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At least 199 records · Page 11Linked to original sources
PubMed2003

Genetic mapping and QTL analysis of fiber-related traits in cotton ( Gossypium).

Cotton, the leading natural fiber crop, is largely produced by two primary cultivated allotetraploid species known as Upland or American cotton ( Gossypium hirsutum L.) and Pima or Egyptian cotton ( G. barbadense L.). The allotetraploid species diverged from each other and from their diploid progenitors (A or D genome) through selection and domestication after polyploidization. To analyze cotton AD genomes and dissect agronomic traits, we have developed a genetic map in an F2 population derived from interspecific hybrids between G. hirsutum L. cv. Acala-44 and G. barbadense L. cv. Pima S-7. A total of 392 genetic loci, including 333 amplified fragment length polymorphisms (AFLPs), 47 simple sequence repeats (SSRs), and 12 restriction fragment length polymorphisms (RFLPs), were mapped in 42 linkage groups, which span 3,287 cM and cover approximately 70% of the genome. Using chromosomal aneuploid interspecific hybrids and a set of 29 RFLP and SSR framework markers, we assigned 19 linkage groups involving 223 loci to 12 chromosomes. Comparing four pairs of homoeologous chromosomes, we found that with one exception linkage distances in the A-subgenome chromosomes were larger than those in their D-subgenome homoeologues, reflecting higher recombination frequencies and/or larger chromosomes in the A subgenome. Segregation distortion was observed in 30 out of 392 loci mapped in cotton. Moreover, approximately 29% of the RFLPs behaved as dominant loci, which may result from rapid genomic changes. The cotton genetic map was used for quantitative trait loci (QTL) analysis using composite interval mapping and permutation tests. We detected seven QTLs for six fiber-related traits; five of these were distributed among A-subgenome chromosomes, the genome donor of fiber traits. The detection of QTLs in both the A subgenome in this study and the D subgenome in a previous study suggests that fiber-related traits are controlled by the genes in homoeologous genomes, which are subjected to selection and domestication. Some chromosomes contain clusters of QTLs and presumably contribute to the large amount of phenotypic variation that is present for fiber-related traits.

Chromosome Mapping↗
PubMed2000

Facilitating use of analytic methods at a federal agency.

Identification and application of appropriate analytic methods are critical pieces of the foundation of science. Because of the increasingly complex issues federal agencies face and the increasing importance of addressing those issues with multi-disciplinary teams that offer knowledge and skills in many methods areas, it is important that agencies foster coordinated integration of analytic methods. This report discusses the Centers for Disease Control and Prevention's (CDC's) evolving needs regarding analytic methods and includes activities that CDC has undertaken to facilitate a coordinated approach to the use of the statistical sciences. We introduce a new framework for facilitating coordination in analytic methods as a hybrid model, blending attributes of centralized and decentralized resource models. This coordinating focus approach offers assets of timeliness, efficiency, and effectiveness, as well as fosters strengthened relationships among scientists and increased collaboration among scientific disciplines.

Centers for Disease Control and Prevention, U.S.↗
PubMed2002

Relationship between molecular structure and electron targets in the electroreduction of benzocarbazolediones and anilinenaphthoquinones. Experimental and theoretical study.

We report the synthesis and voltamperometric reduction of 5H-benzo[b]carbazole-6,11-dione (BCD) and its 2-R-substituted derivatives (R = -OMe, -Me, -COMe, -CF(3)). The electrochemical behavior of BCDs was compared to that of the 2-[(R-phenyl)amine]-1,4-naphthalenediones (PANs) previously studied. Like PANs, BCDs exhibit two reduction waves in acetonitrile. The first reduction step for the BCDs represents formation of the radical anion, and the half-wave potential (E(1/2)) values for this step are less negative than for that of the PANs. The second reduction wave, corresponding to the formation of dianion hydroquinone, has E(1/2) values that shift to more negative potentials. A good linear Hammett-Zuman (E(1/2) vs sigma(p)) relationship, similar to that for the PAN series, was also obtained for the BCDs. However, unlike the PANs, in the BCDs, the first reduction wave was more susceptible to the effect of the substituent groups than was the second wave, suggesting that the ordering of the two successive one-electron reductions in BCDs is opposite that in PANs. This is explained by the fact that the electron delocalizations in the two systems are different; in the case of BCDs there is an extra aromatic indole ring, which resists loss of its aromatic character. The electronic structures of BCD compounds were, therefore, investigated within the framework of the density functional theory, using the B3LYP hybrid functional with a double zeta split valence basis set. Our theoretical calculations show that the O(1).H-N hydrogen bond, analogous to that previously described for the PAN series, is not observed in the BCDs. Laplacians of the critical points (nabla(2)rho) and the natural charges for the C-O bonds indicate that the first reduction wave for the BCDs corresponds to the C(4)-O(2) carbonyl, while in the PAN series the first one-electron transfer occurred at the C(1)-O(1) carbonyl. Natural bond orbital analysis showed that, in all the BCDs, the lowest unoccupied molecular orbital (LUMO) is located at C(4), whereas for the PANs, the LUMO is found at C(1). The good correlation between the LUMO energy values and the E(1/2) potentials (wave I) established that the first one-electron addition takes place at the LUMO. Analysis of the molecular geometry confirmed that, in both series of compounds, the effect of the substituent groups is mainly on the C(4)-O(2) carbonyl. These results explain the fact that reduction of the C(4)-O(2) carbonyl (voltammetric wave II in the PANs and voltammetric wave I in the BCDs) is more susceptible to the effect of the substituent groups than is reduction of the C(1)-O(1) carbonyl (wave I in the PANs and wave II in the BCDs).

Carbazoles↗
PubMed2007

Moving beyond pure signal-detection models: comment on Wixted (2007).

The dual-process signal-detection (DPSD) model assumes that recognition memory is based on recollection of qualitative information or on a signal-detection-based familiarity process. The model has proven useful for understanding results from a wide range of memory research, including behavioral, neuropsychological, electrophysiological, and neuroimaging studies. However, a number of concerns have been raised about the model over the years, and it has been suggested that an unequal-variance signal-detection (UVSD) model that incorporates separate recollection and familiarity processes (J. T. Wixted, 2007) may provide an equally good, or even better, account of the data. In this article, the authors show that the results of studies that differentiate these models support the predictions of the DPSD model and indicate that recognition does not reflect the summing of 2 signal-detection processes, as the new UVSD model assumes. In addition, the assumptions of the DPSD model are clarified in order to address some of the common misconceptions about the model. Although important challenges remain, hybrid models such as this provide a more useful framework within which to understand human memory than do pure signal-detection models.

Humans↗
PubMed2004

A protein interaction framework for human mRNA degradation.

The degradation of mRNA is an important regulatory step in the control of gene expression. However, mammalian RNA decay pathways remain poorly characterized. To provide a framework for studying mammalian RNA decay, a two-hybrid protein interaction map was generated using 54 constructs from 38 human proteins predicted to function in mRNA decay. The results provide evidence for interactions between many different proteins required for mRNA decay. Of particular interest are interactions between the poly(A) ribonuclease and the exosome and between the Lsm complex, decapping factors, and 5'-->3' exonucleases. Moreover, multiple interactions connect 5'-->3' and 3'-->5' decay proteins to each other and to nonsense-mediated decay factors, providing the opportunity for coordination between decay pathways. The interaction network also predicts the internal organization of the exosome and Lsm complexes. Additional interactions connect mRNA decay factors to many novel proteins and to proteins required for other steps in gene expression. These results provide an experimental insight into the organization of proteins required for mRNA decay and their coupling to other cellular processes, and the physiological relevance of many of these interactions are supported by their evolutionary conservation. The interactions also provide a wealth of hypotheses to guide future research on mRNA degradation and demonstrate the power of exhaustive protein interaction mapping in aiding understanding of uncharacterized protein complexes and pathways.

Carrier Proteins↗
PubMed2003

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.

Comparative-based gene recognition is driven by the principle that conserved regions between related organisms are more likely than divergent regions to be coding. We describe a probabilistic framework for gene structure and alignment that can be used to simultaneously find both the gene structure and alignment of two syntenic genomic regions. A key feature of the method is the ability to enhance gene predictions by finding the best alignment between two syntenic sequences, while at the same time finding biologically meaningful alignments that preserve the correspondence between coding exons. Our probabilistic framework is the generalized pair hidden Markov model, a hybrid of (1). generalized hidden Markov models, which have been used previously for gene finding, and (2). pair hidden Markov models, which have applications to sequence alignment. We have built a gene finding and alignment program called SLAM, which aligns and identifies complete exon/intron structures of genes in two related but unannotated sequences of DNA. SLAM is able to reliably predict gene structures for any suitably related pair of organisms, most notably with fewer false-positive predictions compared to previous methods (examples are provided for Homo sapiens/Mus musculus and Plasmodium falciparum/Plasmodium vivax comparisons). Accuracy is obtained by distinguishing conserved noncoding sequence (CNS) from conserved coding sequence. CNS annotation is a novel feature of SLAM and may be useful for the annotation of UTRs, regulatory elements, and other noncoding features.

Animals↗
PubMed1986

Gene mapping and chromosome 19.

Chromosome 19 is currently the most fully mapped of the smaller chromosomes, with about 40 loci assigned to it (HGM8). Major inherited disorders on this chromosome include myotonic dystrophy and familial hypercholesterolaemia. Other loci include five blood groups, a cluster of apolipoprotein genes, and the receptors for insulin and polio virus. A number of cloned genes and random DNA sequences identify polymorphisms which, together with blood group and other protein polymorphisms, have been used to establish a framework for ordering the loci and estimating genetic distances. Hybrid cell lines allow loci to be assigned to one of eight different regions and a detailed genetic map of the chromosome will be possible in the near future.

ABO Blood-Group System↗
PubMed1998

Inheritance of male hybrid sterility in the house musk shrew (Suncus murinus, Insectivora, Soricidae).

Two geographic races of the house musk shrew (Suncus murinus) were crossed and intercrossed in the laboratory. Many cases of male sterility were detected among the hybrids. Segregation analysis of the pedigree data showed that the inheritance of male sterility in interracial hybrids of S. murinus can be described within the framework of monogene polyallele model with sterility of a single allele combination. This model is similar if not identical to that proposed by Dobzhansky and Muller.

Alleles↗
PubMed1990

Molecular heterogeneity of beta-thalassaemia in the Japanese: identification of two novel mutations.

Five unrelated Japanese beta-thalassaemia genes, from one homozygote and four heterozygotes, have been systematically characterized using DNA polymorphism analysis, polymerase chain reaction, dot-blot hybridization and direct sequencing of amplified genomic DNA. Four different molecular defects were observed on three different beta-globin gene frameworks. One of these, the A----G mutation in the TATA box, a previously described mutation, was detected by dot-blot hybridization in one homozygote and one heterozygote with the beta-globin gene of framework 2. The second mutation is a C----T substitution at position 654 of IVS-2, the mutation commonly found in Chinese, which was associated with the framework 1 gene. Another two mutations, both associated with framework 3 genes, are novel ones; an amber mutation in codon 90 (GAG to TAG) and a frameshift (+G) insertion in codon 54, both of which cause a beta 0-thalassaemia phenotype by premature termination of the beta-globin chain synthesis.

Adult↗
PubMed1999

Java-based framework for the secure distribution of electronic medical records.

In this paper, we present a Java-based framework for the processing, storage and delivery of Electronic Medical Records (EMR). The choice of Java as a developmental and operational environment ensures operability over a wide-range of client-side platforms, with our on-going work emphasising migration towards Extensible Markup Language (XML) capable Web browser clients. Telemedicine in support of womb-to-tomb healthcare as articulated by the Multimedia Supercorridor (MSC) Telemedicine initiative--which motivated this project--will require high-volume data exchange over an insecure public-access Wide Area Network (WAN), thereby requiring a hybrid cryptosystem with both symmetric and asymmetric components. Our prototype framework features a pre-transaction authentication and key negotiation sequence which can be readily modified for client-side environments ranging from Web browsers without local storage capability to workstations with serial connectivity to a tamper-proof device, and also for point-to-multipoint transaction processes.

Computer Communication Networks↗
PubMed2004

Transfer of European mink (Mustela lutreola) embryos into hybrid recipients.

The European mink is considered as a highly endangered Mustelidae species. The objective of this study was to explore the intriguing possibility of embryo transfer from European mink to closely related Mustelidae recipient females. To overcome interspecies pregnancy failure, embryos of European mink (Mustela lutreola) were transferred into hybrid females obtained after mating of European polecat (Mustela putorius) males and European mink (M. lutreola) females and vice versa. A total of 32 blastocysts were surgically flushed from the uteri of nine European mink donors and surgically transferred into six pseudopregnant hybrid recipients. One of the recipients received a single embryo and did not whelp. The remaining five recipients each received five to eight embryos and delivered kits. The overall success rate was 50% (16 kits/32 transferred embryos). For both male and female offspring, the average birth weight was lower in ET group when compared with naturally bred control population of European mink. The postnatal mortality rate was significantly higher in ET group as compared to controls: only 9 of 16 kits survived past the first week. At 10 days of age, the average weight for male offspring from the ET and control groups did not differ, although differences still persisted at this age for female offspring. At 3 months of age, the weight of male and female offspring in the ET group did not differ from European minks born after natural mating. We propose that transfer of European mink embryos to hybrid recipients be considered as a new experimental tool within the framework of ex situ approach conservation of this aboriginal European mustelid.

Animals↗
PubMed1996

Construction of a radiation hybrid map of chromosome 9p.

A radiation hybrid panel has been constructed for chromosome 9 using the somatic cell hybrid GM10611 as the donor cell line fused to the hamster cell line A23. The hybrid GM10611 was characterized by fluorescence in situ hybridization and reverse painting onto spreads of normal human metaphase chromosomes; it contains human chromosome 9 as the only cytogenetically detectable human material. GM10611 was irradiated with 6000 rads of X rays prior to fusion, a total of 93 independent clones were selected, and frozen stocks and DNA were prepared from each clone. These clones were screened by PCR amplification with oligonucleotide primers for sequence-tagged sites specific for 50 single-copy loci mapping to the short arm of chromosome 9. The average retention frequency of these hybrids was approximately 23%. The markers were ordered into a framework map by analyzing coretention patterns, minimizing the number of obligatory chromosome breaks, and finally confirming the order by maximum likelihood methods. A framework map ordering 27 markers with odds greater than 1000:1 was constructed. A further 16 markers that could not be uniquely placed on the map with the required support were positioned within a range of adjacent intervals.

Animals↗
PubMed2000

A dual-color FISH framework map for the characterization of the Sai1 tumor suppression region on rat chromosome 5.

The analysis of cell hybrids between malignant mouse hepatoma cells and normal rat fibroblasts has previously demonstrated the critical role of a deletion in rat chromosome 5 (RNO5) that was related to an anchorage independent phenotype. Those hybrids that were anchorage independent displayed loss of the entire RNO5 or an interstitial deletion in RNO5. These findings suggested that a putative tumor suppressor gene, Sai1 (suppression of anchorage independence 1), was located within the deleted region. To explore the molecular basis of the tumor suppressor activity of the Sai1 region, we analyzed the RNO5q23-q36 region with several genes and microsatellite markers that could be assigned to the region, as well as with new markers derived by representational difference analysis (RDA) or by microdissection. Dual-color FISH was used to construct a detailed physical map of the entire RNO5. These new data can be used to connect the physical and linkage maps in the rat, as well as to identify the details of the comparative map with other mammalian species including humans and mice. Using as FISH reagents genomic YAC, P1, or phage lambda clones corresponding to RNO5 markers, the order and unique positions of 18 markers could be established. The map provided a framework for the detailed characterization of the deletion found in anchorage independent hybrids. All markers within the bands RNO5q31.3-q35 were shown to be lost, including known cancer-related genes such as Ifna (5q32), Cdkn2a, -b (5q32), Jun (5q34), and Cdkn2c (5q35). However, the aberration in the deletion chromosome turned out to be more complex than originally thought in that we detected the presence of a paracentric inversion in addition to a deletion. The inversion led to the juxtaposition of the gene markers Tal2 (5q24.1) and Cd30lg (5q24.3). The framework map will provide the basis for the detailed physical YAC clone contig mapping of this region, and facilitate the identification and characterization of the Sai1 locus.

Animals↗
PubMed1989

SINEs and LINEs cluster in distinct DNA fragments of Giemsa band size.

By in situ hybridization, short interspersed repeated DNA elements (SINEs), exemplified by Alu repeats, are located principally in Giemsa-light human metaphase chromosome bands. In contrast, the L1 family of long interspersed repeats (LINEs) preferentially cluster in Giemsa-dark bands. These SINE/LINE patterns also generally correspond to early and later replication band patterns. In order to provide a molecular link between structurally visible chromosome bands and a framework of interspersed repeats, we investigated patterns of SINE and LINE hybridization using pulse-field gel electrophoresis (PFGE). Interspersed SINEs and LINEs hybridize with high intensity to specific size fragments of 0.2-3 megabase pairs (Mb). Using appropriate restriction enzymes and pulse-field conditions, a number of fragments were delineated that were either SINE or LINE rich, and were mutually exclusive. Control studies with a human endogenous retroviral repeat that is related in sequence to the major LINE family, delineated a subset of fragments of 0.07-0.4 Mb with unequal intensity. Thus these less numerous repeats also appear to cluster selectively in DNA domains that are larger than a chromosome loop (60-120 kb). In summary, PFGE studies independently confirm the clustering of interspersed repeats on contiguous DNA loops. Selective clustering of repeat motifs may contribute to special structural or functional properties of large chromosome domains, such as chromatin extension/condensation or replication characteristics. In some cases the DNA fragments defined by these repeats approach the size of tandem satellite arrays.

Animals↗
PubMed1997

An integrated transcript map of human chromosome 1p35-p36.

The distal short arm of human chromosome 1 (1p) is rearranged in a variety of malignancies, and several genetic diseases also map to this region. We have constructed an integrated transcript map to precisely define the positions of genes and expressed sequence tags (ESTs) previously mapped to 1p35-p36, a region spanning approximately 40 Mb. To anchor the integrated map, a framework genetic map was constructed with 24 genetic markers and a marker order of 1000:1 odds, yielding an average resolution of 2.8 cM. An additional 106 genetic markers were localized relative to the framework genetic map. To place markers more precisely within 1p35-p36, a chromosome 1-specific, radiation-reduced hybrid (RH) panel was created. Individual DNA fragments of the RH panel were identified and ordered by PCR with the framework genetic map. A total of 250 markers, including 142 genes and ESTs, were mapped by PCR against the RH panel. The map has an observed resolution of 800 kb, and the results closely match and more precisely define previous mapping information for most markers. This map will help to identify candidate genes for genetic diseases mapping to distal 1p and is fully integrated with existing genetic and RH maps of the human genome.

Animals↗
PubMed2005

Comparison of all sites for Ti substitution in zeolite TS-1 by an accurate embedded-cluster method.

We studied the preferential location of Ti centers in the framework of the Ti-containing MFI zeolite TS-1 using a hybrid DFT/MM embedding method developed recently. This "covalent elastic polarizable environment" (covEPE) cluster embedding allows a complete and self-consistent treatment of solid covalent systems such as zeolites. For the present study, we used a gradient-corrected density functional approach. The resulting structural features of both Si- and Ti-substituted forms of the zeolite framework fit well with available experimental information. The calculated substitution energy of Ti at the 12 crystallographically different tetrahedral sites of the MFI structure vary within 19 kJ/mol with T12 and T2 as most and least preferred sites, respectively. On the basis of these computational results and the preferential sites for Ti substitution reported from different experimental investigations, we concluded that the Ti distribution in the TS-1 framework is not governed by the thermodynamic stability of the pure material.

Journal Article↗