Integrative plasmid vector for constructing single-copy reporter systems to study gene regulation in Rhizobium meliloti and related species

Plasmid ◽  
2004 ◽  
Author(s):  
S FERENCZI
Keyword(s):  
Gene Regulation ◽  
Related Species ◽  
Rhizobium Meliloti ◽  
Plasmid Vector ◽  
Single Copy ◽  
Integrative Plasmid ◽  
Reporter Systems ◽  
Study Gene Regulation

Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 423-434
Author(s):  
Jan Dvorřák ◽  
Ming-Cheng Luo ◽  
Zu-Li Yang
Keyword(s):  
Related Species ◽  
Gene Diversity ◽  
Single Copy ◽  
Species Variation ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Phylogenetic Status ◽  
Average Gene ◽  
Genomic Regions ◽  
Chromosome Regions

Abstract RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

scholarly journals Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sajjad Asaf ◽  
Abdul Latif Khan ◽  
Muhammad Numan ◽  
Ahmed Al-Harrasi
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Evolutionary Genetics ◽  
Single Copy ◽  
Avicennia Marina ◽  
Pairwise Distance ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mangrove Tree ◽  
High Degree

AbstractAvicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

scholarly journals Expression of thaumatin, a new type of alternative sweetener in rice

2020 ◽  
Vol 48 (3) ◽  
pp. 1276-1291
Author(s):  
Shahina AKTER ◽  
Md. Amdadul HUQ ◽  
Yu-Jin JUNG ◽  
Kwon-Kyoo KANG
Keyword(s):  
Transgenic Rice ◽  
Oryza Sativa L ◽  
Plasmid Vector ◽  
Single Copy ◽  
Cauliflower Mosaic Virus ◽  
Pcr Analysis ◽  
35S Promoter ◽  
Alternative Sweetener ◽  
Sweet Proteins ◽  
Transgenic Lines

  Sweet proteins are the natural alternative to the artificial sweeteners as well as flavor enhancers. Among other sweet protein, thaumatin protein was isolated from Thaumatococcus daniellii Benth plant fruit. In this study, pinII Ti plasmid vector was constructed with thaumatin gene, where thaumatin was placed under the control of the duel cauliflower mosaic virus 35S promoter into rice (Oryza sativa L. var. japonica cv. ‘Dongjinbyeo’) by Agrobacterium-mediated transformation to generate transgenic plants. Thirteen plant lines were regenerated and the transgenic rice lines were confirmed by different molecular analysis. The genomic PCR result revealed that all of the plant lines were transgenic. The single copy and intergenic plant lines were selected by Taqman PCR analysis and FST analysis, respectively. Expression of thaumatin gene in transgenic rice resulted in the accumulation of thaumatin protein in the leave. Thaumatin protein was also accumulated in leave of T1 generation. Sensory analysis result suggested that the thaumatin protein expressing transgenic lines exerted sweet tasting activity. These results demonstrated that thaumatin was expressed in transgenic rice plants.

scholarly journals Independent Regulation of MucD, an HtrA-Like Protease in Pseudomonas aeruginosa, and the Role of Its Proteolytic Motif in Alginate Gene Regulation

2006 ◽  
Vol 188 (8) ◽  
pp. 3134-3137 ◽  
Author(s):  
Lynn F. Wood ◽  
Dennis E. Ohman
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Regulation ◽  
Transcriptional Start Site ◽  
Single Copy ◽  
Start Site ◽  
Temperature Resistance

ABSTRACT Expression of mucD, encoding a homologue of the HtrA(DegP) family of endoserine proteases, was investigated in Pseudomonas aeruginosa. Expressed from the algT-mucABCD operon, MucD was detected in mucoid (FRD1) and nonmucoid (PAO1) parental strains and also when polar insertions were placed upstream in algT or mucB. A transcriptional start site for a mucD promoter (PmucD) was mapped within mucC. Expression of single-copy mucD217, encoding MucD altered in the protease motif (S217A), was defective in temperature resistance and alginate gene regulation.

scholarly journals Hematopoietic Differentiation of Embryonic Stem Cells: An In Vitro Model to Study Gene Regulation during Megakaryocytopoiesis

Stem Cells ◽  
1996 ◽  
Vol 14 (S1) ◽  
pp. 194-199 ◽  
Author(s):  
Georges Uzan ◽  
Marie‐Hélène Prandini ◽  
Jean‐Philippe Rosa ◽  
Rolande Berthier
Keyword(s):  
Stem Cells ◽  
Gene Regulation ◽  
Embryonic Stem Cells ◽  
In Vitro Model ◽  
Embryonic Stem ◽  
Hematopoietic Differentiation ◽  
Vitro Model ◽  
Study Gene Regulation

scholarly journals Internally Controlled Poly(A) Tail Assay to Study Gene Regulation

BioTechniques ◽  
2002 ◽  
Vol 33 (3) ◽  
pp. 476-480
Author(s):  
Chiara Gamberi ◽  
Ellen Gottlieb
Keyword(s):  
Gene Regulation ◽  
Study Gene Regulation

scholarly journals Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model

2021 ◽  
Author(s):  
Genevieve Housman ◽  
Emilie Briscoe ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Bone Cells ◽  
Cell Types ◽  
Differentially Expressed ◽  
Functional Genomic ◽  
Cell Culture Model ◽  
Culture Model ◽  
Study Gene Regulation

AbstractThe evolution of complex skeletal traits in primates was likely influenced by both genetic and environmental factors. Because skeletal tissues are notoriously challenging to study using functional genomic approaches, they remain poorly characterized even in humans, let alone across multiple species. The challenges involved in obtaining functional genomic data from the skeleton, combined with the difficulty of obtaining such tissues from nonhuman apes, motivated us to consider an alternative in vitro system with which to comparatively study gene regulation in skeletal cell types. Specifically, we differentiated six human and six chimpanzee induced pluripotent stem cell lines (iPSCs) into mesenchymal stem cells (MSCs) and subsequently into osteogenic cells (bone cells). We validated differentiation using standard methods and collected single-cell RNA sequencing data from over 100,000 cells across multiple samples and replicates at each stage of differentiation. While most genes that we examined display conserved patterns of expression across species, hundreds of genes are differentially expressed (DE) between humans and chimpanzees within and across stages of osteogenic differentiation. Some of these interspecific DE genes show functional enrichments relevant in skeletal tissue trait development. Moreover, topic modeling indicates that interspecific gene programs become more pronounced as cells mature. Overall, we propose that this in vitro model can be used to identify interspecific regulatory differences that may have contributed to skeletal trait differences between species.Author SummaryPrimates display a range of skeletal morphologies and susceptibilities to skeletal diseases, but the molecular basis of these phenotypic differences is unclear. Studies of gene expression variation in primate skeletal tissues are extremely restricted due to the ethical and practical challenges associated with collecting samples. Nevertheless, the ability to study gene regulation in primate skeletal tissues is crucial for understanding how the primate skeleton has evolved. We therefore developed a comparative primate skeletal cell culture model that allows us to access a spectrum of human and chimpanzee cell types as they differentiate from stem cells into bone cells. While most gene expression patterns are conserved across species, we also identified hundreds of differentially expressed genes between humans and chimpanzees within and across stages of differentiation. We also classified cells by osteogenic stage and identified additional interspecific differentially expressed genes which may contribute to skeletal trait differences. We anticipate that this model will be extremely useful for exploring questions related to gene regulation variation in primate bone biology and development.

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