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PubMed2001

Fucosyltransferases: structure/function studies.

Alpha3-fucosyltransferases (alpha3-FucTs) catalyze the final step in the synthesis of a range of important glycoconjugates that function in cell adhesion and lymphocyte recirculation. Six members of this family of enzymes have been cloned from the human genome, and their expression pattern has been shown to be highly regulated. Each enzyme has a unique acceptor substrate binding pattern, and each generates a unique range of fucosylated products. Results from a range of studies have provided information on amino acids in the FucT sequence that contribute to the differential acceptor specificity for the FucTs, and to the binding of the nucleotide sugar donor GDP-fucose. These results, in conjunction with results obtained from the analysis of the disulfide bond pattern, have provided useful clues about the spatial distribution of amino acids that influence or directly contribute to substrate binding. This information is reviewed here, and a molecular fold prediction is presented which has been constructed based on the available information and current modeling methodology.

Chromosome Mapping↗

PubMed1993

Patterns of gene expression in Bacillus subtilis colonies.

Bacillus subtilis 5:7, a derivative of macrofiber-producing strain FJ7, carries the lacZ reporter gene within Tn917 at an unknown location in the host genome. Expression of the host gene carrying lacZ within colonies of 5:7 was observed by examining growth under different conditions in the presence of 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal). At a high plating density small colonies arose that expressed the host gene early and throughout the colony, whereas at a low density large colonies were produced that expressed the host gene late in development and only in cells forming a ring pattern close to the colony periphery. A highly regulated spatial and temporal gene expression pattern was observed in growth from cross-streaks, suggesting that gene expression is responsive to concentration gradient fields established by neighboring growth. Colonies cultured on agar blocks revealed that expression was governed by depletion of a medium component and also by the geometry of the substrate upon which the colonies grew. At least three factors influenced the control of expression: (i) the concentration of a diffusible component of the medium exhausted by cell growth, (ii) a spatial-temporal factor related to growth within the colony, and (iii) the geometry of the growth substrate.

Bacillus subtilis↗

PubMed2005

Contrasting patterns of floral and molecular variation across a cline in Mimulus aurantiacus.

Steep clines in ecologically important traits may be caused by divergent natural selection. However, processes that do not necessarily invoke ongoing selection, such as secondary contact or restricted gene flow, can also cause patterns of phenotypic differentiation over short spatial scales. Distinguishing among all possible scenarios is difficult, but an attainable goal is to establish whether scenarios that imply selection need to be invoked. We compared the extent of morphological and genetic differentiation between geographically structured red and yellow floral races of Mimulus aurantiacus (bush monkeyflower; Phrymaceae). Flower color was assessed in a common garden as well as in the field to determine whether variation was genetic and to quantify the extent of geographical differentiation. Population genetic differentiation at marker loci was measured for both chloroplast and nuclear genomes, and the degree of population structure within and among the floral races was evaluated. Flower color shows both a strong genetic basis and a sharp geographic transition, with pure red-flowered populations in western San Diego County and pure yellow-flowered populations to the east. In the zone of contact, both pure and intermediate phenotypes occur. Patterns of genetic differentiation at marker loci are far less pronounced, as little of the variation is partitioned according to the differences in flower color. Phenotypic differentiation (Q(ST)) between populations with different flower colors is much greater than neutral genetic differentiation (F(ST)). When comparisons are made between populations of the same flower color, the opposite trend is evident. Limited neutral genetic structure between the floral races, combined with sharp differentiation in flower color, is consistent with the hypothesis that current or recent natural selection maintains the cline in flower color.

Biological Evolution↗

PubMed1996

The Drosophila brain revisited by enhancer detection.

The patterns of gene expression in the Drosophila brain were studied by using the lacZ reporter gene carried on an enhancer detector element. From the analysis of serial sections of the heads of 6000 enhancer detector lines, reporter gene expression in some lines was found to generally follow boundaries established by cell type or anatomy, revealing distinct patterns of lacZ expression restricted to the lamina, the medulla, mushroom bodies, antennal lobes, or other anatomical subdivisions. About 15% of the lines showed ubiquitous expression in most or all head tissues and 25% of the lines showed expression throughout the CNS. Another quarter of the lines showed widespread expression in the CNS, with large regions of the brain showing expression. This suggests that the majority of detected genes are expressed with little spatial specificity. The expression patterns produced by 12 different insertions at the rutabaga locus were found to be extremely similar in the brain and offer strong evidence that the enhancer detector elements generally report the activity of an adjacent gene. Only 15% of the lines were judged to have relatively specific expression in one brain region, including those with preferential or specific expression in the mushroom bodies, antennal lobes, lamina, medulla, etc. The cytological insertion sites for elements showing preferential mushroom body expression were found to be dispersed in the genome at approximately 50 different chromosomal regions. In addition to providing a broad picture of the transcriptional activity in the Drosophila brain, these enhancer detector lines offer access to interesting new genes and form a novel collection of lines in which identifiable brain cells are marked in a reproducible way.

Animals↗

PubMed2026

Liquid biopsy: a new window on the BRCA genes.

The Breast Cancer Susceptibility Gene (BRCA)-associated tumors represent a constantly evolving and intriguing scenario in oncology, in which the availability of novel systemic treatment, mainly including the poly (ADP-ribose) polymerase (PARP) inhibitors, has enabled an improved survival benefit in clinical subgroups. The expanding regulatory approvals of PARP inhibitors have inevitably reshaped the clinical indications for BRCA testing, moving the BRCA1/2 profiling from the traditional and preventive workflows to therapeutic paths. Despite advances in technology and treatment, substantial limitations remain in current genetic and genomic tools for the detection of deleterious BRCA1/2 variants. Germline and tumor tissue testing provide only a snapshot of a patient's disease, failing to capture the dynamic and longitudinal aspects of tumor clonal evolution. In this scenario, liquid biopsy (LB) profiling of BRCA1/2 genes, primarily as circulating tumor DNA, represents a highly active area of research potentially affecting many aspects of cancer screening, diagnosis, and monitoring in individuals who are carriers of BRCA1/2 deleterious variants. Beyond the attractive potential to surrogate the tumor tissue testing, to overcome the cancer spatial and temporal heterogeneity, and to monitor the tumor mutational profile over time, accurately detecting all clinically relevant BRCA genetic variants and epigenetic modifications using LB remains technically challenging.

BRCA1/2↗

PubMed2006

Efficient prediction of nucleic acid binding function from low-resolution protein structures.

Structural genomics projects as well as ab initio protein structure prediction methods provide structures of proteins with no sequence or fold similarity to proteins with known functions. These are often low-resolution structures that may only include the positions of C alpha atoms. We present a fast and efficient method to predict DNA-binding proteins from just the amino acid sequences and low-resolution, C alpha-only protein models. The method uses the relative proportions of certain amino acids in the protein sequence, the asymmetry of the spatial distribution of certain other amino acids as well as the dipole moment of the molecule. These quantities are used in a linear formula, with coefficients derived from logistic regression performed on a training set, and DNA-binding is predicted based on whether the result is above a certain threshold. We show that the method is insensitive to errors in the atomic coordinates and provides correct predictions even on inaccurate protein models. We demonstrate that the method is capable of predicting proteins with novel binding site motifs and structures solved in an unbound state. The accuracy of our method is close to another, published method that uses all-atom structures, time-consuming calculations and information on conserved residues.

Binding Sites↗

PubMed2006

The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus.

Little information is presently available on the factors promoting genetic divergence in eukaryotic microbes. We studied the spatial distribution of genetic variation in Saccharomyces paradoxus, the wild relative of Saccharomyces cerevisiae, from the scale of a few centimetres on individual oak trees to thousands of kilometers across different continents. Genealogical analysis of six loci shows that isolates from Europe form a single recombining population, and within this population genetic differentiation increases with physical distance. Between different continents, strains are more divergent and genealogically independent, indicating well-differentiated lineages that may be in the process of speciation. Such replicated populations will be useful for studies in population genomics.

Base Sequence↗

PubMed2005

Somatic transgenesis in the avian model system.

The chick embryo is a versatile model system, in which classical embryology can be combined with modern molecular approaches. In the last two decades, several efficient methods have been developed to introduce exogenous genes into the chick embryo. These techniques allow alteration of gene expression levels in a spatially and temporally restricted manner, thereby circumventing embryonic lethality and/or eliminating secondary effects in other tissues. Here, we present the current status of avian somatic transgenic techniques, focusing on electroporation and retrovirus-mediated gene transfer. Electroporation allows quick and efficient gain-of-function studies based on transient misexpression of genes. Retroviral vectors, which are capable of integrating exogenous genes into the host chromosome, permit analysis of long-term effects of gene misexpression. The variety of methods available for somatic transgenesis, along with the recent completion of the chicken genome, are transforming the chick embryo into one of the most attractive model systems to examine function of genes that are important for embryonic development.

Animals↗

PubMed2001

Genetic engineering of neural function in transgenic rodents: towards a comprehensive strategy?

As mammalian genome projects move towards completion, the attention of molecular neuroscientists is currently moving away from gene identification towards both cell-specific gene expression patterns (neuronal transcriptions) and protein expression/interactions (neuronal proteomics). In the long term, attention will increasingly be directed towards experimental interventions which are able to question neuronal function in a sophisticated manner that is cognisant of both transcriptomic and proteomic organization. Central to this effort will be the application of a new generation of transgenic approaches which are now evolving towards an appropriate level of molecular, temporal and spatial resolution. In this review, we summarize recent developments in transgenesis, and show how they have been applied in the principal model species for neuroscience, namely rats and mice. Current concepts of transgene design are also considered together with an overview of new genetically-encoded tools including both cellular indicators such as fluorescent activity reporters, and cellular regulators such as dominant negative signalling factors. Application of these tools in a whole animal context can be used to question both basic concepts of brain function, and also current concepts of underlying dysfuction in neurological diseases.

Animals↗

PubMed2005

Dynamic patterns of adaptive radiation.

Adaptive radiation is defined as the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. When it occurs, adaptive radiation typically follows the colonization of a new environment or the establishment of a "key innovation," which opens new ecological niches and/or new paths for evolution. Here, we take advantage of recent developments in speciation theory and modern computing power to build and explore a large-scale, stochastic, spatially explicit, individual-based model of adaptive radiation driven by adaptation to multidimensional ecological niches. We are able to model evolutionary dynamics of populations with hundreds of thousands of sexual diploid individuals over a time span of 100,000 generations assuming realistic mutation rates and allowing for genetic variation in a large number of both selected and neutral loci. Our results provide theoretical support and explanation for a number of empirical patterns including "area effect," "overshooting effect," and "least action effect," as well as for the idea of a "porous genome." Our findings suggest that the genetic architecture of traits involved in the most spectacular radiations might be rather simple. We show that a great majority of speciation events are concentrated early in the phylogeny. Our results emphasize the importance of ecological opportunity and genetic constraints in controlling the dynamics of adaptive radiation.

Adaptation, Biological↗

PubMed2004

Decoding human regulatory circuits.

Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de novo, the cis features of these CRMs, their component TFBSs, and the properties of their spatial distribution. The algorithm finds 69% of experimentally reported TFBSs and 85% of the CRMs in a reference data set of regions upstream of genes differentially expressed in skeletal muscle cells. A discriminant procedure based on the output of the model specifically discriminated regulatory sequences in muscle-specific genes in an independent test set. Application of the method to the analysis of 2710 10-kb fragments upstream of annotated human genes identified 17 novel candidate modules with a false discovery rate </=0.05, demonstrating the applicability of the method to genome-scale data.

Algorithms↗

PubMed1985

Developmental and molecular aspects of nephroblastomas induced by avian myeloblastosis-associated virus 2-O.

Avian myeloblastosis-associated virus-induced nephroblastomas are tumors consisting mainly of mesenchymal and epithelial renal elements with variable degrees of differentiation. The spatial distribution of developmental stages reflects a gradient of differentiation from less differential structures in the periphery towards more differentiated structures in the center of the lobules formed in the nephroblastomas. These heterogenic tumors contain discrete virus-cell DNA junction fragments and are therefore clonal outgrowths of a single transformed cell. These findings support the hypothesis that a mesenchymal, nephrogenic cell residual in the postembryonic kidney is the origin of the tumor, which grows by proliferation and differentiation of this target cell. All the tumors expressed higher levels of viral genomic and env messages than nontransformed tissue from the same kidney. A screening of oncogene expression with 13 different oncogenes revealed enhanced myc levels. There was, however, no rearrangement of c-myc or of the other oncogenes detected with EcoRI-digested tumor DNAs. This suggests that there is no insertion of viral elements adjacent to a c-myc. The levels of myc expression in embryonic kidneys were as high as in the tumors. Therefore, the enhanced myc expression in nephroblastomas is a reflection of the embryonic status of the tumor rather than a newly acquired function. This finding, plus the similarity of development and morphology of nephroblastomas and embryonic kidneys, suggests that the tumors arise as a result of a deficiency in a function which turns the embryonic status off.

Animals↗

PubMed1991

Homeobox genes in mouse development.

Following the discovery of the homeobox as a conserved sequence in developmentally important genes of Drosophila, a plethora of such sequences have been identified in evolutionarily distant organisms. Among mammals, the mouse homeobox genes have been studied most intensively with a hope of deciphering basic mechanisms of embryonic development. The genomic arrangement of many mouse homeobox genes is similar to the organization of the Drosophila genes, suggesting that they arose as a consequence of gene duplication and divergence from a primordial cluster during evolution. Homeobox genes encode proteins that may form a part of the autoregulatory and transregulatory network specifying positional value in the embryo. Supporting this view, the more diverged members of this growing family function as transcription factors, some of which regulate the expression of tissue-specific genes. Mouse homeobox genes are expressed during embryonic development in a spatially restricted manner and alterations in their expression pattern can disrupt embryonic development. The implications of these findings will be discussed in the context of the role of homeobox genes in the embryonic development of Drosophila and other organisms.

Amino Acid Sequence↗

PubMed1994

Adenovirus-mediated transfer of a human dystrophin gene to skeletal muscle of mdx mouse.

Due to their quiescent nature and spatial complexity, many target tissues for gene therapy will require novel strategies. An alternative to ex vivo gene transfer, providing many technical advantages and possibly allowing sufficient transfer of the therapeutic gene, is direct in vivo delivery of the vehicle. For a favorable outcome, this procedure is dependent on a high-titer vector, fully competent before post-mitotic cells. In view of the restrictions with the use of retroviruses, we investigated the potentials of adenovirus. Adenoviruses have as primary targets of infection the differentiated epithelial cell. The large DNA genome of the virus hints to a large cloning capacity. Furthermore, the wild type adenovirus has been largely used in man as a vaccine against adenovirus-induced respiratory disease. Taken together, the biological characteristics of adenovirus and the precedent of administration to humans are suggestive of adenovirus-based gene therapy for diseases involving a variety of quiescent tissues. The use of a replication-defective adenovirus carrying a gene encoding a nuclearly-targeted beta-galactosidase Ad.RSV beta gal demonstrated that replication-defective adenovirus offers an efficient means to transfer a gene for extended periods of time in the liver, muscle, lung and brain (1-6).

Adenoviridae↗

PubMed1998

Molecular and genetic ecotoxicologic approaches to aquatic environmental bioreporting.

Molecular and population genetic ecotoxicologic approaches are being developed for the utilization of arthropods as bioreporters of heavy metal mixtures in the environment. The explosion of knowledge in molecular biology, molecular genetics, and biotechnology provides an unparalleled opportunity to use arthropods as bioreporter organisms. Interspecific differences in aquatic arthropod populations have been previously demonstrated in response to heavy metal insult in the Arkansas River (AR) California Gulch Superfund site (CGSS). Population genetic analyses were conducted on the mayfly Baetis tricaudatus. Genetic polymorphisms were detected in polymerase chain reaction amplified 16S mitochondrial rDNA (a selectively neutral gene) of B tricaudatus using single-strand conformation polymorphism analysis. Genetic differences may have resulted from impediments to gene flow in the population caused by mortality arising from exposure to heavy metal mixture pollution. In laboratory studies a candidate metal-responsive mucinlike gene, which is metal and dose specific, has been identified in Chironomus tentans and other potential AR-CGSS bioreporter species. Population genetic analyses using the mucinlike gene may provide insight into the role of this selectable gene in determining the breeding structure of B. tricaudatus in the AR-CGSS and may provide mechanistic insight into determinants of aquatic arthropod response to heavy metal insult. Metal-responsive (MR) genes and regulatory sequences are being isolated, characterized, and assayed for differential gene expression in response to heavy metal mixture pollution in the AR-CGSS. Identified promoter sequences can then be engineered into previously developed MR constructs to provide sensitive in vitro assays for environmental bioreporting of heavy metal mixtures. The results of the population genetic studies are being entered into an AR geographic information system that contains substantial biological, chemical, and geophysical information. Integrated spatial, structural, and temporal analyses of these parameters will provide invaluable information concerning environmental determinants that restrict or promote gene flow in bioreporter populations.

Aedes↗

PubMed1987

Molecular analysis of the neurogenic locus Enhancer of split of Drosophila melanogaster.

Enhancer of split [E(spl)], one of the neurogenic loci of Drosophila, is located in bands 96F8-13. One hundred and fifty kilobases of genomic DNA, spanning the E(spl) locus, were cloned by chromosomal walking. DNA heterogeneities associated with eleven E(spl) mutations, including three Pr alleles, were mapped to a region of 36 kb, and an additional one outside of this region. One of these mutations is a deletion of 34 kb that causes severe neural hyperplasia of homozygous embryos with complete penetrance. Mutations associated with DNA polymorphisms mapping within smaller regions do not lead to a fully penetrant neurogenic phenotype. The 36-kb region encodes 11 major transcripts, which exhibit distinct temporal and/or spatial patterns of expression. The expression of one of these transcripts is modified in two different mutants. In addition, one of the mutants [E(spl)] shows another transcript, which is not present in the wild-type and co-exists with the remaining transcripts. We suggest that more than one of the 11 transcripts are necessary for a normal function of the E(spl) locus. The spatial distribution of four of these RNAs, which exhibit almost identical patterns of expression, strongly suggests that the encoded proteins are required for the process of segregation of neural and epidermal lineages.

Journal Article↗

PubMed1991

Molecular evolution of eastern equine encephalomyelitis virus in North America.

We examined the rate and spatial pattern of eastern equine encephalomyelitis virus (EEEV) evolution in North America using primer-extension sequencing of viral RNA. Nucleotide sequences of the entire 26 S structural gene region of four EEEV strains revealed remarkable conservation between 1933 and 1985, with an estimated 0.7% divergence or 1.4 x 10(-4) nucleotide substitutions per site per year. Sequences from smaller 26 S regions of nine additional strains suggested that EEEV evolves in North America in a single lineage, with genetic exchange regularly occurring among enzootic transmission foci. In these limited 26 S genome regions, only synonymous nucleotide substitutions became fixed between 1933 and 1988, implying a high degree of conservation in protein structure. Short nucleotide sequences from a Panamanian, South American variety isolate revealed a relatively distant relationship to North American serotype viruses. This suggested genetic divergence between antigenic varieties, and independent evolution of EEEV in North and South America. Factors related to replication and epidemiology of EEEV, which may constrain its evolution in nature, are discussed. Possible mechanisms of genetic exchange among enzootic foci are also considered.

Amino Acid Sequence↗

PubMed2002

Developmental expression of the T-box transcription factor T-bet/Tbx21 during mouse embryogenesis.

A novel type of DNA-binding domain, the 'T-box' domain, characterizes an increasingly large family of transcription factors (Trends Genet. 15 (1999) 154). We have identified and characterized the expression pattern of a new member of the Tbr1 subfamily of T-box genes; this gene has been recently named T-bet/Tbx21 (Genomics 70 (2000) 41; Cell 17 (2000) 655; Science 292 (2001) 1907; Science 295 (2002) 338). The sequence and expression of Tbr1 and eomesodermin/Tbr2 are closely related to T-bet/Tbx21. The expression of Tbr1 (Neuron 15 (1995) 63) and Tbr2 (Mech Dev 84 (1999) 133) have virtually identical onset, at around E10.5, and expression domains in the mouse telencephalon. While Tbr1 is expressed in postmitotic neurons, Tbr2 (which is also expressed during gastrulation is also expressed in neural progenitors. We have used in situ hybridization to determine the temporal and spatial distribution of T-bet/Tbx21 expression during mouse development. T-bet/Tbx21 expression is exclusively restricted to the olfactory bulb and the thymus. To assess the distribution of T-BET/TBX21 expression in the haematopoietic compartment we used reverse transcriptase-polymerase chain reaction and found its expression in several human blood cell lineages, including progenitors/stem cells, immature B cells and peripheral T cells.

Amino Acid Sequence↗