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At least 541 records · Page 30Linked to original sources
PubMed2002

Spatial organisation and behaviour of the parental chromosome sets in the nuclei of Saccharomyces cerevisiae x S. paradoxus hybrids.

We demonstrate that the genomes of Saccharomyces cerevisiae and S. paradoxus are sufficiently divergent to allow their differential labeling by genomic in situ hybridisation (GISH). The cytological discrimination of the genomes allowed us to study the merging of the two genomes during hybrid mating. GISH revealed that in hybrid nuclei the two genomes are intermixed. In hybrid meiosis, extensive intraspectific nonhomologous pairing takes place. GISH on chromosome addition and substitution strains (with chromosomes of S. paradoxus added to or replacing the homoeologous chromosome of an otherwise S. cerevisiae background) was used to delineate individual chromosomes at interphase and to examine various aspects of chromosome structure and arrangement.

Cell Nucleus↗
PubMed2006

Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex.

We have determined the genomic sequences of four virulent myophages, Bcep1, Bcep43, BcepB1A, and Bcep781, whose hosts are soil isolates of the Burkholderia cepacia complex. Despite temporal and spatial separations between initial isolations, three of the phages (Bcep1, Bcep43, and Bcep781, designated the Bcep781 group) exhibit 87% to 99% sequence identity to one another and most coding region differences are due to synonymous nucleotide substitutions, a hallmark of neutral genetic drift. Phage BcepB1A has a very different genome organization but is clearly a mosaic with respect to many of the genes of the Bcep781 group, as is a defective prophage element in Photorhabdus luminescens. Functions were assigned to 27 out of 71 predicted genes of Bcep1 despite extreme sequence divergence. Using a lambda repressor fusion technique, 10 Bcep781-encoded proteins were identified for their ability to support homotypic interactions. While head and tail morphogenesis genes have retained canonical gene order despite extreme sequence divergence, genes involved in DNA metabolism and host lysis are not organized as in other phages. This unusual genome arrangement may contribute to the ability of the Bcep781-like phages to maintain a unified genomic type. However, the Bcep781 group phages can also engage in lateral gene transfer events with otherwise unrelated phages, a process that contributes to the broader-scale genomic mosaicism prevalent among the tailed phages.

Amino Acid Sequence↗
PubMed2005

Genotypic diversity within a natural coastal bacterioplankton population.

The genomic diversity and relative importance of distinct genotypes within natural bacterial populations have remained largely unknown. Here, we analyze the diversity and annual dynamics of a group of coastal bacterioplankton (greater than 99% 16S ribosomal RNA identity to Vibrio splendidus). We show that this group consists of at least a thousand distinct genotypes, each occurring at extremely low environmental concentrations (on average less than one cell per milliliter). Overall, the genomes show extensive allelic diversity and size variation. Individual genotypes rarely recurred in samples, and allelic distribution did not show spatial or temporal substructure. Ecological considerations suggest that much genotypic and possibly phenotypic variation within natural populations should be considered neutral.

Alleles↗
PubMed2026

Convergent methodologies in prosthetic joint infection research: integrating transdisciplinary approaches to understand and prevent biofilm-driven failure of orthopaedic prostheses.

Prosthetic joint infections (PJIs) remain among the most devastating complications of arthroplasty, imposing substantial clinical, economic and patient burdens. Although culture-based diagnostics underpin current clinical practice, PJIs are biofilm-driven infections shaped by taxonomic diversity, spatial organization, host responses and surface interactions, meaning conventional approaches provide only a partial and often decontextualized view of the infection process. We examine how convergent methodologies can transform PJI research by integrating approaches that have traditionally been studied in isolation, including sequencing, transcriptomics, metabolomics, advanced imaging and culture-based characterization. We discuss how whole-genome sequencing, shotgun metagenomics, transcriptomic and metabolomic approaches resolve pathogen identity, functional activity and adaptive persistence and how cross-scale imaging and spatial biology techniques reveal where microbes colonize, interact and survive across implant surfaces. We highlight emerging opportunities to unify these datasets into coherent frameworks that capture both the molecular and physical dimensions of PJIs. Integrating these complementary approaches will enable a multi-layered understanding of PJIs that link composition, function and spatial organization. Ultimately, this provides a foundation for predictive diagnostics, precision antimicrobial strategies and improved implant design and supports a shift towards more effective, mechanism-informed management of implant-associated infection.

Prosthesis-Related Infections↗
PubMed2005

Evidence for a dispersed Hox gene cluster in the platyhelminth parasite Schistosoma mansoni.

In most bilaterian organisms so far studied, Hox genes are organized in genomic clusters and determine development along the anteroposterior axis. It has been suggested that this clustering, together with spatial and temporal colinearity of gene expression, represents the ancestral condition. However, in organisms with derived modes of embryogenesis and lineage-dependent mechanisms for the determination of cell fate, temporal colinearity of expression can be lost and Hox cluster organization disrupted, as is the case for the ecdysozoans Drosophila melanogaster and Caenorhabditis elegans and the urochordates Ciona intestinalis and Oikopleura dioica. We sought to determine whether a lophotrochozoan, the platyhelminth parasite Schistosoma mansoni, possesses a conserved or disrupted Hox cluster. Using a polymerase chain reaction (PCR)-based strategy, we have cloned and characterized three novel S. mansoni genes encoding orthologues of Drosophila labial (SmHox1), deformed (SmHox4), and abdominal A (SmHox8), as well as the full-length coding sequence of the previously described Smox1, which we identify as an orthologue of fushi tarazu. Quantitative reverse transcriptase-PCR showed that the four genes were expressed at all life-cycle stages but that levels of expression were differentially regulated. Phylogenetic analysis and the conservation of "parapeptide" sequences C-terminal to the homeodomains of SmHox8 and Smox1 support the grouping of platyhelminths within the lophotrochozoan clade. However, Bacterial Artificial Chromosome (BAC) library screening followed by genome walking failed to reconstitute a cluster. The BAC clones containing Hox genes were sequenced, and in no case were other Hox genes found on the same clone. Moreover, the SmHox4 and SmHox8 genes contained single very large introns (>40 kbp) further indicating that the schistosome Hox cluster is highly extended. Localization of the Hox genes to chromosomes using fluorescence in situ hybridization showed that SmHox4 and SmHox8 are on the long arm of chromosome 4, whereas SmHox1 and Smox1 are on chromosome 3. In silico screening of the available genome sequences corroborated results of Southern blotting and BAC library screening that indicate that there are no paralogues of SmHox1, SmHox4, or SmHox8. The schistosome Hox cluster is therefore not duplicated, but is both dispersed and disintegrated in the genome.

Amino Acid Sequence↗
PubMed2006

Insect iron binding proteins: insights from the genomes.

Sequencing of the genomes of Drosophila melanogaster, Anopheles gambiae, Apis mellifera, and Bombyx mori provided an opportunity to examine the diversity and organization of genes encoding insect transferrins (Tsf) and ferritins. Information obtained from the genomes significantly advances our knowledge of these major players in insect iron metabolism and complements the results of molecular studies on their temporal, spatial, and inducible expression pattern and regulatory mechanisms conducted in diverse insect species. Analysis of genes encoding new members of the Tsf family and non-secreted ferritin subunits allows making preliminary hypotheses about their possible functions and opens possibilities to study lesser-known aspects of insect iron homeostasis. Proteomic and gene expression studies that followed the whole genome sequencing quickly contribute to defining or better understanding of the important and diverse biological roles of Tsf and ferritin, particularly their involvement in insect's defenses against oxidative stress and infection.

Amino Acid Sequence↗
PubMed1986

Large mitochondrial genome and mitochondrial DNA size polymorphism in the mosquito parasite, Romanomermis culicivorax.

Physical characterization of the mitochondrial genome derived from the obligate mosquito parasite, Romanomermis culicivorax has generated some surprising physical properties regarding the molecular structure of nematode mitochondrial DNA (mtDNA). Restriction enzyme analysis of this mtDNA has revealed a mitochondrial genome size of approximately 26 kb, the largest metazoan mtDNA reported to date. Isofemale lineages are monomorphic for one of three size variants, differing by 500-1,000 base pairs, present in our original field population. Cloned hybridization probes derived from a single region exhibiting a 600 bp size polymorphism share strong homology with several spatially separated sites distributed about the mtDNA. This suggests that the homology is a result of repeated DNA sequence elements contained within this mitochondrial genome that contribute to mtDNA size polymorphism.

Animals↗
PubMed2025

The functional organization of chromosome territories in single nuclei during zygotic genome activation.

Chromosome territories (CTs) are intricately organized and regulated within the nucleus. Despite remarkable advances in our understanding of genome packaging and gene expression, the interplay among CTs, pairing of parental homologous chromosomes, and genome function during development remains elusive. Here, we employ an Oligopaints-based high-resolution imaging approach to examine variable CT organization in single nuclei during the developmental process of zygotic genome activation. We reveal large-scale chromosome changes with extensive homolog pairing at the whole-chromosome level that decreases locally due to spatial variability in chromosome conformations. In the absence of one homolog copy, the dynamics of CT compaction and RNA polymerase II recruitment are supported by transcriptional changes in haploid embryos. Finally, global inhibition of transcription results in decreased CT opening and no significant impact on CT pairing levels. These findings enhance our understanding of parental genome folding and regulation, which may inform strategies for chromosome-based diseases.

RNA polymerase II↗
PubMed2005

Single-cell genomics.

The evolution of higher plants depended on the ability of cells to express hereditary information in many different ways and led to the development of specialized cell types, reflecting an elaborate system of control over gene expression in the individual component cells of various tissues. Bulk tissue sampling results in the loss of spatial resolution, and recent efforts have been directed toward improving access to specialized cell types in plants. Access to the contents of individual cells followed by analyses using post-genomic technologies promise to revolutionize our understanding of the differentiation of specialized cell types, and to enable downstream applications aimed at harnessing their unique biochemical properties.

Genetic Techniques↗
PubMed2026

From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.

Sugarcane (Saccharum spp.) underpins global sugar and bioenergy supply and is increasingly valued as a renewable biomass feedstock. Sustained improvement in commercial traits and resilience is constrained by long breeding cycles, clonal propagation, multi-stage testing, and a highly polyploid, heterozygous, and frequently aneuploid genome with substantial non-additive genetic variation. Genomic selection has demonstrated value for predicting elite-clone performance, yet its operational use remains limited at earlier decision points, including family selection, parent evaluation, and cross design. This review examines the biological, statistical, and genomic factors that shape these decisions, with emphasis on the Australian breeding context based on progeny assessment trials (PATs), clonal assessment trials (CATs), and final assessment trials (FATs). We evaluate challenges arising from family plot means, the use of different full-sib samples as nominal family replicates, spatial heterogeneity, competition, genotype-by-environment interaction, and the partitioning of additive and non-additive effects. We also assess the integration of pedigree and genomic relationship, genotype representation, allele-dosage estimation, aneuploidy, genomic prediction models, and training-population design. We then consider genomic prediction of cross performance and constrained mate allocation as approaches for improving expected family performance, accounting for cross-specific non-additive effects and managing relatedness. We propose a decision-centred framework that links family and clonal data across breeding stages, tracks the propagation of information and uncertainty, and supports parent recycling and cross allocation. We conclude with a practical research agenda for stage-integrated mixed-model and single-step analyses that connect early family evaluation with genomic prediction and cross-level decision support in sugarcane breeding.

Saccharum↗
PubMed2005

Using genome scans of DNA polymorphism to infer adaptive population divergence.

Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome-wide patterns of DNA polymorphism to detect the locus-specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying selection on polygenic traits can be expected to produce predictable patterns of allelic variation at the underlying quantitative trait loci (QTL), and whether the locus-specific effects of selection can be reliably detected against the genome-wide backdrop of stochastic variability. I then review different approaches that have been developed to identify loci involved in adaptive population divergence and I discuss the relative merits of model-based approaches that rely on assumptions about population structure vs. model-free approaches that are based on empirical distributions of summary statistics. Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence.

Adaptation, Biological↗
PubMed2006

Natural selection and climate change: temperature-linked spatial and temporal trends in gene frequency in Fagus sylvatica.

Rapid increases in global temperature are likely to impose strong directional selection on many plant populations, which must therefore adapt if they are to survive. Within populations, microgeographic genetic differentiation of individuals with respect to climate suggests that some populations may adapt to changing temperatures in the short-term through rapid changes in gene frequency. We used a genome scan to identify temperature-related adaptive differentiation of individuals of the tree species Fagus sylvatica. By combining molecular marker and dendrochronological data we assessed spatial and temporal variation in gene frequency at the locus identified as being under selection. We show that gene frequency at this locus varies predictably with temperature. The probability of the presence of the dominant marker allele shows a declining trend over the latter half of the 20th century, in parallel with rising temperatures in the region. Our results show that F. sylvatica populations may show some capacity for an in situ adaptive response to climate change. However as reported ongoing distributional changes demonstrate, this response is not enough to allow all populations of this species to persist in all of their current locations.

Alleles↗
PubMed2006

Spatial and temporal expression of MFRP and its interaction with CTRP5.

PURPOSE: Mutations in the membrane frizzled-related protein (MFRP) gene cause nanophthalmos in humans, and a splice site mutation causes recessive retinal degeneration in the rd6 mouse. In human and mouse genomes, the MFRP gene lies adjoining to the complement 1q tumor necrosis factor-related protein 5 (CTRP5/C1QTNF5) gene involved in causing retinal degeneration and abnormal lens zonules in human. The purpose of this study was to characterize the spatial and temporal expression of the mouse Mfrp gene, determine tissue and subcellular localization of MFRP protein, and study its interaction with CTRP5. METHODS: Expression of the Mfrp gene in the mouse was studied by quantitative (q)RT-PCR. MFRP protein expression and distribution were studied by Western blot analysis, immunohistochemistry, and immunoelectron microscopy. Interaction with CTRP5 was studied by immunoprecipitation and immunoblot analysis, using mouse eye and human retinal pigmented epithelium (RPE) choroid extracts and by expressing full-length CTRP5 and MFRP in a heterologous system. RESULTS: The Mfrp gene is specifically expressed in RPE and ciliary body (CB), and its expression starts during early stages of embryogenesis. In the albino mouse eye, MFRP is localized to the apical and basal membranes of RPE and ciliary epithelium (CE). In addition, MFRP and CTRP5 were found to colocalize in RPE, CE, and MDCK cells, a general model of polarized epithelia. These proteins interact with each other in ocular tissues and also in a heterologous system. CONCLUSIONS: MFRP is localized to the plasma membrane of CE and RPE, and colocalizes and interacts with CTRP5 indicating a functional relationship between these two proteins.

Animals↗
PubMed1998

Dissection of cis-regulatory elements of the Drosophila gene Serrate.

The Drosophila gene Serrate encodes a membrane spanning protein, which is expressed in a complex pattern during embryogenesis and larval stages. Loss of Serrate function leads to larval lethality, which is associated with several morphogenetic defects, including the failure to develop wings and halteres. Serrate has been suggested to act as a short-range signal during wing development. It is required for the induction of the organising centre at the dorsal/ventral compartment boundary, from which growth and patterning of the wing is controlled. In order to understand the regulatory network required to control the spatially and temporally dynamic expression of Serrate, we analysed its cis-regulatory elements by fusing various genomic fragments upstream of the reporter gene lacZ. Enhancer elements reflecting the expression pattern of endogenous Serrate in embryonic and postembryonic tissues could be confined to 26 kb of genomic DNA, including 9 kb of transcribed region. Expression in some embryonic tissues is under the control of multiple enhancers located in the 5' region and in intron sequences. The data presented here provide the tools to unravel the genetic network which regulates Serrate during different developmental stages in diverse tissues.

Animals↗
PubMed2002

Antiprogestin-controllable transgene regulation in vivo.

Gene control systems that provide temporal and spatial regulation of transgene expression in response to orally delivered drugs are needed for advances in functional genomics, models of human disease and gene therapy. A regulation system based on the altered binding and activation properties of a truncated ligand-binding domain derived from the progesterone receptor has been shown to be effective in providing tissue-specific, antiprogestin-controllable gene expression in transgenic mice, transgenic fruit flies and animals that have been administered viral-based or plasmid-based gene therapy vectors.

Animals↗
PubMed1998

Cloning and characterization of the Drosophila homologue of the AP-2 transcription factor.

The AP-2 family of transcription factors (AP-2alpha, AP-2beta and AP-2gamma) is temporally and spatially regulated in mammals and has also been implicated in oncogenesis. Here we report the isolation of genomic and cDNA clones encoding the Drosophila homologue of AP-2, designated DAP-2. The predicted amino acid sequence exhibits 42-45% overall identity with the vertebrate AP-2 proteins. A sequence of 107 amino acids within the DNA binding and dimerization domain of the vertebrate AP-2 proteins is highly conserved (90-92%) with the DAP-2 homologue. An in vitro translation product of DAP-2 cDNA binds specifically to AP-2 consensus binding sites. DAP-2 was also shown to be functionally conserved in vivo because transient transfection of a DAP-2 expression plasmid activated transcription through AP-2 binding sites in both mammalian and Drosophila cell lines. DAP-2 is expressed during early embryogenesis and DAP-2 transcripts are also detected in the adult. Whole-mount in situ hybridizations demonstrated that DAP-2 is expressed initially at stage 9 of Drosophila embryonic development and that DAP-2 transcripts are detected in regions of the brain, eye-antennal disc, optical lobe, antenno-maxillary complex, and in a subset of cells of the ventral nerve cord. The cloning of DAP-2 and the identification of the DAP-2 expression pattern during embryogenesis provides a starting point to address the function of AP-2 during differentiation and development in a well understood model system.

Amino Acid Sequence↗
PubMed1996

Embryonic development and pattern formation.

During embryogenesis, information encoded in the genome is translated into cell proliferation, morphogenesis, and early stages of differentiation. Embryonic pattern arises from the spatial and temporal regulation and coordination of these events. The vitamin A (retinol) derivative retinoic acid (RA) is essential for normal development. Mammalian embryos are protected against vitamin A deficiency by maternal retinoid homeostasis until stored retinoids fall to very low levels. Retinol binding protein, which is synthesized in the yolk sac placenta of rodent embryos and in the syncytiotrophoblast of the human placenta, is essential for access of retinol to the embryo. Synthesis and metabolism of RA may involve cytoplasmic binding proteins, but the observation that mutants lacking these proteins are normal or near-normal suggests that they are not essential. Severe congenital vitamin A deficiency results in a spectrum of malformations including defects of the eye, lungs, cardiovascular system, and urogenital system. Extreme deficiency results as well in forelimb abnormalities and cleft face, but the embryos are not viable. Similar abnormalities are observed in embryos lacking two retinoid receptors, but loss of one receptor results in either normal development or mild abnormalities. Two single-receptor null mutants, RARgamma-/- and RXRalpha-/-, show regional pattern-specific resistance to teratogenic levels of RA. Mutations leading to abnormality of the structure or regulation of RA signaling pathway genes may be an important cause of human congenital abnormality.

Abnormalities, Multiple↗
PubMed1993

The irregular chiasm C-roughest locus of Drosophila, which affects axonal projections and programmed cell death, encodes a novel immunoglobulin-like protein.

The axonal projection mutations irregular chiasm C of Drosophila melanogaster comap and genetically interact with the roughest locus, which is required for programmed cell death in the developing retina. We cloned the genomic region in 3C5 by transposon tagging and identified a single transcription unit that produces a major, spatially and temporally regulated mRNA species of approximately 5.0 kb. Postembryonic expression is strong in the developing optic lobe and in the eye imaginal disc. The gene encodes a transmembrane protein of 764 amino acids with five extracellular immunoglobulin-like domains and similarity to the chicken axonal surface glycoprotein DM-GRASP/SC1/BEN. Both known irreC alleles reduce the level of transcription, whereas the roughestCT mutation disrupts the intracellular domain of the protein.

Alleles↗