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Hybridization in East African swarm-raiding army ants
Daniel JC Kronauer, Marcell K Peters, Caspar Sch?ning, Jacobus J Boomsma
Frontiers in Zoology , 2011, DOI: 10.1186/1742-9994-8-20
Abstract: While the mitochondrial phylogeny had a strong geographic signal, different species were not recovered as monophyletic. At our main study site at Kakamega Forest, a mitochondrial haplotype was shared between a "Dorylus molestus-like" and a "Dorylus wilverthi-like" form. This pattern is best explained by introgression following hybridization between D. molestus and D. wilverthi. Microsatellite data from workers showed that the two morphological forms correspond to two distinct genetic clusters, with a significant proportion of individuals being classified as hybrids.We conclude that hybridization and gene-flow between the two army ant species D. molestus and D. wilverthi has occurred, and that mating between the two forms continues to regularly produce hybrid workers. Hybridization is particularly surprising in army ants because workers have control over which males are allowed to mate with a young virgin queen inside the colony.While botanists have long accepted that hybridization plays an important role in plant evolution and regularly leads to the emergence of new species [1], zoologists have traditionally regarded hybridization and interspecific gene flow as rare exceptions [2]. However, the advent of molecular genetic markers has changed this view during the last decade and it is now widely accepted that hybridization between closely related species is also common in animals [3-5]. Hybrids are often non-viable or sterile due to negative epistasis and therefore tend to be rather efficiently removed from the population by natural selection [6]. However, in situations where this is not the case, hybridization can lead to the collapse of closely related species into a single panmictic population [e.g. [7]], or to speciation events when some form of reproductive isolation between parental species and hybrids emerges [3-5].In haplodiploid eusocial animals such as ants, the consequences of hybridization can be strikingly different from those in other organisms. First,
Trypetidae (Diptera) associated with the plant Monechma (Acanthaceae) in the Kalahari Gemsbok National Park  [cached]
H. K. Munro
Koedoe : African Protected Area Conservation and Science , 1963, DOI: 10.4102/koedoe.v6i1.812
Abstract: Trypetidae (Diptera) associated with the plant Monechma (Acanthaceae) in the Kalahari Gemsbok National Park
Genome-Wide Association Studies of the PR Interval in African Americans  [PDF]
J. Gustav Smith equal contributor ,Jared W. Magnani equal contributor,Cameron Palmer,Yan A. Meng,Elsayed Z. Soliman,Solomon K. Musani,Kathleen F. Kerr,Renate B. Schnabel,Steven A. Lubitz,Nona Sotoodehnia,Susan Redline,Arne Pfeufer,Martina Müller,Daniel S. Evans,Michael A. Nalls,Yongmei Liu,Anne B. Newman,Alan B. Zonderman,Michele K. Evans,Rajat Deo,Patrick T. Ellinor,Dina N. Paltoo,Christopher Newton-Cheh equal contributor,Emelia J. Benjamin equal contributor,Reena Mehra equal contributor,Alvaro Alonso equal contributor,Susan R. Heckbert equal contributor,Ervin R. Fox equal contributor,Candidate-gene Association Resource (CARe) Consortium
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1001304
Abstract: The PR interval on the electrocardiogram reflects atrial and atrioventricular nodal conduction time. The PR interval is heritable, provides important information about arrhythmia risk, and has been suggested to differ among human races. Genome-wide association (GWA) studies have identified common genetic determinants of the PR interval in individuals of European and Asian ancestry, but there is a general paucity of GWA studies in individuals of African ancestry. We performed GWA studies in African American individuals from four cohorts (n = 6,247) to identify genetic variants associated with PR interval duration. Genotyping was performed using the Affymetrix 6.0 microarray. Imputation was performed for 2.8 million single nucleotide polymorphisms (SNPs) using combined YRI and CEU HapMap phase II panels. We observed a strong signal (rs3922844) within the gene encoding the cardiac sodium channel (SCN5A) with genome-wide significant association (p<2.5×10?8) in two of the four cohorts and in the meta-analysis. The signal explained 2% of PR interval variability in African Americans (beta = 5.1 msec per minor allele, 95% CI = 4.1–6.1, p = 3×10?23). This SNP was also associated with PR interval (beta = 2.4 msec per minor allele, 95% CI = 1.8–3.0, p = 3×10?16) in individuals of European ancestry (n = 14,042), but with a smaller effect size (p for heterogeneity <0.001) and variability explained (0.5%). Further meta-analysis of the four cohorts identified genome-wide significant associations with SNPs in SCN10A (rs6798015), MEIS1 (rs10865355), and TBX5 (rs7312625) that were highly correlated with SNPs identified in European and Asian GWA studies. African ancestry was associated with increased PR duration (13.3 msec, p = 0.009) in one but not the other three cohorts. Our findings demonstrate the relevance of common variants to African Americans at four loci previously associated with PR interval in European and Asian samples and identify an association signal at one of these loci that is more strongly associated with PR interval in African Americans than in Europeans.
Molecular verification of the integration ofTripsacum dactyloides DNA into wheat genome through wide hybridization
Jiwen Qiu,Demin Jin,Chuanyou Li,Jianhang Jia,Ping Ouyang,William Tai,Bin Wang,Dawei Li
Chinese Science Bulletin , 2000, DOI: 10.1007/BF02887099
Abstract: RAPD and RFLP analyses of double haploid lines which derived from hybridization between hexaploid wheat (Triticum aestivum L. 2n=42) and eastern gamagrass (Tripsacum dactyloides L.2n=4x=72) are reported. Two of the 340 Operon primers have been screened, which stably amplifiedTripsacum dactyloides (male parent) specific bands in the double haploid lines. These results confirm the fact thatTripsacum dactyloides DNA has been integrated into wheat genome by sexual hybridization at molecular level. This idea has been further testified by RFLP analysis. Application and potentials of transferringTripsacum dactyloides DNA into wheat genome by sexual hybridization in wheat breeding are discussed.
GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
Heidi Lyng, Malin Lando, Runar S Br?vig, Debbie H Svendsrud, Morten Johansen, Eivind Galteland, Odd T Brustugun, Leonardo A Meza-Zepeda, Ola Myklebost, Gunnar B Kristensen, Eivind Hovig, Trond Stokke
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-5-r86
Abstract: Array comparative genomic hybridization (aCGH) is widely used for genome-wide mapping of DNA copy number changes in malignant cells [1,2]. Genetic gains and losses impact gene expression levels, and thereby promote tumor growth and progression [3-5]. Numerous clinical studies have been performed to find tumor characteristics and to classify patients with respect to their prognosis based on the copy number changes [6,7]. The usefulness of the aCGH data is limited, however, because only relative and not absolute copy numbers are achieved, making the interpretation of the data and comparisons across experiments difficult. Absolute DNA copy numbers can be obtained only on a single gene basis by the use of fluorescence in situ hybridization (FISH). Development of genome-wide methods for this purpose would enable generation of universal gene copy number databases of individual diseases that could be utilized more widely, as is the goal of several public repositories like the Mitelman Database of Chromosome Aberrations in Cancer [8].The relative values achieved in aCGH experiments are influenced by the total DNA content (ploidy) of the tumor cells, the proportion of normal cells in the sample, and the experimental bias, in addition to the DNA copy numbers. The values are presented as intensity ratios between tumor and normal DNA [2]. The data are normalized so that the ratio of 1.0 is the baseline for the analysis, and corresponds to two DNA copies in near diploid (2n) tumors. The copy number changes are identified from the ratios deviating from the baseline, using statistical methods for ratio smoothing and breakpoint detection [9-12]. To assign an absolute copy number to each ratio level identified by the statistical analysis and thereby score genetic aberrations are, however, challenging. In aneuploid tumors with gross alterations in the DNA content, the baseline represents a copy number other than 2, like 3 or 4 in tri- or tetraploid tumors, or a non-integer value when
Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma
Tsz-Kwong Man, Xin-Yan Lu, Kim Jaeweon, Laszlo Perlaky, Charles P Harris, Shishir Shah, Marc Ladanyi, Richard Gorlick, Ching C Lau, Pulivarthi H Rao
BMC Cancer , 2004, DOI: 10.1186/1471-2407-4-45
Abstract: We used a genome-wide screening method – array based comparative genomic hybridization (array-CGH) to identify DNA copy number changes in 48 patients with osteosarcoma. We applied fluorescence in situ hybridization (FISH) to validate some of amplified clones in this study.Clones showing gains (79%) were more frequent than losses (66%). High-level amplifications and homozygous deletions constitute 28.6% and 3.8% of tumor genome respectively. High-level amplifications were present in 238 clones, of which about 37% of them showed recurrent amplification. Most frequently amplified clones were mapped to 1p36.32 (PRDM16), 6p21.1 (CDC5L, HSPCB, NFKBIE), 8q24, 12q14.3 (IFNG), 16p13 (MGRN1), and 17p11.2 (PMP22 MYCD, SOX1,ELAC27). We validated some of the amplified clones by FISH from 6p12-p21, 8q23-q24, and 17p11.2 amplicons. Homozygous deletions were noted for 32 clones and only 7 clones showed in more than one case. These 7 clones were mapped to 1q25.1 (4 cases), 3p14.1 (4 cases), 13q12.2 (2 cases), 4p15.1 (2 cases), 6q12 (2 cases), 6q12 (2 cases) and 6q16.3 (2 cases).This study clearly demonstrates the utility of array CGH in defining high-resolution DNA copy number changes and refining amplifications. The resolution of array CGH technology combined with human genome database suggested the possible target genes present in the gained or lost clones.Osteosarcoma (OS) is a primary malignant tumor of bone arising from primitive bone-forming mesenchymal cells and it accounts for approximately 60% of malignant bone tumors in the first two decades of life [1]. These tumors typically arise in the metaphyseal regions of long bones, with the distal femur, proximal tibia and proximal humerus. A significant number of osteosarcomas are of conventional type which can be subdivided into three major categories based on their predominant differentiation of tumor cells: osteoblastic, chondroblastic, and fibroblastic. Currently, only the histological response (degree of necrosis) to therapy
Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization
Gui Lee, Woo Yang, Hei Jeung, Sang Kim, Min Seo, Chan Park, Hyun Chung, Sun Rha
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-305
Abstract: We investigated the molecular characteristics of genetic changes variation of thymoma using cDNA microarray based-comparative genomic hybridization (CGH) with a 17 K cDNA microarray in an indirect, sex-matched design. Genomic DNA from the paraffin embedded 39 thymoma tissues (A 6, AB 11, B1 7, B2 7, B3 8) labeled with Cy-3 was co-hybridized with the reference placenta gDNA labeled with Cy-5. Using the CAMVS software, we investigated the deletions on chromosomes 1, 2, 3, 4, 5, 6, 8, 12, 13 and 18 throughout the thymoma. Then, we evaluated the genetic variations of thymoma based on the subgroups and the clinical behavior. First, the 36 significant genes differentiating five subgroups were selected by Significance Analysis of Microarray. Based on these genes, type AB was suggested to be heterogeneous at the molecular level as well as histologically. Next, we observed that the thymoma was divided into A, B (1, 2) and B3 subgroups with 33 significant genes. In addition, we selected 70 genes differentiating types A and B3, which differ largely in clinical behaviors. Finally, the 11 heterogeneous AB subtypes were able to correctly assign into A and B (1, 2) types based on their genetic characteristics.In our study, we observed the genome-wide chromosomal aberrations of thymoma and identified significant gene sets with genetic variations related to thymoma subgroups, which might provide useful information for thymoma pathobiology.Thymoma is a thymic epithelial cell tumor having organotypic features and no overt cytologic atypia. Although controversy still remains, the classical histological classifications of thymoma based on the proportion of reactive lymphocytes and tumor epithelial cells have been replaced by a histogenetic classification that basically subdivides thymoma into medullary, cortical, and mixed types, according to cytological features of epithelial cells [1-5]. Several studies supported the validity of the histogenetic classification and the World Health Org
Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation
Tracy Tucker, Alexandre Montpetit, David Chai, Susanna Chan, Sébastien Chénier, Bradley P Coe, Allen Delaney, Patrice Eydoux, Wan L Lam, Sylvie Langlois, Emmanuelle Lemyre, Marco Marra, Hong Qian, Guy A Rouleau, David Vincent, Jacques L Michaud, Jan M Friedman
BMC Medical Genomics , 2011, DOI: 10.1186/1755-8794-4-25
Abstract: We studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500 K GeneChip SNP arrays, Agilent Human Genome 244 K oligonucleotide arrays and NimbleGen 385 K Whole-Genome oligonucleotide arrays. We also determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32 K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP arrays.The Affymetrix 500 K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosomal CNVs in the 30 trios. 147 of these CNVs appeared to be de novo, but only 34 (22%) were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 most likely pathogenic and 2 possibly pathogenic CNVs for MR. All 9 of these putatively pathogenic CNVs were detected by the Affymetrix 500 K, Agilent, NimbleGen and the Illumina arrays, and 5 were found by the SMRT BAC array. Both putatively pathogenic CNVs identified in the 15 trios tested with the Affymetrix 6.0 were identified by this platform.Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology.Chromosomal abnormalities, the most frequently diagnosed cause of mental retardation (MR)[1], are routinely identified by cytogenetic analysis. Studies using array genomic hybridization (AGH) have found apparently-pathogenic gains or losses of genetic material in at least 10% of children with MR and normal conventional cytogenetic analysis[2-4]. These apparently pathogenic deletions and duplications range in size from < 100 Kb to 15 Mb. Such submicroscopic chromosomal gains or losses are collectively called pathogenic copy number variants (CNVs).However, most CNVs, despite producing gen
Linkage of cDNA expression profiles of mesencephalic dopaminergic neurons to a genome-wide in situ hybridization database
Kambiz N Alavian, Horst H Simon
Molecular Neurodegeneration , 2009, DOI: 10.1186/1750-1326-4-6
Abstract: The population of dopaminergic (DA) neurons in the ventral midbrain is divided into three distinct groups, substantia nigra pars compacta (SNpc) or the A9 group, ventral tegmental area (VTA) or the A10 group, and retrorubral field. The A9 and A10 groups are the main source of dopamine in the central nervous system and give rise to two major dopaminergic pathways. Neurons of the VTA innervate the nucleus accumbens and olfactory tubercle, comprising the mesolimbic and mesocortical pathways, and the target for SNpc innervation is the dorsal striatum, thereby constituting the nigrostriatal pathway [1]. These three pathways are involved in control of emotion, motivation and motor behavior and are connected to neurological conditions such as addiction, schizophrenia and to the second most common neurodegenerative disorder, Parkinson's disease (PD) [2,3]. The main pathological characteristic of PD is the progressive degeneration of DA neurons in the SNpc. The functional and pathological relevance of the neurons in SNpc and VTA necessitates in depth study of their gene expression profile. In recent years, several such studies have been carried out to identify the genes, expressed in these neuronal populations [4-9].Allen Brain Atlas (ABA) is a large-scale collection of gene expression patterns, using high throughput, semi-automated in situ hybridization (ISH) on mouse brain sections. The expression patterns of over 21,000 genes have been uploaded so far. Taking a genomic style approach, ABA shows above background expression, in different regions of the brain, for approximately 80% of the genes. The ISH data is searchable either by anatomical structure or using a finer (100–300 μm) resolution geometric grid [10]. The data is also available as three dimensional images and graphs, through the usage of a web browser and Brain Explorer. Another function of ABA, Neuroblast, allows identification of genes with similar expression patterns within the ABA dataset [11]. In this study,
Wing pollination by bees in Mexacanthus (Acanthaceae)?  [cached]
J. Per-Henrik Holmqvist,Mariette Manktelow,Thomas F. Daniel
Acta botánica mexicana , 2005,
Abstract: El género monotípico Mexacanthus de la familia Acanthaceae es endémico del centro occidente de México, donde está representado por la especie M. mcvaughii T.F. Daniel. La estructura de la flor es poco usual, con las anteras y el estigma en posición lateral y una barrera de néctar que no se abre sin el ejercicio de fuerza. El estudio de la polinización muestra que las flores son visitadas principalmente por el colibrí tijereta esmeralda Chlorostilbon canivetii (Lesson) y por el abejorro Xylocopa mexicanorum (Cockerell). Ambas especies abren sin problemas la barrera de néctar y se comportan como polinizadores. Los colibríes transfieren el polen en su área auricular; la abeja lo hace en sus alas, en las cuales lleva numerosos granos. La polinización por alas anteriormente se conocía sólo de lo registrado en representantes del grupo de las mariposas.
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