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Gene Analysis (gene + analysis)
Kinds of Gene Analysis Selected Abstracts2435: Control of the Meibomian gland in health and diseaseACTA OPHTHALMOLOGICA, Issue 2010DA SULLIVAN Purpose The meibomian gland is extremely important in maintaining the health and integrity of the ocular surface. This gland, through its lipid synthesis and secretion, promotes the stability and prevents the evaporation of the tear film. Conversely, meibomian gland dysfunction (MGD) leads to a decreased stability and increased evaporation of the tear film. Indeed, meibomian gland dysfunction is thought to be the major cause of dry eye syndromes throughout the world. Our goal is to advance understanding of the regulation of meibomian gland function and the mechanisms underlying MGD. Methods Procedures included the immortalization of human meibomian gland epithelial cells with human telomerase reverse transcriptase, the evaluation of cellular responsiveness, and the identification of glandular gene expression changes in MGD. Gene analyses were conducted with Illumina HumanHT-12 v3 Expression BeadChips and Geospiza bioinformatics software. Results To date we have [a] immortalized human meibomian gland epithelial cells that respond to secretagogue, growth factor, neurotransmitter and hormone exposure with alterations in proliferation, differentiation, signaling, gene expression and/or lipogenesis; [b] discovered human meibomian gland genes that may facilitate the development and/or progression of MGD. These genes encode proteins that promote keratinization and amplify inflammation. Conclusion Our findings advance our understanding of the control of the meibomian gland in both health and disease. [Acknowledgments: S.M. Richards, M. Hatton, A.M. Fay and K. Lo; Supported by grants from NIH (R01EY05612) and Alcon] Commercial interest [source] New mechanism of transforming growth factor-, signaling in hepatoma: Dramatic up-regulation of tumor initiating cells and epidermal growth factor receptor expressionHEPATOLOGY RESEARCH, Issue 5 2009Takeshi Nishimura Aim:, Transforming growth factor-, (TGF-,) has dual activity in tumor cells. We studied the effect of TGF-, on tumor-initiating cells (TICs), which are similar in self-renewal and differentiation features to normal adult stem cells. Methods:, We used side population (SP) cells that exclude DNA binding dye Hoechst 33342 to obtain TICs, studied the differences in the kinetics of the SP cell response to TGF-, treatment between hepatic tumor cell lines, and performed gene analysis. Results:, SP cells from all cell lines have higher proliferative ability compared to non-SP cells and they are drug resistant. TGF-, treatment increased the percentage of SP cells (%SP) and the survival rate; chemotherapeutic drug resistance developed only in K-251 SP cells. Gene analysis showed that TGF-, up-regulated epidermal growth factor receptor (EGFR) only in K-251 cells. There were no EGFR mutations in K-251, which had been reported in lung cancer. Knockdown of Smad4 using the small-interfering RNA technique in K-251 cells inhibited EGFR overexpression and significantly decreased the %SP. In contrast, the JNK inhibitor had little effect on EGFR expression or the %SP. Conclusion:, TGF-, treatment of K-251 cells causes tumor progression and the anti-cancer drug resistant phenotype by increasing SP. [source] Epidermolysis bullosa nevus arising in a patient with Dowling,Meara type epidermolysis bullosa simplex with a novel K5 mutationTHE JOURNAL OF DERMATOLOGY, Issue 8 2009Hiroko SUGIYAMA-FUKAMATSU Abstract We report herein a 4-year-old girl with Dowling,Meara type epidermolysis bullosa (EB) who presented with peculiar pigmented nevi. Blister formation had repeatedly occurred on the erythematous plaques in a circinate fashion since birth, and marked hyperkeratosis was observed on the palms and soles associated with nail deformity. Her mother and maternal grandmother also had similar symptoms. In addition to the blistering lesions, the patient had three large, asymmetrical, pigmented plaques with color variegation. Light and electron microscopic findings of the blistering lesions showed a subepidermal blister with intracytoplasmic granules in keratinocytes as well as degeneration of basal cells and aggregation of tonofilaments. The pigmented lesions revealed histopathological features of compound nevus without malignant changes. Gene analysis revealed an E478K (Glu to Lys) mutation in exon 5 of the keratin 5 (K5) gene. These findings, together with clinical features, were consistent with those of Dowling,Meara type EB associated with so-called EB nevus. [source] Nuclear receptor NR5A2 is required for proper primitive streak morphogenesisDEVELOPMENTAL DYNAMICS, Issue 12 2006Cassandre Labelle-Dumais Abstract NR5A2, also known as liver receptor homologue 1 (LRH-1) and fetoprotein transcription factor (FTF), is an orphan nuclear receptor involved in the regulation of cholesterol metabolism and steroidogenesis in the adult. NR5A2 was also shown to be expressed during early mouse embryogenesis. Consistent with its early expression pattern, a targeted disruption of this gene leads to embryonic lethality around the gastrulation period. To characterize the embryonic phenotype resulting from NR5A2 loss of function, we undertook morphological and marker gene analyses and showed that NR5A2,/, embryos display growth retardation, epiblast disorganization, a mild embryonic,extraembryonic constriction, as well as abnormal thickening of the proximo-posterior epiblast. We demonstrated that, although initial specification of the anterior,posterior axis occurred in the absence of NR5A2, primitive streak formation was impaired and neither embryonic nor extraembryonic mesoderm was generated. Moreover, although the visceral endoderm does not show major morphological abnormalities in NR5A2,/, embryos, a decrease in the expression level of HNF4 and GATA4 was observed. Aggregation experiments demonstrated that, in the presence of wild-type tetraploid cells, NR5A2 mutant cells in the epiblast are capable of undergoing normal gastrulation. Therefore, our results suggest a requirement for NR5A2 in extraembryonic tissues and identify a novel role of this gene in proper primitive streak morphogenesis. Developmental Dynamics 235:3359,3369, 2006. © 2006 Wiley-Liss, Inc. [source] Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease,HUMAN MUTATION, Issue 6 2008Veerle Bogaerts Abstract In one genetic study, the high temperature requirement A2 (HTRA2) mitochondrial protein has been associated with increased risk for sporadic Parkinson disease (PD). One missense mutation, p.Gly399Ser, in its C-terminal PDZ domain (from the initial letters of the postsynaptic density 95, PSD-95; discs large; and zonula occludens-1, ZO-1 proteins [Kennedy, 1995]) resulted in defective protease activation, and induced mitochondrial dysfunction when overexpressed in stably transfected cells. Here we examined the contribution of genetic variability in HTRA2 to PD risk in an extended series of 266 Belgian PD patients and 273 control individuals. Mutation analysis identified a novel p.Arg404Trp mutation within the PDZ domain predicted to freeze HTRA2 in an inactive form. Moreover, we identified six patient-specific variants in 5, and 3, regulatory regions that might affect HTRA2 expression as supported by data of luciferase reporter gene analyses. Our study confirms a role of the HTRA2 mitochondrial protein in PD susceptibility through mutations in its functional PDZ domain. In addition, it extends the HTRA2 mutation spectrum to functional variants possibly affecting transcriptional activity. The latter underpins a previously unrecognized role for altered HTRA2 expression as a risk factor relevant to parkinsonian neurodegeneration. Hum Mutat 29(6), 832,840, 2008. © 2008 Wiley-Liss, Inc. [source] Influence of cancer-related gene polymorphisms on clinicopathological features in colorectal cancerJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 6 2008Gen Yoshiya Abstract Background and Aim:, Single nucleotide polymorphisms (SNP) are shown to be related with cancer incidence. It has been reported that CCND1, p21cip1DCC, MTHFR, and EXO1 are related with the risk of malignant neoplasm, but few studies have mentioned the prognosis of the patients. We investigated the SNP of patients and related this to clinicopathological features, including survival rate. Method:, DNA from the tissues of primary colorectal cancer was obtained from surgical resections of 114 patients (68 males and 46 females, 29,83 years). The CCND1 polymorphism was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and those of other genes were investigated by the TaqMan method. The polymorphisms obtained were statistically analyzed for the relationship with clinicopathological features. Results:, The CG + GG allele was more invasive than the CC allele in histological tumor depth in the DCC codon 201 (P = 0.0086). The 677TT allele in MTHFR had a larger tumor size than the 677CC allele (P = 0.028). In EXO1 P757L polymorphism, patients with the TT allele had a statistically reduced survival rate compared with the other alleles. In CCND1 polymorphisms, we found no statistical significance in clinicopathological features. Conclusions:, From these preliminary data, these polymorphisms would be candidates predicting the clinicopathological features of colorectal cancer, but further more systematic gene analyses are warranted. [source] Inferring the evolutionary history of Drosophila americana and Drosophila novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analysesMOLECULAR ECOLOGY, Issue 12 2008RAMIRO MORALES-HOJAS Abstract The evolutionary history of closely related organisms can prove sometimes difficult to infer. Hybridization and incomplete lineage sorting are the main concerns; however, genome rearrangements can also influence the outcome of analyses based on nuclear sequences. In the present study, DNA sequences from 12 nuclear genes, for which the approximate chromosomal locations are known, have been used to estimate the evolutionary history of two forms of Drosophila americana (Drosophila americana americana and Drosophila americana texana) and Drosophila novamexicana (virilis group of species). The phylogenetic analysis of the combined data set resulted in a phylogeny showing reciprocal monophyly for D. novamexicana and D. americana. Single gene analyses, however, resulted in incongruent phylogenies influenced by chromosomal rearrangements. Genetic differentiation estimates indicated a significant differentiation between the two species for all genes. Within D. americana, however, there is no evidence for differentiation between the chromosomal forms except at genes located near the X/4 fusion and Xc inversion breakpoint. Thus, the specific status of D. americana and D. novamexicana is confirmed, but there is no overall evidence for genetic differentiation between D. a. americana and D. a. texana, not supporting a subspecific status. Based on levels of allele and nucleotide diversity found in the strains used, it is proposed that D. americana has had a stable, large population during the recent past while D. novamexicana has speciated from a peripheral southwestern population having had an ancestral small effective population size. The influence of chromosomal rearrangements in single gene analyses is also examined. [source] Genetics and Asthma Disease Susceptibility in the US Latino PopulationMOUNT SINAI JOURNAL OF MEDICINE: A JOURNAL OF PERSONALIZED AND TRANSLATIONAL MEDICINE, Issue 2 2010Joan Reibman MD Abstract The US Latino population is heterogeneous with diversity in environmental exposures and socioeconomic status. Moreover, the US Hispanic population derives from numerous countries previously under Spanish rule, and many Hispanics have complex proportions of European, Native American, and African ancestry. Disparities in asthma severity and control are due to complex interactions between environmental exposures, socioeconomic factors, and genetic variations. In addition, diseases within the Latino community may also differ by country of origin. Although US Census data show low asthma rates in the Hispanic population as a whole, there is a lot of variability in the prevalence and morbidity of asthma, with a prevalence of 5.0% in Mexican Americans versus 17.0% in Puerto Ricans. The diversity and population admixture make the study of the genetics of asthma complex in Latino populations. However, an understanding of the genetics of asthma in all populations, including the Latino population, can enhance risk identification, help us to target pharmacological therapy, and guide environmental regulations, all of which can promote a reduction in health disparities. The inclusion of markers of ancestral diversity and the incorporation of techniques to adjust for stratification now make these studies feasible in complex populations, including the Latino population. To date, studies using linkage analyses, genome-wide associations, or candidate gene analyses have identified an association of asthma or asthma-related phenotypes with candidate genes, including interleukin 13, ,-2 adrenergic receptor, a disintegrin and metalloproteinase 33, orosomucoid 1-like 3, and thymic stromal lymphopoietin. As reviewed here, although these genes have been identified in diverse populations, limited studies have been performed in Latino populations, and they have had variable replication. There is a need for the development of registries with well-phenotyped pediatric and adult Latino populations and subgroups for inclusion in the rapidly expanding field of genetic studies, and these studies need to be used to reduce health disparities. Mt Sinai J Med 77:140,148, 2010. © 2010 Mount Sinai School of Medicine [source] Acute lymphoblastic leukemia with the phenotype of a putative B-cell/T-cell bipotential precursorAMERICAN JOURNAL OF HEMATOLOGY, Issue 2 2004Lee Gong Lau Abstract Biphenotypic acute leukemias (BALs) are uncommon. Most are of myeloid-B-cell or myeloid-T-cell lineage. We report herein a 70-year-old man with an unusual acute leukemia where the blasts expressed both B- and T-lymphoid markers. He presented to us with an enlarging cutaneous tumor. The presenting peripheral blood and bone marrow aspirate showed 40% and 90% blasts, respectively, which were negative for the usual cytochemical stains. The flow cytometric analysis revealed that the blasts were positive for CD19, CD20, CD22, cytoplasmic (Cyt) CD79a, CD10, Cyt CD3, CD5, CD7, CD4, HLA-DR, TdT, and were negative for myeloid markers. According to the scoring system from the European Group for the Immunological Characterization of Acute Leukaemias (EGIL), this case was an unequivocal B-cell/T-cell BAL. Conventional cytogenetic analysis revealed 46XY [t(4;11)(q31;q13), add(8)(q24), der(9)del(9)(p21)del(9)(q32q34), ,13, +mar] in all 25 metaphases analyzed. Fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) for 11q23 rearrangements as well as t(9;22) were negative. PCR for both TCR- , and IgH gene analyses revealed polyclonal rearrangements. We postulate that this case of BAL might have arisen from the putative common lymphoid progenitor cell. Am. J. Hematol. 77:156,160, 2004. © 2004 Wiley-Liss, Inc. [source] Expression of the AtSUC1 gene in the female gametophyte, and ecotype-specific expression differences in male reproductive organsPLANT BIOLOGY, Issue 2010A. Feuerstein Abstract Based on analyses in Arabidopsis thaliana ecotype C24, the AtSUC1 protein was previously characterised as a male gametophyte-specific H+/sucrose symporter. Later, expression analyses in ecotype Columbia-0 (Col-0) identified AtSUC1 expression also in trichomes (not detected in trichome-less C24 plants) and roots, suggesting ecotype-specific differences in AtSUC1 expression. Here, we present data on additional ecotype-specific differences in AtSUC1 expression in other tissues. Using different AtSUC1 promoter,reporter gene lines, we performed comparative analyses of AtSUC1 expression in floral tissues of C24 and Col-0 plants, and using an AtSUC1 -specific antiserum, we performed immunohistochemical analyses on tissue sections from C24, Col-0, Landsberg erecta (Ler) and Wassilewskaija (Ws) ecotypes. We show that AtSUC1 expression occurs in the funicular epidermis of C24, Ler and Ws, but not in Col-0. In contrast, we observed high levels of AtSUC1 protein in pollen grains of Col-0, lower levels in pollen of C24 and Ler, and no AtSUC1 protein in Ws pollen. Moreover, our reporter gene analyses identified a previously undetected expression of AtSUC1 in the female gametophyte, and revealed that AtSUC1 expression in the funicular epidermis is absent from unpollinated siliques and is induced upon successful pollination. The impact of these findings on the potential physiological role of AtSUC1 is discussed. [source] Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence DataPLANT BIOLOGY, Issue 5 2000H. T. Lumbsch Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets. [source] Genetic variation of the human glycine receptor subunit genes GLRA3 and GLRB and susceptibility to idiopathic generalized epilepsiesAMERICAN JOURNAL OF MEDICAL GENETICS, Issue 6 2001Diana Sobetzko Abstract Alterations of glycine receptor ,1 and , subunit genes have been associated with hypertonic motor disorders in both mice and humans. Mutations in genes encoding other ligand- and voltage-gated ion channels have been identified in rare monogenic forms of idiopathic generalized epilepsies (IGE). We tested the hypothesis that allelic variants of the glycine receptor subunit genes, GLRA3 and GLRB, both localized on chromosome 4q, confer susceptibility to common subtypes of IGE. Mutation screening was carried out in index patients of 14 IGE families. No pathogenic mutation was found, but two intronic polymorphisms were detected in the GLRB gene, and four intronic, three exonic, and one 3,-UTR polymorphisms were identified for the GLRA3 gene. Subsequent screening for exonic and 3,-UTR polymorphisms in GLRA3 showed no statistical difference between a group of sporadic IGE patients (n,=,104) and a control group (n,=,141). The genotype frequencies for exonic and 3,-UTR polymorphisms in GLRA3 showed no statistically significant difference between IGE patients (n,=,104) and an ethnically matched control group (n,=,141). Thus, no association between IGE and alterations in GLRA3 or GLRB genes could be detected, indicating that both genes do not play a major causative role in the epileptogenesis of common IGE subtypes. Still, these novel single nucleotide polymorphisms may be useful markers for candidate gene analyses of other disorders. © 2001 Wiley-Liss, Inc. [source] Survival After Lung Transplantation of Cystic Fibrosis Patients Infected with Burkholderia cepacia ComplexAMERICAN JOURNAL OF TRANSPLANTATION, Issue 5 2008B. D. Alexander Within the Burkholderia cepacia complex (Bcc), B. cenocepacia portends increased mortality compared with other species. We investigated the impact of Bcc infection on mortality and re-infection following lung transplant (LT). Species designation for isolates from Bcc-infected patients was determined using 16S rDNA and recA gene analyses. Of 75 cystic fibrosis patients undergoing LT from September 1992 to August 2002, 59 had no Bcc and 16 had Bcc (including 7 B. cenocepacia) isolated in the year before LT. Of the latter, 87.5% had Bcc recovered after transplantation, and all retained their pretransplant strains. Survival was 97%, 92%, 76% and 63% for noninfected patients; 89%, 89%, 67% and 56% for patients infected with Bcc species other than B. cenocepacia; and 71%, 29%, 29% and 29% for patients with B. cenocepacia (p = 0.014) at 1 month, 1 year, 3 years and 5 years, respectively. Patients infected with B. cenocepacia before transplant were six times more likely to die within 1 year of transplant than those infected with other Bcc species (p = 0.04) and eight times than noninfected patients (p < 0.00005). Following LT, infection with Bcc species other than B. cenocepacia does not significantly impact 5-year survival whereas infection with B. cenocepacia pretransplant is associated with decreased survival. [source] Abundance of sulphur-oxidizing bacteria in coastal aquaculture using soxB gene analysesAQUACULTURE RESEARCH, Issue 9 2010Kishore K Krishnani Abstract Molecular techniques based on sequencing of metagenomic clone libraries provide an insight into the diversity of microbial populations. Using nucleic acid-based methods, the diversity of soxB genes was examined to detect and characterize sulphur-oxidizing bacteria in Indian coastal aquaculture environments. Gene-specific degenerate primers were used to amplify various fragments (710, 753, 483,503, 280 and 239 bp) of soxB genes. Metagenomic clone libraries were constructed for 753, 483,503 and 239 bp fragments of soxB genes. The abundance of soxB revealed the presence of sulphur-oxidizing organisms. Amino acids in parts of the soxB -encoded proteins were aligned to known conserved amino acid residues. The level of conservation ranged from 23% to 30%. A phylogenetic tree constructed from aligned amino acid sequences of SoxB revealed different clusters associated with the branches of phototrophic ,- and ,-proteobacteria. In general, soxB is widespread among the various phylogenetic groups, although this does not necessarily mean that the organism can use sulphur compounds. Our results suggest that the chemolithoautotrophy based on sulphur oxidation in coastal aquaculture is primarily sustained by the presence of sulphur oxidizers, which involve the soxB gene. This study aids identification of the phylogenetic characteristics related to sulphur bioremediation in poorly characterized coastal aquaculture environments. [source] Prolonged expression of CD154 on CD4 T cells from pediatric lupus patients correlates with increased CD154 transcription, increased nuclear factor of activated T cell activity, and glomerulonephritisARTHRITIS & RHEUMATISM, Issue 8 2010Jay Mehta Objective To assess CD154 expression in patients with pediatric systemic lupus erythematosus (SLE) and to explore a transcriptional mechanism that may explain dysregulated expression of CD154. Methods Cell surface CD154 expression (pre- and postactivation) in peripheral blood CD4 T cells from 29 children with lupus and 29 controls matched for age, sex, and ethnicity was examined by flow cytometry. CD154 expression was correlated with clinical features, laboratory parameters, and treatments received. Increased CD154 expression on CD4 T cells from the SLE patients was correlated with CD154 message and transcription rates by real-time reverse transcription,polymerase chain reaction (RT-PCR) and nuclear run-on assays, respectively. Nuclear factor of activated T cell (NF-AT) transcription activity and mRNA levels in CD4 T cells from SLE patients were explored by reporter gene analysis and real-time RT-PCR, respectively. Results CD154 surface protein levels were increased 1.44-fold in CD4 T cells from SLE patients as compared with controls in cells evaluated 1 day postactivation ex vivo. This increase correlated clinically with the presence of nephritis and an elevated erythrocyte sedimentation rate. Increased CD154 protein levels also correlated with increased CD154 mRNA levels and with CD154 transcription rates, particularly at later time points following T cell activation. Reporter gene analyses revealed a trend for increased NF-AT, but decreased activator protein 1 and similar NF-,B, activity in CD4 T cells from SLE patients as compared with controls. Moreover, NF-AT1 and, in particular, NF-AT2 mRNA levels were notably increased in CD4 T cells from SLE patients as compared with controls. Conclusion Following activation, cell surface CD154 is increased on CD4 T cells from pediatric lupus patients as compared with controls, and this increase correlates with the presence of nephritis, increased CD154 transcription rates, and increased NF-AT activity. These results suggest that NF-AT/calcineurin inhibitors, such as tacrolimus and cyclosporine, may be beneficial in the treatment of lupus nephritis. [source] Embryonic holoprosencephaly: pathology and phenotypic variabilityCONGENITAL ANOMALIES, Issue 4 2006Shigehito Yamada ABSTRACT Holoprosencephaly (HPE) is one of the major brain anomalies caused by the failure of cleavage of the prosencephalon during the early stage of development. Over 200 cases of HPE in the Kyoto Collection of Human Embryos were observed grossly and histologically, with special emphasis on the anomalies of the brain, face and eye. The facial anomalies of HPE human embryos after Carnegie stage (CS) 18 could be classified into cyclopia, synophthalmia, ethmocephaly, cebocephaly, and premaxillary agenesis, similarly as the classical classification for postnatal cases. On the other hand, HPE embryos at CS 13,17 showed some characteristic facies which are different from those in older embryos. In the present paper, pathology and phenotypic variability in HPE embryos were discussed from the embryopathological point of view. Recently, the molecular mechanism of HPE has been clarified by the techniques of gene manipulation, and various HPE genes have been identified by gene analysis of familial HPE cases. HPE is one of the major CNS anomalies which have been extensively studied and provides a clue to the mechanisms of normal and abnormal development of craniofacial structures. [source] Guest Lecture 9.00,9.45 Wednesday 17 September 2003CYTOPATHOLOGY, Issue 2003Peter A. Hall MD PhD FRCPath The past decades have seen an explosion in our knowledge of the molecular events underpinning the pathogenesis of many disease processes. Furthermore, there have been enormous technical advances with the ability to identify, clone and sequence genes and to characterize their protein products now being common place in research settings. However, despite many claims as to the utility of molecular and biochemical methods in pathology only very few laboratories employ such methods in a clinical setting. Indeed the impact of molecular medicine has been more talked about than real. Why is this? The goal of this presentation is to address this question and present some perspectives on the future of Molecular Pathology. I shall overview, for the BSCC, the current state of the technology available for gene analysis and to explore the developments needed before the mirage of molecular pathology becomes a clinical reality. [source] Renal vascular disease in neurofibromatosis type 2: association or coincidence?DEVELOPMENTAL MEDICINE & CHILD NEUROLOGY, Issue 1 2006Nuno JV Cordeiro MBChB MRCPCH Neurofibromatosis type 2 (NF2) remains a challenging diagnosis in childhood where there may be no neurological involvement. A 12-month-old male in whom NF2 was suspected because of characteristic ophthalmological and cutaneous lesions is reported. Cranial MRI showed no tumours. A pathogenic mutation was identified on NF2 gene analysis. The child developed hypertension due to renal vascular disease. Although renal vascular disease is a recognized complication of neurofibromatosis type 1 (NF1), it has not been reported in NF2. [source] Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environmentsENVIRONMENTAL MICROBIOLOGY, Issue 2 2009N. Hamamura Summary The identification and characterization of genes involved in the microbial oxidation of arsenite will contribute to our understanding of factors controlling As cycling in natural systems. Towards this goal, we recently characterized the widespread occurrence of aerobic arsenite oxidase genes (aroA -like) from pure-culture bacterial isolates, soils, sediments and geothermal mats, but were unable to detect these genes in all geothermal systems where we have observed microbial arsenite oxidation. Consequently, the objectives of the current study were to measure arsenite-oxidation rates in geochemically diverse thermal habitats in Yellowstone National Park (YNP) ranging in pH from 2.6 to 8, and to identify corresponding 16S rRNA and aroA genotypes associated with these arsenite-oxidizing environments. Geochemical analyses, including measurement of arsenite-oxidation rates within geothermal outflow channels, were combined with 16S rRNA gene and aroA functional gene analysis using newly designed primers to capture previously undescribed aroA -like arsenite oxidase gene diversity. The majority of bacterial 16S rRNA gene sequences found in acidic (pH 2.6,3.6) Fe-oxyhydroxide microbial mats were closely related to Hydrogenobaculum spp. (members of the bacterial order Aquificales), while the predominant sequences from near-neutral (pH 6.2,8) springs were affiliated with other Aquificales including Sulfurihydrogenibium spp., Thermocrinis spp. and Hydrogenobacter spp., as well as members of the Deinococci, Thermodesulfobacteria and ,- Proteobacteria. Modified primers designed around previously characterized and newly identified aroA -like genes successfully amplified new lineages of aroA- like genes associated with members of the Aquificales across all geothermal systems examined. The expression of Aquificales aroA- like genes was also confirmed in situ, and the resultant cDNA sequences were consistent with aroA genotypes identified in the same environments. The aroA sequences identified in the current study expand the phylogenetic distribution of known Mo-pterin arsenite oxidase genes, and suggest the importance of three prominent genera of the order Aquificales in arsenite oxidation across geochemically distinct geothermal habitats ranging in pH from 2.6 to 8. [source] Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateauENVIRONMENTAL MICROBIOLOGY, Issue 10 2007Hongchen Jiang Summary Previous investigations of the salinity effects on the microbial community composition have largely been limited to dynamic estuaries and coastal solar salterns. In this study, the effects of salinity and mineralogy on microbial community composition was studied by using a 900-cm sediment core collected from a stable, inland hypersaline lake, Lake Chaka, on the Tibetan Plateau, north-western China. This core, spanning a time of 17 000 years, was unique in that it possessed an entire range of salinity from freshwater clays and silty sands at the bottom to gypsum and glauberite in the middle, to halite at the top. Bacterial and archaeal communities were studied along the length of this core using an integrated approach combining mineralogy and geochemistry, molecular microbiology (16S rRNA gene analysis and quantitative polymerase chain reaction), cultivation and lipid biomarker analyses. Systematic changes in microbial community composition were correlated with the salinity gradient, but not with mineralogy. Bacterial community was dominated by the Firmicutes -related environmental sequences and known species (including sulfate-reducing bacteria) in the freshwater sediments at the bottom, but by halophilic and halotolerant Betaproteobacteria and Bacteroidetes in the hypersaline sediments at the top. Succession of proteobacterial groups along the salinity gradient, typically observed in free-living bacterial communities, was not observed in the sediment-associated community. Among Archaea, the Crenarchaeota were predominant in the bottom freshwater sediments, but the halophilic Halobacteriales of the Euryarchaeota was the most important group in the hypersaline sediments. Multiple isolates were obtained along the whole length of the core, and their salinity tolerance was consistent with the geochemical conditions. Iron-reducing bacteria were isolated in the freshwater sediments, which were capable of reducing structural Fe(III) in the Fe(III)-rich clay minerals predominant in the source sediment. These data have important implications for understanding how microorganisms respond to increased salinity in stable, inland water bodies. [source] Phylogenetic diversity of non-nodulating Rhizobium associated with pine ectomycorrhizaeFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Megumi Tanaka Abstract Most Rhizobium species described are symbionts that form nodules on legume roots; however, non-nodulating strains of Rhizobium are also widespread in nature. Unfortunately, knowledge of non-nodulating Rhizobium is quite limited compared with nodulating Rhizobium. Here, we studied the phylogenetic diversity of Rhizobium species that inhabit Japanese red pine roots (Pinus densiflora). Because fine roots of pine trees are usually colonized by ectomycorrhizal fungi in nature, we mainly used ectomycorrhizal root tips for bacterial isolation. Out of 1195 bacteria isolated from 75 independent root samples from the field and greenhouse experiments, 102 isolates were confirmed to be Rhizobium following partial 16S rRNA gene analysis. Rhizobium species were occasionally dominant in culturable bacterial communities, whereas no Rhizobium species were isolated from the soil itself. Molecular phylogenetic analyses using 16S rRNA, atpD, and recA gene sequences revealed that isolated Rhizobium strains were phylogenetically diverse and that several were distantly related to known Rhizobium species. Considering that a single species of pine is associated with unique and phylogenetically diverse Rhizobium populations, we should pay more attention to non-nodulating strains to better understand the diversity, ecology, and evolution of the genus Rhizobium and plant,Rhizobium associations. [source] Changes in microbial diversity in industrial wastewater evaporation ponds following artificial salinationFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Eitan Ben-Dov Abstract The salinity of industrial wastewater evaporation ponds was artificially increased from 3,7% to 12,16% (w/v), in an attempt to reduce the activity of sulfate-reducing bacteria (SRB) and subsequent emission of H2S. To investigate the changes in bacterial diversity in general, and SRB in particular, following this salination, two sets of universal primers targeting the 16S rRNA gene and the functional apsA [adenosine-5,-phosphosulfate (APS) reductase ,-subunit] gene of SRB were used. Phylogenetic analysis indicated that Proteobacteria was the most dominant phylum both before and after salination (with 52% and 68%, respectively), whereas Firmicutes was the second most dominant phylum before (39%) and after (19%) salination. Sequences belonging to Bacteroidetes, Spirochaetes and Actinobacteria were also found. Several groups of SRB from Proteobacteria and Firmicutes were also found to inhabit this saline environment. Comparison of bacterial diversity before and after salination of the ponds revealed both a shift in community composition and an increase in microbial diversity following salination. The share of SRB in the 16S rRNA gene was reduced following salination, consistent with the reduction of H2S emissions. However, the community composition, as shown by apsA gene analysis, was not markedly affected. [source] Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probingFEMS MICROBIOLOGY ECOLOGY, Issue 1 2007Aurélie Cébron Abstract A considerable amount of methane produced during decomposition of landfill waste can be oxidized in landfill cover soil by methane-oxidizing bacteria (methanotrophs) thus reducing greenhouse gas emissions to the atmosphere. The identity of active methanotrophs in Roscommon landfill cover soil, a slightly acidic peat soil, was assessed by DNA-stable isotope probing (SIP). Landfill cover soil slurries were incubated with 13C-labelled methane and under either nutrient-rich nitrate mineral salt medium or water. The identity of active methanotrophs was revealed by analysis of 13C-labelled DNA fractions. The diversity of functional genes (pmoA and mmoX) and 16S rRNA genes was analyzed using clone libraries, microarrays and denaturing gradient gel electrophoresis. 16S rRNA gene analysis revealed that the cover soil was mainly dominated by Type II methanotrophs closely related to the genera Methylocella and Methylocapsa and to Methylocystis species. These results were supported by analysis of mmoX genes in 13C-DNA. Analysis of pmoA gene diversity indicated that a significant proportion of active bacteria were also closely related to the Type I methanotrophs, Methylobacter and Methylomonas species. Environmental conditions in the slightly acidic peat soil from Roscommon landfill cover allow establishment of both Type I and Type II methanotrophs. [source] Targeted gene analysis in Ulmus americana and U. pumila tissuesFOREST PATHOLOGY, Issue 2 2008C. Nasmith Summary Steady-state gene expression was compared between Dutch elm disease (DED)-susceptible Ulmus americana and DED-resistant U. pumila callus, leaf midrib, root and inner bark tissues. Stress-related cDNAs including phenylalanine ammonia-lyase (PAL), chitinase (CHT) and polygalacturonase-inhibiting protein (PGIP) were isolated and compared following RT-PCR of elm tissues. Complete CHT and partial PAL and PGIP cDNA transcripts were identified, each displaying sequence variation between elm species. These transcripts were Dig-labelled and subsequently used for northern analyses of the elm tissues. Midrib and root tissue displayed highest steady-state gene expression compared with inner bark and callus tissues. A modified nucleic acid isolation technique was necessary for downstream RNA analyses. Lithium chloride and polyvinylpyrrolidone were critical for efficient removal of polysaccharides and phenolics associated with some of the elm tissues. Steady-state gene expression is discussed in relation to the tissues investigated. The use of tissues other than in vitro callus culture more closely represents the tissues associated with the elm's vascular response to DED. [source] Identification and characterization of a novel progesterone receptor-binding element in the mouse prostaglandin E receptor subtype EP2 geneGENES TO CELLS, Issue 9 2003Sohken Tsuchiya Background:, Gene expression of prostaglandin E receptor EP2 is induced in the luminal epithelium of the mouse uterus during peri-implantation period (day-5 of pseudopregnancy), suggesting the involvement of progesterone and its receptor (PR) in this expression. However it remains unclear whether PR affects EP2 gene expression through its binding. Results:, We investigated transcriptional regulation of EP2 gene expression with reporter gene analysis using HeLa cells with or without expression of the PR. The 5,-flanking region (,3260 to ,27, upstream of the translation initiation site) exhibited progesterone-induced promoter activation and basal promoter activity in the presence of PR. Using successive deletion analysis, we determined the six regulatory regions in the EP2 gene. Three regions were found to be involved in progesterone-induced promoter activation, whereas the other three regions were involved in basal promoter activity in the presence of PR. We identified a novel PR-binding sequence, 5,-G(G/A)CCGGA-3,, in the two basal promoter regions and Sp1- and Sp3-binding in the other basal promoter region. Conclusions:, We identified a novel PR-binding sequence, which may be involved in the regulation of basal promoter activity in the EP2 gene. [source] Power calculations for likelihood ratio tests for offspring genotype risks, maternal effects, and parent-of-origin (POO) effects in the presence of missing parental genotypes when unaffected siblings are availableGENETIC EPIDEMIOLOGY, Issue 1 2007E. Rampersaud Abstract Genotype-based likelihood-ratio tests (LRT) of association that examine maternal and parent-of-origin effects have been previously developed in the framework of log-linear and conditional logistic regression models. In the situation where parental genotypes are missing, the expectation-maximization (EM) algorithm has been incorporated in the log-linear approach to allow incomplete triads to contribute to the LRT. We present an extension to this model which we call the Combined_LRT that incorporates additional information from the genotypes of unaffected siblings to improve assignment of incompletely typed families to mating type categories, thereby improving inference of missing parental data. Using simulations involving a realistic array of family structures, we demonstrate the validity of the Combined_LRT under the null hypothesis of no association and provide power comparisons under varying levels of missing data and using sibling genotype data. We demonstrate the improved power of the Combined_LRT compared with the family-based association test (FBAT), another widely used association test. Lastly, we apply the Combined_LRT to a candidate gene analysis in Autism families, some of which have missing parental genotypes. We conclude that the proposed log-linear model will be an important tool for future candidate gene studies, for many complex diseases where unaffected siblings can often be ascertained and where epigenetic factors such as imprinting may play a role in disease etiology. Genet. Epidemiol. © 2006 Wiley-Liss, Inc. [source] New mechanism of transforming growth factor-, signaling in hepatoma: Dramatic up-regulation of tumor initiating cells and epidermal growth factor receptor expressionHEPATOLOGY RESEARCH, Issue 5 2009Takeshi Nishimura Aim:, Transforming growth factor-, (TGF-,) has dual activity in tumor cells. We studied the effect of TGF-, on tumor-initiating cells (TICs), which are similar in self-renewal and differentiation features to normal adult stem cells. Methods:, We used side population (SP) cells that exclude DNA binding dye Hoechst 33342 to obtain TICs, studied the differences in the kinetics of the SP cell response to TGF-, treatment between hepatic tumor cell lines, and performed gene analysis. Results:, SP cells from all cell lines have higher proliferative ability compared to non-SP cells and they are drug resistant. TGF-, treatment increased the percentage of SP cells (%SP) and the survival rate; chemotherapeutic drug resistance developed only in K-251 SP cells. Gene analysis showed that TGF-, up-regulated epidermal growth factor receptor (EGFR) only in K-251 cells. There were no EGFR mutations in K-251, which had been reported in lung cancer. Knockdown of Smad4 using the small-interfering RNA technique in K-251 cells inhibited EGFR overexpression and significantly decreased the %SP. In contrast, the JNK inhibitor had little effect on EGFR expression or the %SP. Conclusion:, TGF-, treatment of K-251 cells causes tumor progression and the anti-cancer drug resistant phenotype by increasing SP. [source] Third international meeting on the genetic epidemiology of complex traits, April 4,6, 2002, Cambridge, UKHUMAN MUTATION, Issue 3 2002Sally John Abstract The Third International Meeting on the Genetic Epidemiology of Complex Traits was held at Churchill College, Cambridge, UK on April 4,6, 2002. The event was organized by the Twin Research and Genetic Epidemiology Unit, St Thomas' Hospital, London and sponsored by Roche Genetics and Insightful. It provided an interactive forum for discussion of topical issues relating to the genetic analysis of complex diseases and traits. Topics discussed included linkage disequilibrium mapping and candidate gene analysis, as well as cutting edge advances in both technologies and statistical analysis methods. Details of the meeting can be found at http://www.twin-research.ac.uk/. Hum Mutat20:227,229, 2002. © 2002 Wiley-Liss, Inc. [source] Analysis of a non-functional HNF-1, (TCF1) mutation in Japanese subjects with familial type 1 diabetesHUMAN MUTATION, Issue 4 2001Issei Yoshiuchi Abstract Mutations in the transcription factor hepatocyte nuclear factor-1, (HNF-1,; gene symbol TCF1) cause maturity-onset diabetes of the young type 3 (MODY3), a form of diabetes mellitus characterized by autosomal dominant inheritance, early onset, and pancreatic ,-cell dysfunction. Recent genetic studies, however, also found mutations in patients diagnosed with idiopathic (non-autoimmune based) type 1 diabetes. We identified a novel frameshift mutation (142delG) in the TCF1 gene in a family with a strong family history of type 1 diabetes and examined the functional properties of the mutant HNF 1,. The expression of the mutant protein was not detected in COS-7 cells by Western blot analysis after transfection of the mutant cDNA. This is the first case of an unstable mutant HNF-1, protein. Reporter gene analysis indicated that the mutant HNF-1, had no transactivation activity in HeLa and MIN6 cells. Haploinsufficiency for HNF-1, may lead to severe forms of diabetes like type 1 diabetes. Hum Mutat 18:345,351, 2001. © 2001 Wiley-Liss, Inc. [source] HLA haplotypes in recurrent aphthous stomatitis: a mode of inheritance?INTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 6 2008E. Albanidou-Farmaki Summary The aim of this study was to investigate the genetic association between recurrent aphthous stomatitis (RAS) and human leucocyte antigen (HLA) class I and II alleles and HLA haplotypes. Families selected had at least one child suffering from recurrent aphthous stomatitis in addition to one or both of the parents. HLA-A, -B and -DR alleles were typed in 29 families, 27 nuclear and two extended (121 subjects). HLA haplotypes of all family members with RAS were compared with those who were RAS negative. Although major histocompatibility complex class I and II gene analysis failed to demonstrate any significant association between RAS and HLA antigens, the study of HLA haplotypes revealed a significant association between HLA haplotypes and susceptibility to RAS. The results indicate that susceptibility to RAS segregates in families in association with HLA haplotypes. [source] | ||||||||||||||||||||||||||||||||||