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At least 739 records · Page 41Linked to original sources
PubMed1988

Transposable and nontransposable elements similar to the I factor involved in inducer-reactive (IR) hybrid dysgenesis in Drosophila melanogaster coexist in various Drosophila species.

The I factor is a transposable element controlling inducer-reactive (IR) hybrid dysgenesis in Drosophila melanogaster, which occurs when males from the class of inducer strains are crossed with females from the class of reactive strains. Inducer strains contain several copies of the complete 5.4-kilobase (kb) I factor at various sites on the chromosomal arms; reactive strains contain no complete I factor. Incomplete and defective I elements occur at constant locations in pericentromeric heterochromatin of both types of strains. The 5.4-kb I factors transpose, whereas incomplete I elements do not transpose. The constant location of defective I elements in all strains indicates that they were in the genome before the spread of D. melanogaster throughout the world. Sequences homologous to I occur in other Drosophila species, and their distribution correlates with the phylogenetic relationships between species. We have studied the organization of I homologues in Drosophila simulans and Drosophila teissieri. These species seem to contain both transposable I elements, even though their structure may differ from that of the 5.4-kb I factors of the inducer strains of D. melanogaster, and nontransposable I elements, which are always at the same place in the genome when different stocks of the same species are compared. These results suggest that both mobile and nonmobile I elements are very old components of the Drosophilidae genome.

Animals↗
PubMed1992

Reovirus genome segment assortment into progeny genomes studied by the use of monoclonal antibodies directed against reovirus proteins.

Using a panel of monoclonal antibodies (MABs) against reovirus proteins, we have identified proteins that associate with reovirus messenger RNA molecules prior to the generation of progeny double-stranded (ds) genome segments and proteins that are components of the structures within which progeny ds genome segments are generated. The following conclusions can be drawn from the results obtained. (1) Three proteins rapidly become associated with mRNA molecules to form single-stranded RNA-containing complexes (ssRCCs): the nonstructural protein microNS, the nonstructural protein sigma NS, and protein sigma 3. (2) Analysis of populations of ssRCCs in density gradients and by sequential exposure to various MABs indicates that some ssRCCs contain only microNS, others microNS and sigma NS or sigma 3, and others all three proteins. Each ssRCC contains one RNA molecule and, depending on the size of the RNA, 10-30 protein molecules. (3) The relative proportions of the individual RNA species in the ssRCC populations reflect the composition of the total mRNA population present in infected cells (which differs substantially from equimolarity). (4) RCCs that contain dsRNA, which become detectable as early as 4 hr after infection, contain not only microNS, sigma NS, and sigma 3, but also lambda 2. (5) The relative proportions of the 10 genome segments in dsRCCs are equimolar. This suggests that genome segment assortment into progeny genomes is linked to the transcription of plus strands into minus strands.

Animals↗
PubMed2006

Genomewide linkage scan for quantitative trait loci underlying variation in age at menarche.

CONTEXT: Age at menarche (AAM) is an important anthropological variable that has major implications for a woman's health later in life. Genetic influence has been shown to contribute greatly to AAM, but the specific genetic determinants are largely unknown. OBJECTIVE: The objective of this study was to identify the quantitative trait loci (QTL) underlying the variations in AAM. METHODS: We performed a large-scale, genomewide, linkage scan in 2461 Caucasian women from 402 pedigrees. All subjects were genotyped with 410 microsatellite markers spaced approximately 8.9 cM apart across the human genome. Using the variance component method, we conducted multipoint linkage analyses and two-locus tests for epistatic interaction. RESULTS: The strongest linkage signal was obtained at the genomic region of 22q13 (LOD, 3.70); the other two suggestive linkages were on 22q11 (LOD, 2.68) and 11q23 (LOD, 1.98), respectively. We also detected significant epistatic interaction between genomic regions 22q13 and 3q13. CONCLUSIONS: The identification of QTL and epistatic interaction in a large female sample laid a foundation for independent replication and fine-mapping studies as well as positional and functional candidate gene studies aimed at finding the causal genetic variants and hidden mechanisms concerning the variations in AAM.

Age Factors↗
PubMed1999

The involvement of genome researchers in high school science education.

The rapid accumulation of genetic information generated by the Human Genome Project and related research has heightened public awareness of genetics issues. Education in genome science is needed at all levels in our society by specific audiences and the general public so that individuals can make well-informed decisions related to public policy and issues such as genetic testing. Many scientists have found that an effective vehicle for reaching a broad sector of society is through high school biology courses. From an educational perspective, genome science offers many ways to meet emerging science learning goals, which are influencing science teaching nationally. To effectively meet the goals of the science and education communities, genome education needs to include several major components-accurate and current information about genomics, hands-on experience with DNA techniques, education in ethical decision-making, and career counseling and preparation. To be most successful, we have found that genome education programs require the collaborative efforts of science teachers, genome researchers, ethicists, genetic counselors, and business partners. This report is intended as a guide for genome researchers with an interest in participating in pre-college education, providing rationale for their involvement and recommendations for ways they can contribute, and highlighting a few exemplary programs. World Wide Web addresses for all of the programs discussed in this report are given in Table 1. We are developing a database of outreach programs offering genetics education () and request that readers submit an entry describing their programs. We invite researchers to contact us for more information about activities in their local area.

Adolescent↗
PubMed1983

The distribution of CR1, and Alu-like family of interspersed repeats, in the chicken genome.

We have studied the distribution of CR1, a family of short interspersed repeats, in the chicken genome; this family is homologous to the AluI family of man and to the B1-B2 families of mouse. Hybridization with a suitable probe showed that the vase majority of CR1 are located on the heaviest major component (1.708) of the genome which only represents 9% of chicken DNA. Some repeats were also found on the 1.702 and 1.704 components, but none on the 1.699 component (components are denoted by their buoyant densities in CsCl). The GC content of the repeats, 48%, matches that, 47%, of the major component mainly harboring it.

Animals↗
PubMed2001

Genome-wide linkage analyses of total serum IgE using variance components analysis in asthmatic families.

Variance components models were used to analyze total IgE levels in families ascertained though the Collaborative Study of the Genetics of Asthma (CSGA) using a genome-wide array of polymorphic markers. While IgE levels are known to be associated with clinical asthma and recognized to be under strong genetic control (here the heritability was estimated at 44-60% in the three racial groups), specific genes influencing this trait are still largely unknown. Multipoint analysis of 323 markers yielded little indication of specific regions containing a trait locus controlling total serum IgE levels (adjusted for age and gender). Although a number of regions showed LOD statistics above 1.5 in Caucasian families (chromosome 4) and in African-American families (chromosomes 2 and 4), none yielded consistent evidence in all three racial groups. Analysis of total IgE adjusted for gender, age and Allergy Index (a quantitative score of skin test sensitivity to 14 common aeroallergens) was conducted on these data. In this analysis, a much stronger signal for a trait locus controlling adjusted log[total IgE] was seen on the telomeric end of chromosome 18, but only in Caucasian families. This region accounted for most of the genetic variation in log[total IgE], and may represent a quantitative trait locus for IgE levels independent of atopic response. Oligogenic analysis accounting simultaneously for the contribution of this locus on chromosome 18 and other chromosomal regions showing some evidence of linkage in these Caucasian families (on chromosomes 2, 4 and 20) failed to yield significant evidence for interaction.

Asthma↗
PubMed1998

Bioenergetics of the obligate intracellular parasite Rickettsia prowazekii.

Mitochondria are thought to be derived from an ancestor of the alpha-proteobacteria and more specifically from the Rickettsiaceae. The bioenergetic repertoire of the obligate intracellular parasite Rickettsia prowazekii is consistent with its postulated role as the ancestor of the mitochondria. For example, the R. prowazekii genome contains genes encoding components of the tricarboxylic acid cycle as well as of the electron transport system, but lacks genes to support glycolysis. In addition, the R. prowazekii genome contains multiple genes coding for adenine nucleotide translocators which enables this intracellular parasite to exploit the cytoplasmic ATP of its host cell as a source of energy. The aim of this review is to describe the different aspects of the bioenergetic system in R. prowazekii and to discuss the results of phylogenetic reconstructions based on a variety of bioenergetic molecules which shed light on the origin and evolution of the mitochondrial genomes.

Citric Acid↗
PubMed1978

DNA-binding nonhistone proteins: DNA site reassociation.

The DNA-binding nonhistone proteins (NHP) have been demonstrated to fractionate the rat genome into protein-bound and unbound DNA sequences. Twenty percent of highly sheared rat DNA [approximately 350 base pair (bp)] can be retained on membrane filters as protein complexes. When extracted from the filter and retitrated with the NHP, a 4- to 5-fold enrichment of binding sites is present in the bound DNA with few, if any, sites detected in the unbound DNA. Rat DNA restricted by EcoRI endonuclease can be fractionated by its DNA-binding NHP retention characteristics. Reassociation kinetics of the bound restricted sequences indicate that 45.6% is a subset of total single-copy sequence of the rat genome an 26.9% is repetitive sequences. Cross hybridization studies indicate the repetitive sequences of the bound DNA are not enriched as much as the slow component of the rat genome. Thus a 4-fold enrichment of a subset of the rat genome has been observed via NHP-DNA interactions.

Animals↗
PubMed1983

Preimplantation development: biology, genetics, and mutagenesis.

After fertilization, the one-cell zygote grows to the morula stage and then the blastocyst stage prior to its implantation in the uterus. This series of events is under the control of the embryonic genome, although maternal cytoplasmic components may initially play a major role. The study of molecular biology has revealed a great deal concerning the organization and expression of the eukaryotic genome. Particular interest has been focused on the mechanism of control of gene expression. These mechanisms must ultimately control cellular differentiation and the early development of the embryo. The study of reproductive toxicology requires a sound molecular appreciation of gene expression and cell differentiation. Mutations of the genome can dramatically affect the embryo. Although repair mechanisms have evolved to compensate for these mutations, repairs are not uniformly successful and unrepaired mutations can lead to early fetal loss.

Animals↗
PubMed2005

Grain yield responses to moisture regimes in a rice population: association among traits and genetic markers.

Drought is a major constraint to rice (Oryza sativa L.) production in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid our understanding of the genetic mechanism of drought tolerance (DT) of rice and the development of DT varieties. Grain yield (GY) and its components of a recombinant inbred population developed from a lowland rice and an upland rice were investigated under different water levels in 2003 and 2004 in a rainout DT screening facility. Correlation and path analysis indicated that spikelet fertility (SF) was particularly important for grain yield with direct effect (P=0.60) under drought stress, while spikelet number per panicle (SN) contributed the most to grain yield (P=0.41) under well-watered condition. A total of 32 quantitative trait loci (QTLs) for grain yield and its components were identified. The phenotypic variation explained by individual QTLs varied from 1.29% to 14.76%. Several main effect QTLs affecting SF, 1,000-grain weight (TGW), panicle number (PN), and SN were mapped to the same regions on chromosome 4 and 8. These QTLs were detected consistently across 2 years and under both water levels in this study. Several digenic interactions among yield components were also detected. The identification of genomic regions associated with GY and its components under stress will be useful to improve drought tolerance of rice by marker-aided approaches.

Chromosome Mapping↗
PubMed1978

An analysis of the bovine genome by density-gradient centrifugation. Preparation of the dG+dC-rich DNA components.

The dG+dC-rich fractions obtained by density gradient centrifugation of bovine DNA in Cs2SO4/BAMD [J. Cortadas, G. Macaya & G. Bernardi (1977) Eur. J. Biochem. 76, 13--19] were centrifuged in Cs2SO4/Ag+ density gradients. These experiments led to the preparation of the DNA components which had been detected (by analytical centrifugation in CsCl) in the Cs2SO4/BAMD fractions, and also of DNA components which had identical behaviors in Cs2SO4/BAMD gradients and identical buoyant densities in CsCl. A total of eight satellite components and 11 minor components, accounting for 23% and 4% of the bovine genome, respectively, were thus isolated and charcterized in their relative amounts and buoyant densities. The implications of these results on the interpretation of renaturation kinetic data on the bovine genome are discussed.

Animals↗
PubMed1988

Properties of two 5'-coterminal RNAs transcribed part way and across the S component origin of DNA synthesis of the herpes simplex virus 1 genome.

In cells infected with herpes simplex virus 1 the domains of the two identical origins of viral DNA synthesis in the S component (Oris) are transcribed in two 5'-coterminal RNAs. OriSRNA1, synthesized early in infection and also in the absence of protein synthesis by infected cells, runs antisense to and terminates at the transcription initiation site for alpha genes 22 or 47. OriSRNA2, reported earlier, was detected in cells 14 hr after infection; it extends across the origin and is coterminal with the alpha 4 mRNA. Whereas the OriSRNA2 of herpes simplex virus 1 (HSV-1) contains an open reading frame, the corresponding herpes simplex virus 2 (HSV-2) transcript does not. However, in the two viruses, the transcription initiation sites are 260 (HSV-1) to 180 (HSV-2) nucleotides distant from the corresponding origins of DNA synthesis.

Animals↗
PubMed1995

Sequence analysis of a faba bean necrotic yellows virus DNA component containing a putative replicase gene.

Faba bean necrotic yellows virus (FBNYV) has a circular ssDNA genome possibly consisting of several components of about 1 kb each. The complete nucleotide sequence of one component of FBNYV (FBNYV DNA 1) containing a putative replicase gene is presented. This component consists of 1002 nucleotides and, in the virion orientation, contains one large open reading frame (ORF1) potentially encoding a 32.3 kDa replicase with the NTP-binding motif GGEGKS. No obvious functions could be assigned to two smaller ORFs (7.4 and 9.3 kDa) occurring in the complementary orientation. Amino acid sequence comparisons of the putative replicase of FBNYV with that of other similar ssDNA viruses yielded higher homologies to subterranean clover stunt virus than to banana bunchy top and coconut foliar decay viruses. A potential stem-loop structure and a TATA box were identified within the noncoding region. Two oligonucleotides derived from FBNYV DNA 1 were used for direct sequencing of the virion ssDNA to determine its virion polarity and for amplifying part of this component by immunocapture PCR in extracts from from FBNYV-infected plants.

Amino Acid Sequence↗
PubMed2003

A genome-wide survey of the genes for planar polarity signaling or convergent extension-related genes in Ciona intestinalis and phylogenetic comparisons of evolutionary conserved signaling components.

Non-canonical Wnt signals similar to planar cell polarity (PCP) signaling in the fly control convergent extension (CE) of the dorsal mesoderm during gastrulation in vertebrates. Using the Ciona complete genome sequence and EST sequence data, we present here an initial and exhaustive search in non-vertebrate chordates, Ciona intestinalis for the family members as well as homologs or orthologs that are involved in PCP/CE signaling cascades. We clarified 7 cardinal gene families, including the MAPK, STE20 group kinase, Rho small GTPase, STAT, Glypican, Fz and Wnt gene families, as well as gene homologs or orthologs for known PCP/CE signaling components with their phylogenetic nature. As a result, we characterized 62 Ciona component genes. Among them, 59 genes were novel and functional genes which were supported by EST expressions and 15 genes belonged to PCP/CE component orthologs of other organisms or common ancestor genes. Moreover, from the phylogenetic point of view, we compared these components genome-widely with the PCP signaling components of fly and the CE signaling components of vertebrates. We then discovered not only that ascidians contain the basic ancestral signaling pathway components in chordates but also that several signaling components have not found in ascidian, indicating that ascidian CE pathway might have several gaps from vertebrate CE pathway. The present study provides an initial step for the subsequent analysis of CE in the non-vertebrate chordates, ascidians. In addition, this phylogenetic approach will help to facilitate understanding of the relationship between fly PCP signaling and the vertebrate CE pathway.

Adaptor Proteins, Signal Transducing↗
PubMed1985

Isomerization of herpes simplex virus 1 genome: identification of the cis-acting and recombination sites within the domain of the a sequence.

Previous studies have shown that the a sequence located at the termini and at the junction between the L and S components is the site-specific, cis-acting sequence mediating the inversions of herpes simplex virus 1 DNA. We constructed mutated a sequences, inserted them into the thymidine kinase gene, and recombined them into the L component of the viral genome. Deletion of Uc or Ub domains of the a sequence did not affect inversions, whereas the deletion of direct repeat #4 (DR4) drastically reduced their frequency. Deletion of both direct repeat #2 (DR2) and DR4 abolished inversions. Recombinational events leading to inversions appear to occur through DR2, and possibly DR4. These results complement previous studies showing that most of one DR1 sequence can also be dispensed with and are consistent with the hypothesis that DR4 and possibly DR2 are the cis-acting sites for the inversions mediated by the a sequence.

Base Sequence↗
PubMed1997

The characterization of two new clusters of duplicated genes suggests a 'Lego' organization of the yeast Saccharomyces cerevisiae chromosomes.

The systematic sequencing of 42,485 bp of yeast chromosome VII (nucleotides 377948 to 420432) has revealed the presence of 27 putative open reading frames (ORFs) coding for proteins of at least 100 amino acids. The degree of redundancy observed is elevated since five of the 27 ORFs are duplications of a previously identified gene. These duplicated copies may be classified in two types of cluster organization. The first type includes genes sharing a significant level of identity in the amino acid sequences of their predicted protein product. They are recovered on two different chromosomes, transcribed in the same orientation and the distance between them is conserved. The second type of cluster is based on one gene unit tandemly repeated. This duplication is itself repeated elsewhere in the genome. The level of nucleic acid identity is high within the coding sequence and the non-coding region between the two repeats. In addition, the basic gene unit is recovered many times in the genome and is a component of a multigene family of unknown function. These organizations in clusters of genes suggest a 'Lego organization' of the yeast chromosomes, as recently proposed for the genome of plants (Moore, 1995). The sequence is deposited in the Yeast Genome Databank under Accession Number from Z72562 to Z72586.

Amino Acid Sequence↗
PubMed1998

MITOMAP: a human mitochondrial genome database--1998 update.

We have continued to develop MITOMAP (http://www.gen.emory. edu/MITOMAP ), a comprehensive database for the human mitochondrial DNA (mtDNA). MITOMAP uses the mtDNA sequence as the unifying element for bringing together information on mitochondrial genome structure and function, pathogenic mutations and their clinical characteristics, population associated variation, and gene-gene interactions. Over the past year we have increased the degree of interlinking of MITOMAP information available on the web page, by using our generalized information management system, GENOME. As increasingly larger regions of the human genome are sequenced and characterized, the need for integrating such information is growing. Consequently, MITOMAP and GENOME provide a valuable reference for the mitochondrial biologist, in addition to being a model for the development of comprehensive, information storage and retrieval systems for other components of the human genome. This paper documents the changes to MITOMAP which have been implemented over the past year.

Computer Communication Networks↗
PubMed2005

A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway.

Members of the Hedgehog (Hh) family of signaling proteins are powerful regulators of developmental processes in many organisms and have been implicated in many human disease states. Here we report the results of a genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. The screen identified hundreds of potential new regulators of Hh signaling, including many large protein complexes with pleiotropic effects, such as the coat protein complex I (COPI) complex, the ribosome and the proteasome. We identified the multimeric protein phosphatase 2A (PP2A) and two new kinases, the D. melanogaster orthologs of the vertebrate PITSLRE and cyclin-dependent kinase-9 (CDK9) kinases, as Hh regulators. We also identified a large group of constitutive and alternative splicing factors, two nucleoporins involved in mRNA export and several RNA-regulatory proteins as potent regulators of Hh signal transduction, indicating that splicing regulation and mRNA transport have a previously unrecognized role in Hh signaling. Finally, we showed that several of these genes have conserved roles in mammalian Hh signaling.

Animals↗