is unclear what general conclusions can be drawn after 15 years of empirical research that documented MHC diversity in the wild. The general objective of this review is to complement earlier literature syntheses on this topic by focusing on MHC studies other than humans and mice. This review first revealed a strong taxonomic bias, whereby many more studies of MHC diversity in natural populations have dealt with mammals than all other vertebrate classes combined. Secondly, it confirmed that positive selection has a determinant role in shaping patterns of nucleotide diversity in MHC genes in all vertebrates studied. Yet, future tests of positive selection would greatly benefit from making better use of the increasing number of models potentially offering more statistical rigour and higher resolution in detecting the effect and form of selection. Thirdly, studies that compared patterns of MHC diversity within and among natural populations with neutral expectations have reported higher population differentiation at MHC than expected either under neutrality or simple models of balancing selection. Fourthly, several studies showed that MHC-dependent mate preference and kin recognition may provide selective factors maintaining polymorphism in wild outbred populations. However, they also showed that such reproductive mechanisms are complex and context-based. Fifthly, several studies provided evidence that MHC may significantly influence fitness, either by affecting reproductive success or progeny survival to pathogens infections. Overall, the evidence is compelling that the MHC currently represents the best system available in vertebrates to investigate how natural selection can promote local adaptation at the gene level despite the counteracting actions of migration and genetic drift. We conclude this review by proposing several directions where future research is needed. [source] Periodontitis-induced lipid peroxidation in rat descending aorta is involved in the initiation of atherosclerosisJOURNAL OF PERIODONTAL RESEARCH, Issue 4 2009D. Ekuni Background and Objective:, Periodontitis is a risk factor for the development of atherosclerosis. Recent studies indicate that oxidative mechanisms, including lipid peroxidation, are involved not only in periodontitis but also in atherosclerosis. Lipid peroxidation may play an important role in the pathogenesis of atherosclerosis, particularly during its earliest stages. The purpose of this study was to investigate the relationship between lipid peroxidation induced by periodontitis and the initiation of atherosclerosis. Material and Methods:, Sixteen rats were randomly divided into two groups of eight rats each. Periodontitis was ligature-induced for 4 wk in the experimental group, whereas the control group was left untreated. After the experimental period, the mandibular first molar regions were resected and then subjected to histological analysis and measurement of hexanoyl-lysine expression as an indicator of lipid peroxidation. Descending aorta was used for measuring the levels of hexanoyl-lysine, reactive oxygen species and lipid deposits, and for real-time polymerase chain reaction microarray analysis. The level of hexanoyl-lysine was also measured in serum. Results:, In the experimental group, the levels of hexanoyl-lysine in periodontal tissue and serum increased. Only aorta samples in the experimental group showed lipid accumulation, with increased expression of hexanoyl-lysine, reactive oxygen species and oxidative stress-related genes (including nitric oxide synthases 2 and 3), whereas the superoxide dismutase 1 gene level was down-regulated. Conclusion:, In a ligature-induced periodontitis rat model, increased lipid peroxidation was found in serum and aorta as well as in periodontal tissue. Atherosclerosis-related gene expression and histological changes were also stimulated. Periodontitis-induced lipid peroxidation in the aorta may be involved in the early stage of atherosclerosis. [source] Early Electrophysiological Changes In Transgenic Rat Model Of Charcot-Marie-ToothJOURNAL OF THE PERIPHERAL NERVOUS SYSTEM, Issue 1 2001M Grandis Recently, a reliable transgenic rat model of human Charcot-Marie-Tooth type 1 A has been developed. So far, neurophysiological studies have been performed only in advanced stages of rat disease. Moreover, axonal involvement, which is known to occur in human CMT1A, has never been observed in this rat model. Affected rats show overexpression of Peripheral Myelin Protein (PMP-22) and a peripheral hypomyelinating neuropathy. We perfomed an electrophysiological study in two heterozygous PMP-22 transgenic rats and in one normal control, matched for age (3 weeks) and weight (average: 60 g). Recordings were performed in vivo by stimulating the sciatic nerve at both sciatic notch and ankle sites and recording the Hoffman reflex and direct muscle responses (CMAP). The H-reflex related SNCV and MNCV were calculated by measuring the distance between the sciatic notch and the ankle sites and the respective latencies. The two transgenic rats showed different levels of PMP-22 overexpression, as judged by quantitative PCR. The rat with a lower PMP-22 gene level showed a 30% reduction of MNCV compared to the normal control, while SNCV was not reduced. The CMAP was sized approximately 45% of the normal rat while the ratio between H wave amplitude and CMAP was 30% of the normal, the H wave amplitude being more affected than the CMAP. The action potentials in the rat with a higher transgene level were not recordable. Our data demonstrate that slowing of MNCV is an early finding in the CMT1A rat model. The marked reduction of H wave amplitude in front of a normal SNCV suggests a possible early axonal damage of sensory fibers. The entity of electrophysiological compromission positively correlated with the number of copies for PMP-22 gene. All together these considerations prove the sensitivity of this method, however further studies are needed to confirm these results and to prove that this model may be suitable to investigate the effects of therapeutic approaches. [source] A proteomic approach to immune-mediated epithelial-mesenchymal transitionPROTEOMICS - CLINICAL APPLICATIONS, Issue 7-8 2008Ronan Feighery Dr. Abstract Increasing evidence suggests epithelial-mesenchymal transition (EMT) plays an important role in renal fibrosis. Initial renal injury enables the infiltration of mononuclear cells into the interstitium, and the resulting generation of inflammatory mediators that favour EMT may have a direct role in the development of renal fibrosis. The aim of this study was to investigate the proteome of renal tubular epithelial cells undergoing EMT in vitro. The human proximal tubular cell line (HK-2), exposed to conditioned medium from activated peripheral blood mononuclear cells (PBMC-CM), undergo phenotypic change, from an epithelial towards a fibroblastic phenotype, as evidenced by decreased E-cadherin and increased fibronectin protein expression. Further proteomic analysis, using 2-DE and Progenesis software, revealed the down-regulation of 4 proteins and up-regulation of 23 proteins. MS analysis allowed the positive identification of 15 differentially expressed proteins, including annexin A2, adipocyte plasma membrane-associated protein, T-complex protein 1, reticulocalbin-1 precursor and moesin among others. Western blotting and quantitative real-time PCR confirmed the increase in annexin A2 at the protein and gene level, respectively. Since annexin A2 and S100A6 exist as complexes in B-1 cells, we investigated the S100A6 gene expression further and show an increased expression in HK-2 cells following exposure to activated PBMC-CM. Therefore, we have identified several potential proteins that could play key roles in immune-mediated EMT. [source] N -acetylcysteine augments adenovirus-mediated gene expression in human endothelial cells by enhancing transgene transcription and virus entryTHE JOURNAL OF GENE MEDICINE, Issue 1 2002L. Jornot Abstract Background It has previously been shown that oxidants reduce the efficiency of adenoviral transduction in human umbilical vein endothelial cells (HUVECs). In this study, the effect of the antioxidant N -acetylcysteine (NAC) in adenovirus-mediated gene transfer has been investigated. Methods HUVECs were pretreated or not with NAC, and infected with E1E3-deleted adenovirus (Ad) containing the LacZ gene expressed from the RSV-LTR promoter/enhancer in the presence and absence of NAC. Transgene expression was assessed at the protein level (histochemical staining, measurement of ,-Gal activity, and western blot), mRNA level (real-time RT-PCR) and gene level (nuclear run on) 24,h and 48,h after infection. Adenoviral DNA was quantitated by real-time PCR, and cell surface expression of Coxsackie/adenovirus receptors (CAR) was determined by FACS analysis. Results Pretreatment of cells with NAC prior to Ad infection enhanced ,-Gal activity by two-fold due to an increase in viral DNA, which was related to increased CAR expression. When NAC was present only during the post-infection period, a five-fold increase in ,-Gal activity and LacZ gene transcriptional activity was observed. When NAC was present during both the pretreatment and the post-infection period, ,-Gal activity was further enhanced, by 15-fold. Augmentation of ,-Gal activity was paralleled by an increase in ,-Gal protein and mRNA levels. NAC did not affect the half-life of LacZ mRNA. Conclusion Pretreatment with NAC prior to Ad infection enhances virus entry, while treatment with NAC post-infection increases transgene transcription. This strategy permits the use of lower adenoviral loads and thus might be helpful for gene therapy of vascular diseases. Copyright © 2001 John Wiley & Sons, Ltd. [source] ORIGINAL RESEARCH: Phosphodiesterase Type 5 Regulation in the Penile Corpora CavernosaTHE JOURNAL OF SEXUAL MEDICINE, Issue S3 2009Ching-Shwun Lin PhD ABSTRACT Introduction., Penile detumescence depends on the hydrolysis of cyclic guanosine monophosphate (cGMP) by phosphodiesterase type 5 (PDE5). It is hoped that a review of publications relevant to the regulation of PDE5 in the penis will be helpful to both scientists and clinicians who are interested in the sciences of erectile function/dysfunction. Aims., The aim of this article is to comprehensively review the mechanisms by which PDE5 activity and expression in the penis are regulated. All published studies relevant to PDE5 regulation in the penis or penile cells will be reviewed. Methods., Entrez (PubMed) was used to search for publications relevant to the topics of this review. Keywords used in the searches included vascular, cavernous, penis, smooth muscle, signaling molecules, erection, priapism, and PDE5. Articles that are dedicated to the study of erectile function/dysfunction were prioritized for citation. Results., Regulation of PDE5 can occur at both protein and gene levels. At protein level, PDE5 is activated by phosphorylation and/or allosteric cGMP binding. Deactivation is carried out by protein phosphatase 1 and thus linked to the Rho-kinase signaling pathway. Cleavage of PDE5 into an inactive form has been shown as carried out by caspase-3. At the gene level, PDE5 expression is regulated at two alternative promoters, PDE5A and PDE5A2, both of which are positively regulated by cyclic adenosine monophosphate and cGMP. Downregulation of PDE5 has been observed in the penis of castrated animals; however, proof of androgen regulation of PDE5 gene requires examination of the smooth muscle content. Hyperoxia and hypoxia, respectively, regulate PDE5 expression positively and negatively. Hypoxic downregulation of PDE5 is a possible mechanism for the development of priapism. Conclusions., PDE5 can be regulated at protein and gene levels. In the penis, changes of PDE5 activity have been linked to its phosphorylation status, and downregulation of PDE5 expression has been associated with hypoxia. Lin CS. PDE5 regulation in the penile corpora nervosa. J Sex Med 2009;6(suppl 3):203,209. [source] Nutrition and immunity: an updateAQUACULTURE RESEARCH, Issue 3 2010Viviane Verlhac Trichet Abstract Immunity encompasses all mechanisms and responses used by the organism to defend itself against bacteria, viruses or parasites. Adequate supply and balance of nutrients are required for proper efficiency of the host defences. Research has identified dietary factors that affect human and animal immune responses like amino acids, fatty acids, minerals and vitamins. Some of these nutrients have been proven to have specific actions on immunity when provided at pharmacological doses. This paper will review these nutrients and their current use in aquaculture. The immune system is an efficient but complex system. Its complexity has made the assessment of the effects of diets difficult. Nevertheless, the standardization of methodology as well as the use of new techniques at the cell or the gene level should help to better understand the mechanisms of immune modulation. This paper will review the major functions of fish and shrimp immune system and the methodologies used. Cellular and humoral functions including cytokines will be discussed in relation to potential means to modulate them and the underlying mechanism. A better understanding of the mechanisms of modulation of the immune functions should help in the discovery of new dietary factors to improve the immune status of the animal, leading to better disease resistance. [source] Ginsenoside Rg1 protects dopaminergic neurons in a rat model of Parkinson's disease through the IGF-I receptor signalling pathwayBRITISH JOURNAL OF PHARMACOLOGY, Issue 3 2009Li Xu Background and purpose:, We have shown that ginsenoside Rg1 is a novel class of potent phytoestrogen and activates insulin-like growth factor-I receptor (IGF-IR) signalling pathway in human breast cancer MCF-7 cells. The present study tested the hypothesis that the neuroprotective actions of Rg1 involved activation of the IGF-IR signalling pathway in a rat model of Parkinson's disease, induced by 6-hydroxydopamine (6-OHDA). Experimental approach:, Ovariectomized rats were infused unilaterally with 6-OHDA into the medial forebrain bundle to lesion the nigrostriatal dopamine pathway and treated with Rg1 (1.5 h after 6-OHDA injections) in the absence or presence of the IGF-IR antagonist JB-1 (1 h before Rg1 injections). The rotational behaviour induced by apomorphine and the dopamine content in the striatum were studied. Protein and gene expression of tyrosine hydroxylase, dopamine transporter and Bcl-2 in the substantia nigra were also determined. Key results:, Rg1 treatment ameliorated the rotational behaviour induced by apomorphine in our model of nigrostriatal injury. This effect was partly blocked by JB-1. 6-OHDA significantly decreased the dopamine content of the striatum and treatment with Rg1 reversed this decrease. Treatment with Rg1 of 6-OHDA-lesioned rats reduced neurotoxicity, as measured by tyrosine hydroxylase, dopamine transporter and Bcl-2 protein and gene level in the substantia nigra. These effects were abolished by JB-1. Conclusions and implications:, These data provide the first evidence that Rg1 has neuroprotective effects on dopaminergic neurons in the 6-OHDA model of nigrostriatal injury and its actions might involve activation of the IGF-IR signalling pathway. [source] Association of glucocorticoid receptor polymorphisms with the susceptibility to major depressive disorder and treatment responses in Korean depressive patientsACTA NEUROPSYCHIATRICA, Issue 1 2009Hwa-Young Lee Objective:, Major depressive disorder (MDD) is closely related to stress reactions and serotonin probably underpins the pathophysiology of MDD. Alterations of the hypothalamic-pituitary-adrenal axis at the gene level have reciprocal consequences on serotonin neurotransmission. Glucocorticoid receptor (GR) polymorphisms affect glucocorticoid sensitivity, which is associated with cortisol feedback effects. Therefore, we hypothesised that GR polymorphisms are associated with the susceptibility to MDD and predict the treatment response. Method:, Ninety-six subjects with a minimum score of 17 on the 21-item Hamilton Depression Scale (HAMD) at baseline were enrolled into the present study. The genotypes of GR (N363S, ER22/23EK, Bcl1, and TthIII1 polymorphisms) were analysed. The HAMD score was again measured after 1, 2, 4 and 8 weeks of antidepressant treatment to detect whether the therapeutic effects differed with the GR genotype. Results:, Our subjects carried no N363S or ER22/23EK genetic polymorphisms and three types of Bcl1 and TthIII1 genetic polymorphisms. The C/C genotype and C allele at Bcl1 polymorphism were more frequent in MDD patients than in normal controls (p < 0.01 and p = 0.01, respectively). The genotype distributions did not differ significantly between responders and non-responders. Conclusion:, These results suggest that GR polymorphism cannot predict the therapeutic response after antidepressant administration. However, GR polymorphism (Bcl1) might play a role in the pathophysiology of MDD. Future studies should check this finding in larger populations with different characteristics. [source] Simulated microgravity activates MAPK pathways in fibroblasts cultured on microgrooved surface topographyCYTOSKELETON, Issue 2 2008W. A. Loesberg Abstract This study evaluated in vitro the differences in morphological behaviour between fibroblast cultured on smooth and microgrooved substrata (groove depth: 0.5 ,m, width: 1 ,m), which were subjected to simulated microgravity. The aim of the study was to clarify which of these parameters was more dominant to determine cell behaviour. Morphological characteristics were investigated using scanning electron microscopy and fluorescence microscopy in order to obtain qualitative information on cell alignment. Expression of collagen type I, and ,1-, ,1-, ,3-integrin were investigated by QPCR. Finally, immunoblotting was applied to visualise MAPK signalling pathways. Microscopy and image analysis showed that the fibroblasts aligned along the groove direction on all textured surfaces. On the smooth substrata, cells had spread out in a random fashion. The alignment of cells cultured on grooved surfaces under simulated microgravity, after 48 h of culturing appeared similar to those cultured at 1g, although cell shape was different. Analysis of variance proved that all main parameters: topography, gravity force, and time were significant. In addition, gene levels were reduced by simulated microgravity particularly those of ,3-integrin and collagen, however alpha-1 and beta-1 integrin levels were up-regulated. ERK1/2 was reduced in RPM, however, JNK/SAPK and p38 remained active. The members of the small GTPases family were stimulated under microgravity, particularly RhoA and Cdc42. The results are in agreement that application of microgravity to fibroblasts promotes a change in their morphological appearance and their expression of cell-substratum proteins through the MAPK intracellular signalling pathways. Cell Motil. Cytoskeleton 2007. © 2007 Wiley-Liss, Inc. [source] The effect of combined simulated microgravity and microgrooved surface topography on fibroblastsCYTOSKELETON, Issue 3 2007W. A. Loesberg Abstract This study evaluated in vitro the differences in morphological behaviour between fibroblast cultured on smooth and microgrooved substrata (groove depth: 0.5 ,m, width: 1, 2, 5, and 10 ,m), which were subjected to simulated microgravity. The aim of the study was to clarify which of these parameters was more dominant to determine cell behaviour. Morphological characteristics were investigated using scanning electron microscopy and fluorescence microscopy in order to obtain qualitative information on cell alignment and area. Confocal laser scanning microscopy visualised distribution of actin filaments and focal adhesion points. Finally, expression of collagen type I, fibronectin, and ,1- and ,1-integrin were investigated by PCR. Microscopy and image analysis showed that the fibroblasts aligned along the groove direction on all textured surfaces. On the smooth substrata, cells had spread out in a random fashion. The alignment of cells cultured on grooved surfaces decreased under simulated microgravity, especially after 24 h of culturing. Cell surface area on grooved substrata were significantly smaller than on smooth substrata, but simulated microgravity on the grooved groups resulted in an enlargement of cell area. ANOVA was performed on all main parameters: topography, gravity force, and time. In this analysis, all parameters proved significant. In addition, gene levels were reduced by microgravity particularly those of ,1-integrin and fibronectin. From our data it is concluded that the fibroblasts primarily adjust their shape according to morphological environmental cues like substratum surface whilst a secondary, but significant, role is played by microgravity conditions. Cell Motil. Cytoskeleton 2007. © 2007 Wiley-Liss, Inc. [source] The effect of combined hypergravity and microgrooved surface topography on the behaviour of fibroblastsCYTOSKELETON, Issue 7 2006W. A. Loesberg Abstract This study evaluated in vitro the differences in morphological behaviour between fibroblast cultured on smooth and microgrooved substrata (groove depth: 1 ,m, width: 1, 2, 5, 10 ,m), which undergo artificial hypergravity by centrifugation (10, 24 and 50 g; or 1 g control). The aim of the study was to clarify which of these parameters was more important to determine cell behaviour. Morphological characteristics were investigated using scanning electron microscopy and fluorescence microscopy in order to obtain qualitative information on cell spreading and alignment. Confocal laser scanning microscopy visualised distribution of actin filaments and vinculin anchoring points through immunostaining. Finally, expression of collagen type I, fibronectin, and ,1 - and ,1 -integrin were investigated by PCR. Microscopy and image analysis showed that the fibroblasts aligned along the groove direction on all textured surfaces. On the smooth substrata (control), cells spread out in a random fashion. The alignment of cells cultured on grooved surfaces increased with higher g-forces until a peak value at 25 g. An ANOVA was performed on the data, for all main parameters: topography, gravity force, and time. In this analysis, all parameters proved significant. In addition, most gene levels were reduced by hypergravity. Still, collagen type 1 and fibronectin are seemingly unaffected by time or force. From our data it is concluded that the fibroblasts primarily adjust their shape according to morphological environmental cues like substratum surface whilst a secondary, but significant, role is played by hypergravity forces. Cell Motil. Cytoskeleton 2006. © 2006 Wiley-Liss, Inc. [source] Abundance of six tetracycline resistance genes in wastewater lagoons at cattle feedlots with different antibiotic use strategiesENVIRONMENTAL MICROBIOLOGY, Issue 1 2007Nicholas Peak Summary The abundance of six tetracycline resistance genes tet(O), tet(Q), tet(W), tet(M), tet(B) and tet(L), were quantified over time in wastewater lagoons at concentrated animal feeding operations (CAFO) to assess how feedlot operation affects resistance genes in downstream surface waters. Eight lagoons at five cattle feedlots in the Midwestern United States were monitored for 6 months. Resistance and 16S-rRNA gene abundances were quantified using real-time PCR, and physicochemical lagoon conditions, tetracycline levels, and other factors (e.g. feedlot size and weather conditions) were monitored over time. Lagoons were sorted according to antibiotic use practice at each site, and designated as ,no-use', ,mixed-use' or ,high-use' for comparison. High-use lagoons had significantly higher detected resistance gene levels (tetR; 2.8 × 106 copies ml,1) relative to no-use lagoons (5.1 × 103 copies ml,1; P < 0.01) and mixed-use lagoons (7.3 × 105 copies ml,1; P = 0.076). Bivariate correlation analysis on pooled data (n = 54) confirmed that tetR level strongly correlated with feedlot area (r = 0.67, P < 0.01) and ,total' bacterial 16S-rRNA gene level in each lagoon (r = 0.51, P < 0.01), which are both characteristic of large CAFOs. tet(M) was the most commonly detected gene, both in absolute number and normalized to 16S-rRNA gene level, although tet(O), tet(Q) and tet(W) levels were also high in the mixed and high-use lagoons. Finally, resistance gene levels were highly seasonal with abundances being 10,100 times greater in the autumn versus the summer. Results show that antibiotic use strategy strongly affects both the abundance and seasonal distribution of resistance genes in associated lagoons, which has implications on water quality and feedlot management practices. [source] PKR, a cognitive decline biomarker, can regulate translation via two consecutive molecular targets p53 and Redd1 in lymphocytes of AD patientsJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 8b 2009Milena Damjanac Abstract In Alzheimer's disease (AD), the control of translation is dysregulated, precisely, two opposite pathways: double-stranded RNA-dependent protein kinase (PKR) is up-regulated and mammalian target of rapamycin (mTOR) is down-regulated. These biochemical alterations were found at the periphery in lymphocytes of AD patients and were significantly correlated with cognitive and memory test scores. However, the molecular crosslink between these two opposite signalling pathways remains unknown. The tumour suppressor p53 and Redd1 (regulated in development and DNA damage response) could be two downstream targets of active PKR to explain the breakdown of translation in AD patients. In this study, the protein and gene levels of p53 and Redd1 were assayed in lymphocytes of AD patients and in age-matched controls by Western blotting and RT-PCR. Furthermore, correlations were analysed with both the level of active PKR and the Mini Mental State Examination score (MMSE). The results show that the gene and protein levels of p53 and Redd1 were significantly increased about 1.5-fold for both gene and Redd1 protein and 2.3-fold for active p53 in AD lymphocytes compared to age-matched controls. Furthermore, statistical correlations between proteins and genes suggest that active PKR could phosphorylate p53 which could induce the transcription of Redd1 gene. No correlations were found between MMSE scores and levels of p53 or Redd1, contrary to active PKR levels. PKR represents a cognitive decline biomarker able to dysregulate translation via two consecutive targets p53 and Redd1 in AD lymphocytes. [source] ORIGINAL ARTICLE: The Role of IL-6, IL-10, TNF-, and its Receptors TNFR1 and TNFR2 in the Local Regulatory System of Normal and Impaired Human SpermatogenesisAMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 1 2009gorzata Bia Problem, To investigate the expression of genes coding for selected cytokines with antagonistic functions (IL-6, IL-10, TNF-,) as well as TNF-, receptors (TNFR1 and TNFR2) in correct spermatogenesis (normal proliferation), maturation arrest (proliferation inhibited) and testicular tumors (overgrowth). Method of study, Transcription levels of genes coding for IL-6, IL-10, TNF-,, TNFR1 and TNFR2 were quantitatively examined using a real-time RT-PCR. Results, Significantly higher amounts of IL-6 mRNA were observed in testicular tumor samples than in normal spermatogenesis or in some syndromes with maturation arrest (MA at spermatid level or SCOS), while IL-10 gene levels were fairly stable. In homogenates with maturation arrest, the expression of TNFR1 gene was markedly higher than in testicular tumors, while the opposite phenomenon was found in respect to TNFR2 gene. Conclusion, The results obtained indicate that changes in activities of intra-testicular cytokines may promote different distinct pathologies such as testicular cancer or infertility. [source] ORIGINAL RESEARCH: Phosphodiesterase Type 5 Regulation in the Penile Corpora CavernosaTHE JOURNAL OF SEXUAL MEDICINE, Issue S3 2009Ching-Shwun Lin PhD ABSTRACT Introduction., Penile detumescence depends on the hydrolysis of cyclic guanosine monophosphate (cGMP) by phosphodiesterase type 5 (PDE5). It is hoped that a review of publications relevant to the regulation of PDE5 in the penis will be helpful to both scientists and clinicians who are interested in the sciences of erectile function/dysfunction. Aims., The aim of this article is to comprehensively review the mechanisms by which PDE5 activity and expression in the penis are regulated. All published studies relevant to PDE5 regulation in the penis or penile cells will be reviewed. Methods., Entrez (PubMed) was used to search for publications relevant to the topics of this review. Keywords used in the searches included vascular, cavernous, penis, smooth muscle, signaling molecules, erection, priapism, and PDE5. Articles that are dedicated to the study of erectile function/dysfunction were prioritized for citation. Results., Regulation of PDE5 can occur at both protein and gene levels. At protein level, PDE5 is activated by phosphorylation and/or allosteric cGMP binding. Deactivation is carried out by protein phosphatase 1 and thus linked to the Rho-kinase signaling pathway. Cleavage of PDE5 into an inactive form has been shown as carried out by caspase-3. At the gene level, PDE5 expression is regulated at two alternative promoters, PDE5A and PDE5A2, both of which are positively regulated by cyclic adenosine monophosphate and cGMP. Downregulation of PDE5 has been observed in the penis of castrated animals; however, proof of androgen regulation of PDE5 gene requires examination of the smooth muscle content. Hyperoxia and hypoxia, respectively, regulate PDE5 expression positively and negatively. Hypoxic downregulation of PDE5 is a possible mechanism for the development of priapism. Conclusions., PDE5 can be regulated at protein and gene levels. In the penis, changes of PDE5 activity have been linked to its phosphorylation status, and downregulation of PDE5 expression has been associated with hypoxia. Lin CS. PDE5 regulation in the penile corpora nervosa. J Sex Med 2009;6(suppl 3):203,209. [source] Perspectives on cancer therapy-induced mucosal injuryCANCER, Issue S9 2004Pathogenesis, consequences for patients, epidemiology, measurement Abstract BACKGROUND A frequent complication of anticancer treatment, oral and gastrointestinal (GI) mucositis, threatens the effectiveness of therapy because it leads to dose reductions, increases healthcare costs, and impairs patients' quality of life. The Multinational Association of Supportive Care in Cancer and the International Society for Oral Oncology assembled an international multidisciplinary panel of experts to create clinical practice guidelines for the prevention, evaluation, and treatment of mucositis. METHODS The panelists examined medical literature published from January 1966 through May 2002, presented their findings at two separate conferences, and then created a writing committee that produced two articles: the current study and another that codifies the clinical implications of the panel's findings in practice guidelines. RESULTS New evidence supports the view that oral mucositis is a complex process involving all the tissues and cellular elements of the mucosa. Other findings suggest that some aspects of mucositis risk may be determined genetically. GI proapoptotic and antiapoptotic gene levels change along the GI tract, perhaps explaining differences in the frequency with which mucositis occurs at different sites. Studies of mucositis incidence in clinical trials by quality and using meta-analysis techniques produced estimates of incidence that are presented herein for what to our knowledge may be a broader range of cancers than ever presented before. CONCLUSIONS Understanding the pathobiology of mucositis, its incidence, and scoring are essential for progress in research and care directed at this common side-effect of anticancer therapies. Cancer 2004;100(9 Suppl):1995,2025. © 2004 American Cancer Society. [source] Conservation of the syntenies between porcine chromosome 7 and human chromosomes 6, 14 and 15 demonstrated by radiation hybrid mapping and linkage analysisANIMAL GENETICS, Issue 4 2003M. Tanaka Summary Comparative mapping studies facilitate the identification of genes located in quantitative trait locus (QTL) regions in domestic animals by utilizing information from the human genome. Radiation hybrid (RH) mapping is effective for this purpose because of its high resolution in ordered gene mapping on chromosomes. We constructed an RH map of pig chromosome 7, by adding 23 markers associated with genes. This RH map clearly demonstrated the mosaic of homology between pig chromosome 7 (SSC7) and human chromosomes 6, 14 and 15 at a ,gene' level, and was confirmed by linkage analysis. Clarification of the homology of SSC7 to human chromosomes will contribute to the elucidation of the gene(s) responsible for QTL detected on this chromosome. [source] | ||||||||||||||||