The Experts below are selected from a list of 153 Experts worldwide ranked by ideXlab platform
Dan Larhammar - One of the best experts on this subject based on the ideXlab platform.
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Evolution of the neuropeptide Y family: new genes by Chromosome Duplications in early vertebrates and in teleost fishes.
General and Comparative Endocrinology, 2007Co-Authors: Görel Sundström, Tomas A. Larsson, Sydney Brenner, Byrappa Venkatesh, Dan LarhammarAbstract:Despite sequence information from many vertebrates the evolution of the neuropeptide Y (NPY) family of peptides has been difficult to resolve, particularly among ray-finned fishes. We have used chromosomal location and sequence analyses to identify orthologs and gene duplicates in teleost fish genomes. Our analyses support origin of NPY and peptide YY (PYY) from a common ancestor in early vertebrate evolution through a Chromosome Duplication. We report here that the teleost tetraploidization generated duplicates of both NPY and PYY and that all four genes are still present in the two sequenced pufferfish genomes Tetraodon nigroviridis and Takifugu rubripes as well as three-spined stickleback, Gasterosteus aculeatus. The zebrafish Danio rerio NPYb gene has probably been lost whereas medaka, Oryzias latipes seems to lack PYYb. Some of the previously published PYY sequences were misidentified and actually constitute NPYb. Our analyses confirm that the peptide previously named PY in some fish species is a duplicate of the PYY gene and hence should be called PYYb. The NPYa and NPYb genes in Takifugu rubripes are predominantly expressed in brain, as detected by RT-PCR, whereas PYYa and PYYb are expressed in several organs including brain, intestine and gonads. Thus, also the resemblance in expression pattern supports the fish gene Duplication scenario. Our study shows that when sequence comparisons give ambiguous results, chromosomal location can serve as a useful criterion to identify orthologs. This strategy may help to resolve relationships in several families of short peptides.
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Novel neuropeptide Y Y2-like receptor subtype in zebrafish and frogs supports early vertebrate Chromosome Duplications.
Journal of Molecular Evolution, 2004Co-Authors: Robert Fredriksson, Earl T. Larson, John H. Postlethwait, Dan LarhammarAbstract:The Y receptors comprise a family of G-protein coupled receptors with neuropeptide Y-family peptides as endogenous ligands. The Y receptor family has five members in mammals and evolutionary data suggest that it diversified in the two genome Duplications proposed to have occurred early in vertebrate evolution. If this theory holds true, it allows for additional family members to be present. We describe here the cloning, pharmacological characterization, tissue distribution, and chromosomal localization of a novel subtype of the Y-receptor family, named Y7, from the zebrafish. We also present Y7 sequences from rainbow trout and two amphibians. The new receptor is most similar to Y2, with 51–54% identity. As Y2 has also been cloned from some of these species, there clearly are two separate Y2-subfamily genes. Chromosomal mapping in zebrafish supports origin of Y7 as a duplicate of Y2 by Chromosome Duplication in an early vertebrate. Y7 has probably been lost in the lineage leading to mammals. The pharmacological profile of the zebrafish Y7 receptor is different from mammalian Y2, as it does not bind short fragments of NPY with a high affinity. The Y7 receptor supports the theory of early vertebrate genome Duplications and suggests that the Y family of receptors is a result of these early genome Duplications.
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The Human Hox-bearing Chromosome Regions Did Arise by Block or Chromosome (or Even Genome) Duplications
Genome Research, 2002Co-Authors: Dan Larhammar, Lars-gustav Lundin, Finn HallböökAbstract:Many Chromosome regions in the human genome exist in four similar copies, suggesting that the entire genome was duplicated twice in early vertebrate evolution, a concept called the 2R hypothesis. Forty-two gene families on the four Hox-bearing Chromosomes were recently analyzed by others, and 32 of these were reported to have evolutionary histories incompatible with Duplications concomitant with the Hox clusters, thereby contradicting the 2R hypothesis. However, we show here that nine of the families have probably been translocated to the Hox-bearing Chromosomes more recently, and that three of these belong to other Chromosome quartets where they actually support the 2R hypothesis. We consider 13 families too complex to shed light on the Chromosome Duplication hypothesis. Among the remaining 20 families, 14 display phylogenies that support or are at least consistent with the Hox-cluster Duplications. Only six families seem to have other phylogenies, but these trees are highly uncertain due to shortage of sequence information. We conclude that all relevant and analyzable families support or are consistent with block/Chromosome Duplications and that none clearly contradicts the 2R hypothesis.
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zebrafish genes for neuropeptide y and peptide yy reveal origin by Chromosome Duplication from an ancestral gene linked to the homeobox cluster
Journal of Neurochemistry, 2002Co-Authors: Charlotte Soderberg, John H. Postlethwait, Amanda Wraith, Maria Ringvall, Lennart Brodin, Dan LarhammarAbstract:Zebrafish genes for neuropeptide Y and peptide YY reveal origin byChromosome Duplication from an ancestral gene linked to the homeoboxcluster.
Karim Labib - One of the best experts on this subject based on the ideXlab platform.
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Chromosome Duplication in saccharomyces cerevisiae
Genetics, 2016Co-Authors: Stephen P Bell, Karim LabibAbstract:The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G 1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation.
Maria Antonietta Germanà - One of the best experts on this subject based on the ideXlab platform.
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Anther culture for haploid and doubled haploid production
Plant Cell Tissue and Organ Culture (PCTOC), 2011Co-Authors: Maria Antonietta GermanàAbstract:Haploids are plants with a gametophytic Chromosome number and doubled haploids are haploids that have undergone Chromosome Duplication. The production of haploids and doubled haploids (DHs) through gametic embryogenesis allows a single-step development of complete homozygous lines from heterozygous parents, shortening the time required to produce homozygous plants in comparison with the conventional breeding methods that employ several generations of selfing. The production of haploids and DHs provides a particularly attractive biotechnological tool, and the development of haploidy technology and protocols to produce homozygous plants has had a significant impact on agricultural systems. Nowadays, these biotechnologies represent an integral part of the breeding programmes of many agronomically important crops. There are several available methods to obtain haploids and DHs, of which in vitro anther or isolated microspore culture are the most effective and widely used. This review article deals with the current status of knowledge on the production of haploids and DHs through pollen embryogenesis and, in particular, anther culture.
Stephen P Bell - One of the best experts on this subject based on the ideXlab platform.
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Chromosome Duplication in saccharomyces cerevisiae
Genetics, 2016Co-Authors: Stephen P Bell, Karim LabibAbstract:The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G 1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation.
Christian J. Rudolph - One of the best experts on this subject based on the ideXlab platform.
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A role for 3′ exonucleases at the final stages of Chromosome Duplication in Escherichia coli
Nucleic Acids Research, 2019Co-Authors: Sarah L. Midgley-smith, Juachi U. Dimude, Christian J. RudolphAbstract:Chromosome Duplication initiates via the assembly of replication fork complexes at defined origins, from where they proceed in opposite directions until they fuse with a converging fork. Recent work highlights that the completion of DNA replication is highly complex in both pro- and eukaryotic cells. In this study we have investigated how 3′ and 5′ exonucleases contribute towards the successful termination of Chromosome Duplication in Escherichia coli. We show that the absence of 3′ exonucleases can trigger levels of over-replication in the termination area robust enough to allow successful Chromosome Duplication in the absence of oriC firing. Over-replication is completely abolished if replication fork complexes are prevented from fusing by Chromosome linearization. Our data strongly support the idea that 3′ flaps are generated as replication fork complexes fuse. In the absence of 3′ exonucleases, such as ExoI, these 3′ flaps can be converted into 5′ flaps, which are degraded by 5′ exonucleases, such as ExoVII and RecJ. Our data support the idea that multiple protein activities are required to process fork fusion intermediates. They highlight the complexity of fork fusions and further support the idea that the termination area evolved to contain fork fusion-mediated pathologies.
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the consequences of replicating in the wrong orientation bacterial Chromosome Duplication without an active replication origin
Mbio, 2015Co-Authors: Juachi U. Dimude, Anna Stockum, Sarah L Midgleysmith, Amy L Upton, Helen A Foster, Arshad Khan, Nigel J Saunders, Renata Retkute, Christian J. RudolphAbstract:ABSTRACT Chromosome replication is regulated in all organisms at the assembly stage of the replication machinery at specific origins. In Escherichia coli, the DnaA initiator protein regulates the assembly of replication forks at oriC. This regulation can be undermined by defects in nucleic acid metabolism. In cells lacking RNase HI, replication initiates independently of DnaA and oriC , presumably at persisting R-loops. A similar mechanism was assumed for origin-independent synthesis in cells lacking RecG. However, recently we suggested that this synthesis initiates at intermediates resulting from replication fork fusions. Here we present data suggesting that in cells lacking RecG or RNase HI, origin-independent synthesis arises by different mechanisms, indicative of these two proteins having different roles in vivo . Our data support the idea that RNase HI processes R-loops, while RecG is required to process replication fork fusion intermediates. However, regardless of how origin-independent synthesis is initiated, a fraction of forks will proceed in an orientation opposite to normal. We show that the resulting head-on encounters with transcription threaten cell viability, especially if taking place in highly transcribed areas. Thus, despite their different functions, RecG and RNase HI are both important factors for maintaining replication control and orientation. Their absence causes severe replication problems, highlighting the advantages of the normal Chromosome arrangement, which exploits a single origin to control the number of forks and their orientation relative to transcription, and a defined termination area to contain fork fusions. Any changes to this arrangement endanger cell cycle control, Chromosome dynamics, and, ultimately, cell viability. IMPORTANCE Cell division requires unwinding of millions of DNA base pairs to generate the template for RNA transcripts as well as Chromosome replication. As both processes use the same template, frequent clashes are unavoidable. To minimize the impact of these clashes, transcription and replication in bacteria follow the same directionality, thereby avoiding head-on collisions. This codirectionality is maintained by a strict regulation of where replication is started. We have used Escherichia coli as a model to investigate cells in which the defined location of replication initiation is compromised. In cells lacking either RNase HI or RecG, replication initiates away from the defined replication origin, and we discuss the different mechanisms by which this synthesis arises. In addition, the resulting forks proceed in a direction opposite to normal, thereby inducing head-on collisions between transcription and replication, and we show that the resulting consequences are severe enough to threaten the viability of cells.