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PubMed2004

A genetic algorithm approach to detecting lineage-specific variation in selection pressure.

The ratio of nonsynonymous (dN) to synonymous (dS) substitution rates, omega, provides a measure of selection at the protein level. Models have been developed that allow omega to vary among lineages. However, these models require the lineages in which differential selection has acted to be specified a priori. We propose a genetic algorithm approach to assign lineages in a phylogeny to a fixed number of different classes of omega, thus allowing variable selection pressure without a priori specification of particular lineages. This approach can identify models with a better fit than a single-ratio model, and with fits that are better than (in an information theoretic sense) a fully local model, in which all lineages are assumed to evolve under different values of omega, but with far fewer parameters. By averaging over models which explain the data reasonably well, we can assess the robustness of our conclusions to uncertainty in model estimation. Our approach can also be used to compare results from models in which branch classes are specified a priori with a wide range of credible models. We illustrate our methods on primate lysozyme sequences and compare them with previous methods applied to the same data sets.

Algorithms↗
PubMed2004

Two-step differential expression analysis reveals a new set of genes involved in thyroid oncocytic tumors.

Thyroid oncocytic adenomas are a class of tumors characterized by the presence of abundant mitochondria. We performed a differential display RT-PCR analysis on two oncocytic adenomas and their paired controls. We then carried out a microarray analysis using the 460 selected, differentially expressed clones on four other oncocytomas and their paired controls. Thirty genes, 12 encoded by mitochondrial DNA and 18 nuclear-encoded, were overexpressed by a factor of at least 2 in the tumors compared with the controls. Seven of the 18 nuclear-encoded genes are involved in protein metabolism: DKFZP434I116, B3GTL, SNX19, RP42, SENP1, UBE2D3, and the CTSB gene, which is known to be particularly deregulated in most thyroid tumors. Other genes are implicated in signal transduction (ITGAV) or tumorigenesis (AF1q). Immunohistochemistry allowed us to confirm overexpression of the ITGAV and CTSB genes at the protein level and showed a marked relocation of the CTSB protein. We confirmed the overexpression of the AF1q oncogene in 56% of 18 oncocytic tumors by quantitative RT-PCR analysis, which attested to the heterogeneity of these tumors. Our results show an increased expression of genes involved in protein metabolism in oncocytoma, the significance of which requires investigation.

Adenine Nucleotide Translocator 2↗
PubMedDate not supplied

Programmed cell death of peripheral myeloid precursor cells in Down patients: effect of zinc therapy.

Hemopoietic stem cell differentiation represents the primary rule of self-renewal, proliferation, and specialization modulated by several mechanisms, including growth factors, cell interactions, and bioavailability of various ions, especially Ca2+ and Zn2+. Apoptotic death, during normal cell turnover, has been widely studied and is recognized as an important pathway for clonal deletion in the hemopoietic system. Multiparametric analyses have shown that subjects with Down syndrome show low levels of plasmic zinc associated with the presence of immature myeloid cells in the peripheral blood. This arrangement is repaired by in vivo zinc therapy. This study presents morphological and biochemical analyses to show that ZnSO4 therapy induces the disappearance of peripheral myeloid precursor cells by a programmed cell death mechanism. The programmed zinc-therapy-induced cell death presumably provides a simple way to regulate the myeloid differentiation selecting appropriate cells.

Adolescent↗
PubMed2001

A century of life-history evolution in grayling.

Synchronic and allochronic data sets consisting of phenotypic values of various life-history traits from five grayling Thymallus thymallus populations with common ancestors were analysed for the purpose of estimating evolution and divergence rates. The synchronic data contained both juvenile and adult traits from populations that have been segregated for 44-88 years (9-22 generations). The allochronic time series contained growth- and maturation data spanning 95 years (16 generations). Estimated evolution and divergence rates were high compared with other life-history studies on the same temporal scale (0.002-1.008 haldanes, 10-30, 500 darwins). The divergence of adult traits were most probably caused by differential mortalities induced by variation in fishing intensity. For the population with allochronic data, 48 years (eight generations) of intense and consistent size-selective gill-net fishing resulted in a constant reduction in age (-0.33 years pr 10 year) and length (-18mm pr 10 year) at maturity. Length-at-age for ages one to five also decreased during the same period. When gill-net fishing was relaxed, age and length at maturity and length-at-age increased. Divergence rates for juvenile traits derived from a common-garden experiment were high, and standardized selection differentials (s') were high, especially for yolk-sac volume (s' = 2.6). We also document that low divergence rates for juvenile traits were lower between populations having similar spawning/nursery habitats (running water) than populations having relatively different habitats (running water v.s. still water). We suggest that the major part of the observed phenotypic divergence is mostly due to adaptive evolution, although microsatellite data indicate that genetic drift also has occurred.

Adaptation, Biological↗
PubMed2003

Evaluation of a dual chamber implantable cardioverter defibrillator for the treatment of atrial and ventricular arrhythmias.

Eighty-nine patients with a documented history of atrial tachyarrhythmias or fibrillation (AF) received a cardioverter defibrillator designed to selectively differentiate and treat atrial and ventricular arrhythmias. Twenty-two patients received a coronary sinus lead and, therefore, could use a separate shock vector for selective treatment of atrial tachyarrhythmias/AF. The device is designed to treat tachyarrhythmias with antitachycardia pacing (ATP) and/or shock therapy using an atrial and/or a ventricular shock vector. Patients underwent induction and shock termination of atrial or dual tachyarrhythmias (AF/VF) to verify proper device function and to measure the arrhythmia detection time with enhancements and preventive algorithms programmed On and Off, respectively. Detection time for 329 VF inductions was 2.41 +/- 0.64 seconds with enhancements On and 2.29 +/- 0.47 with enhancements Off (NS). At implant or predischarge, 283 AF and/or AF/VF (121 atrial and 162 atrial/ventricular fibrillation) were induced. Shock conversion efficacy was 89.8% with AF conversion energies ranging from 0.9 to 27 J. Thirteen of the 23 patients had atrial shock conversions using the separate shock vector with an average conversion energy of 1.9 +/- 1.4 J. (range 0.5-5 J). During follow-up the efficacy of ATP on atrial tachyarrhythmias was 59% and the efficacy of delivered shocks on AF was 85%. This new dual chamber cardioverter defibrillator appropriately detected and classified atrial arrhythmias, and shock therapy for AF was highly effective. The detection algorithm differentiated atrial tachyarrhythmia/AF and did not delay VF detection. The separate shock vector converted induced AF with energies ranging from 0.6 to 5 J.

Atrial Fibrillation↗
PubMed1991

Premature expression of the macrophage colony-stimulating factor receptor on a multipotential stem cell line does not alter differentiation lineages controlled by stromal cells used for coculture.

We are interested to know whether expression of a lineage-specific growth factor receptor is deterministic to lineage commitment during hematopoiesis. For this purpose, we introduced the human c-fms gene into the multipotential stem cell clone LyD9 and two myeloid progenitor clones, L-GM3 and L-G3, cells that differentiate in response to granulocyte/macrophage colony-stimulating factor (GM-CSF) and granulocyte (G)-CSF, respectively. Although LyD9 cells have differentiation potential to become macrophages, c-fms transfectants of LyD9 and L-GM3 cells did not differentiate in response to human macrophage (M)-CSF. However, c-fms transfectants of L-G3 cells differentiated to neutrophils in response to human M-CSF. These results indicate that the M-CSF receptor requires a specific signal transduction pathway to exert its differentiational and proliferative effects. Furthermore, the M-CSF receptor can convey a granulocyte-type differentiation signal possibly by cooperating with the G-CSF receptor signal transduction pathway. The c-fms-transfected LyD9 cells as well as the original LyD9 cells differentiated predominantly into GM-CSF- and G-CSF-responsive cells by coculturing with PA6 and ST2 stromal cells, respectively. The results indicate that differentiation lineage is not affected by premature expression of the M-CSF receptor. Instead, the stromal cell used for coculture apparently controls lineage-selective differentiation of the multi-potential stem cell line.

Animals↗
PubMed2004

Stem cell based therapeutical approach of male infertility by teratocarcinoma derived germ cells.

Infertility affects 13-18% of couples and growing evidence from clinical and epidemiological studies suggests an increasing incidence of male reproductive problems. There is a male factor involved in up to half of all infertile couples. The pathogenesis of male infertility can be reflected by defective spermatogenesis due to failure in germ cell proliferation and differentiation. We report here in vitro generation of a germ cell line (SSC1) from the pluripotent teratocarcinoma cells by a novel promoter-based sequential selection strategy and show that the SSC1 cell line form mature seminiferous tubule structures, and support spermatogenesis after transplantation into recipient testes. To select differentiated germ cell population, we generated a fusion construct (Stra8-EGFP) harbouring the 1.4 kb promoter region of germ line specific gene Stra8 and coding region of enhanced green fluorescence protein. This region was sufficient to direct gene expression to the germinal stem cells in testis of transgenic mice. The purified cells expressed the known molecular markers of spermatogonia Rbm, cyclin A2, Tex18, Stra8 and Dazl and the beta1- and alpha6-integrins characteristic of the stem cell fraction. This cell line undergoes meiosis and can develop into sperm when transplanted into germ cell depleted testicular tubules. Sperm were viable and functional, as shown by fertilization after intra-cytoplasmic injection into mouse oocytes. This approach provides the basis that is essential for studying the development and differentiation of male germ line stem cell, as well as for developing new approaches to reproductive engineering and infertility treatment.

Adaptor Proteins, Signal Transducing↗
PubMedDate not supplied

Stemness, fusion and renewal of hematopoietic and embryonic stem cells.

Development of replacement cell therapies awaits the identification of factors that regulate nuclear reprogramming and the mechanisms that control stem cell renewal and differentiation. Once such factors and signals will begin to be elucidated, new technologies will have to be envisaged where uniform differentiation of adult or embryonic stem cells along one differentiation pathway can be induced. Controlled differentiation of stem cells will require the engineering of niches and extracellular signal combinations that would amplify a particular signaling network and allow uniform and selective differentiation. Three recent advances in stem cell research open the possibility to approach engineering studies for cell replacement therapies. Fusion events between stem cells and adult cells or between adult and embryonic stem cells have been shown to result in altered fates and nuclear reprogramming of cell hybrids. Hematopoietic stem cells were shown to require Wnt signaling in order to renew. The purification of Wnt proteins would allow their use as exogenous purified cytokines in attempts to amplify stem cells before bone marrow transplantation. The homeodomain protein Nanog has been shown to be crucial for the embryonic stem cell renewal and pluripotency. However, the cardinal question of how stemness is preserved in the early embryo and adult stem cells remains opened.

Animals↗
PubMed1990

Plasma cholesterol responses to the adrenocorticotropic hormone in Japanese quail following eighteen generations of divergent selection.

Japanese quail (Coturnix coturnix japonica) lines were divergently selected for plasma cholesterol response to adrenocorticotropin (ACTH). Data for Generations 9 to 18 indicated a greater response in the low (L) line than in the high (H) line, which was contrary to selection responses for the first eight generations. During Generations 9 to 18, selection differentials were greater in the H line; however, heritability estimates were greater in the L line. These data suggest caution in the interpretation of early selection responses for plasma cholesterol. Selection for plasma cholesterol response following ACTH injection also resulted in divergence in plasma cholesterol levels in the H and L lines in the absence of ACTH. Body weights at 31 days were greater in the H line than in the L line, suggesting a possible relationship with the plasma cholesterol level.

Adrenocorticotropic Hormone↗
PubMed2005

Genetic differentiation induced by selection in an inbred population of the silkworm Bombyx mori, revealed by RAPD and ISSR marker systems.

Artificial selection has been widely utilized in breeding programmes concerning the commercially important silk-producing insect Bombyx mori. Selection increases the frequency of homozygotes and makes homozygous effects stronger. Molecular variation induced by selection in the inbred population of B. mori strain Nistari, was assessed in terms of genic differentiation by using a polymorphic profile generated by RAPD and ISSR marker systems. Artificial selection for longer larval duration (LLD) for 4 generations resulted in a significant prolongation of larval duration (F = 89.28; P = 5.14 x 10(-7)). The lines selected for shorter larval duration (SLD) were not significantly different from the control group. RAPD and ISSR primers generated polymorphic profiles when amplified with genomic DNA of individuals of LLD and SLD lines. Distinct markers specific to LLD individuals were observed from the 3rd generation and indicated selection-induced differentiation of allelic variants for longer larval duration. Both SLD and LLD were characterized by high gene diversity (h approximately equal to 0.197) and total heterozygosity (Ht > or =0.26), low homogeneity (chi-square test, p < 0.005) as well as a large coefficient of gene differentiation (Gst > or =0.42) but low gene flow (Nm < or =0.42). Genetic distance was the highest (0.824) between 3rd generations of SLD and LLD. High heterozygosity and prolonged larval duration substituted for shorter larval duration (the traditional trait of fitness) in the Nistari LLD larvae.

Animals↗
PubMed1997

Lambornella clarki (Ciliophora:Tetrahymenidae) resistance in Aedes sierrensis (Diptera:Culicidae):population differentiation in a quantitative trait and allozyme loci.

Heritable variation for resistance to the parasite Lambornella clarki (Corliss & Coats) by its host Aedes sierrensis (Ludlow) and neutral genetic variation among local Oregon mosquito populations were assessed by selection and allozyme frequencies. L. clarki resistance was significantly greater in a population of mosquitoes normally exposed to this parasite than in an unexposed population. Despite this difference between populations, there was no significant increase in heritable resistance to L. clarki within populations of Ae. sierrensis after 1 generation of laboratory selection. Differentiation estimated from allozyme electrophoresis did not coincide with differentiation in L. clarki resistance in Ae. sierrensis populations at the microgeographic scale. Ae. sierrensis has the capacity to respond to foreign clones of the parasite, but electrophoretic surveys may fail to indicate underlying differences in the parasite resistance of mosquito populations.

Aedes↗
PubMed2004

Tissue engineering through autologous mesenchymal stem cells.

The regeneration of damaged cartilage in different pathological situations is a major goal for the future and could be achieved through cell and/or gene therapy. Mesenchymal stem cells (MSCs) are the progenitors of multiple lineages, including bone, cartilage, muscle, fat, and astrocytes. MSCs seem to be the best candidates for cell therapy to regenerate injured tissue, as they are easily isolated from bone marrow and can be rapidly amplified. Full healing is extremely demanding, however, and includes integration of the regenerated tissue within the surrounding host tissue and true differentiation through pathways involved in embryonic development. This goal might be reached through the combined use of scaffolds, MSC-mediated therapy and the expression of selective differentiating factors. The long-term behavior of MSCs associated with biomaterials and implanted in pathological joints remains to be investigated before clinical application in osteoarthritis or rheumatoid arthritis.

Animals↗
PubMed2004

Whole genome expression profiling of advance stage papillary serous ovarian cancer reveals activated pathways.

Ovarian cancer is the most lethal type of gynecologic cancer in the Western world. The high case fatality rate is due in part because most ovarian cancer patients present with advanced stage disease which is essentially incurable. In order to obtain a whole genome assessment of aberrant gene expression in advanced ovarian cancer, we used oligonucleotide microarrays comprising over 40,000 features to profile 37 advanced stage papillary serous primary carcinomas. We identified 1191 genes that were significantly (P < 0.001) differentially regulated between the ovarian cancer specimens and normal ovarian surface epithelium. The microarray data were validated using real time RT-PCR on 14 randomly selected differentially regulated genes. The list of differentially expressed genes includes ones that are involved in cell growth, differentiation, adhesion, apoptosis and migration. In addition, numerous genes whose function remains to be elucidated were also identified. The microarray data were imported into PathwayAssist software to identify signaling pathways involved in ovarian cancer tumorigenesis. Based on our expression results, a signaling pathway associated with tumor cell migration, spread and invasion was identified as being activated in advanced ovarian cancer. The data generated in this study represent a comprehensive list of genes aberrantly expressed in serous papillary ovarian adenocarcinoma and may be useful for the identification of potentially new and novel markers and therapeutic targets for ovarian cancer.

Carcinoma, Papillary↗
PubMed1996

Estimates of genetic trend for yield traits of the registered Jersey population.

Data for American Jersey cattle from 1960 to 1990 were used to study genetic progress achieved by four paths of selection (sires of bulls, dams of bulls, sires of cows, and dams of cows). Possible methods of obtaining optimal genetic gain for the breed were suggested by the analysis. The generation interval by year of birth for parents of AI bulls was greater from 1975 to 1984 than for most recent 5 yr (1983 to 1987) because previously the use of old proven bulls was greater. Sires of bulls tended to have a longer average generation interval (9.3 yr) than the more nearly optimal interval reported in the literature for AI populations (7.0 yr). Selection differentials for the last 5 yr were larger than the average over all years for milk yield, fat yield, protein yield, and fat percentage. More intense selection for sires of bulls gave a larger increase in PTA over time than did other paths of selection. When all paths of selection were combined, estimated annual genetic change for the Jersey breed was greater from 1983 to 1987 than from 1960 to 1987 for milk yield, fat yield, protein yield, and fat percentage. Potential genetic response from the sires and dams that were available to produce sons was greater than the response from parents actually used. Therefore, better sires and dams were available for genetic enhancement of their progeny than those actually used to produce young sires and replacement females.

Animals↗
PubMed1975

The genetic structure of a tribal population, the Yanomama Indians XI. Gene frequencies for 10 blood groups and the ABH-Le secretor traits in the Yanomama and their neighbors; the uniqueness of the tribe.

In this paper we present the results of blood group typings for a total of 33 villages distributed among five South American Indian tribes--Yanomama (21 villages), Makiritare (eight villages), Macushi (two villages), Piaroa (one village), and Wapishana (one village). These new results for the Yanomama and Makiritare tribes have been combined with those previously reported to allow a better appreciation of the distribution of allelic frequencies in the tribes. The relationship of the Yanomama to other South American Indian tribes is investigated using data on six polymorphic loci (Rh, MNS, Fy, Jk, Di, Hp). By use of four genetic measures (two of genetic relationship and two of genetic diversity), we demonstrate that the Yanomama are genetically unique among a sample of 20 South American tribes. In addition, the Yanomama show somewhat less genetic diversity for the six loci analyzed than the average South American tribe. Taken together, these results indicate a rather long period of isolation for the population antecedent to the Yanomama--perhaps since the time of entry of man into the South American continent. The pattern of genetic relationships and genetic diversity for the 20 tribes is consistent with the hypothesis that evolution in South America proceeded by a process of fission-fusion leading to isolation of subpopulations with subsequent genetic differentiation as a consequence of population isolation. The uniqueness of the Yanomama appears to stem entirely from such a process, there being no evidence of any selective differential for the loci analyzed.

ABO Blood-Group System↗
PubMed1998

Regulation of the IL-12 receptor beta2 subunit by soluble antigen and IL-12 in vivo.

Continuous administration of soluble protein antigen to BALB/c mice inhibits the development of Th1 and induces selective differentiation of Th2 cells. Here we show that interleukin (IL)-12, administered together with soluble protein through a mini-osmotic pump implanted subcutaneously, not only prevents the inhibition of Th1 cell development, but stimulates higher interferon (IFN)-gamma production than in mice receiving IL-12 alone. In parallel to co-stimulation of Th1 cell development, co-administration of IL-12 blocks the Th2 response induced by soluble protein. IL-12 administered in adjuvant with antigen or intraperitoneally 2 days after the immunization does not break the inhibition of Th1 but can still decrease the Th2 response induced by pretreatment with soluble protein antigen. In contrast to IL-12, co-administration of IL-2 or IFN-gamma does not affect the diversion to Th2 induced by soluble antigen. Thus IL-12, but not IL-2 nor IFN-gamma, converts in vivo the inhibitory signal for Th1 cell development delivered by soluble antigen into an immunogenic one, while blocking a positive signal for Th2 cell differentiation. A molecular basis for the co-stimulation of Th1 priming and the prevention of Th2 differentiation by IL-12 in vivo is provided by the observation that transcripts encoding the IL-12 receptor beta2 chain, which is required for IL-12 signaling and Th1 cell development, are selectively inhibited by soluble antigen but are enhanced by IL-12 co-administration.

Animals↗
PubMed2005

Analysis of target genes induced by IL-13 cytotoxin in human glioblastoma cells.

IL-13 cytotoxin comprised of IL-13 and a mutated form of Pseudomonas exotoxin (fusion protein termed IL-13-PE38QQR) has been shown to inhibit protein synthesis leading to necrotic and apoptotic cell death in glioblastoma cells that express high levels of interleukin-13 receptors (IL-13R). To identify target genes of cell death and other cellular genes with IL-13 receptors in glioblastoma cells, we utilized the cDNA microarrays to analyze global gene expression profiles after IL-13 cytotoxin and IL-13 treatment. IL-13 cytotoxin mediated cytotoxicity to U251 cells in a dose-dependent manner. Hierarchical cluster analysis of differentially expressed genes in U251 glioma cells at different time points after IL-13 cytotoxin treatment showed three major groups, each representing a specific expression pattern. Randomly selected differentially expressed genes from each group were confirmed by RT-PCR analysis. Most down-regulated genes belong to cell adhesion, motility, angiogenesis, DNA repair, and metabolic pathways. While up-regulated genes belong to cell cycle arrest, apoptosis, signaling and various metabolic pathways. Unexpectedly, at early time points, both IL-13 and IL-13 cytotoxin induced several genes belonging to different pathways most notably IL-8, DIO2, END1, and ALDH1A3 indicating that these genes are early response genes and their products may be associated with IL-13R. In addition, IL-13 cytotoxin induced IL-13Ralpha2 mRNA expression during the treatment in glioma cells. Our results indicate that novel cellular genes are involved with IL-13 receptors and that IL-13 cytotoxin induced cell death involves various target genes in human glioblastoma cells. On going studies will determine the role of associated genes and their products in the IL-13R functions in glioma cells.

ADP Ribose Transferases↗