CRISPR-Associated Transposase System Can Insert Multiple Copies of Donor DNA into the Same Target Locus

2021 ◽  
Author(s):  
Junjie Yang ◽  
Jiawei Yang ◽  
Yiwen Zhang ◽  
Siqi Yang ◽  
Jieze Zhang ◽  
...  
Keyword(s):  
Target Locus ◽  
Multiple Copies

Alkaline Dissociation Products of Lumbricus Terrestris Hemoglobin Viewed with the STEM

1981 ◽  
Vol 39 ◽  
pp. 434-435
Author(s):  
O. H. Kapp ◽  
M. Ohtsuki ◽  
N. Robin ◽  
S. N. Vinogradov ◽  
A. V. Crewe
Keyword(s):  
Carbon Film ◽  
Lumbricus Terrestris ◽  
Uranyl Acetate ◽  
Acetate Solution ◽  
Oxygen Carriers ◽  
Complex Molecules ◽  
Thin Carbon ◽  
Thin Carbon Film ◽  
Multiple Copies ◽  
Hill Coefficients

Annelid extracellular hemoglobins are among the largest known proteins (M.W = 3.9 x 106), and together with the hemocyanins are the largest known oxygen carriers. They display oxygen affinities generally higher than those o vertebrate hemoglobins with Hill coefficients ranging from slightly higher than unity to values as high as 5-6. These complex molecules are composed of multiple copies of as many as six different polypeptides and posse: approximately 150 hemes per molecule.The samples were diluted to 100-200 μg/ml with distilled water just before application to a thin carbon film (∽15 Å thick). One percent (w/v) uranyl acetate solution was used for negative staining for 2 minutes and dried in air. The specimens were examined with the high resolution STEM. Their general appearance is that of a hexagonal bilayer (Fig. 1), each layer consisting of six spheroidal subunits. The corner to corner hexagonal dimensic is approximately 300 Å and the bilayer thickness approximately 200 Å.

scholarly journals Dating the primigenial C4-CYP21 duplication in primates.

Genetics ◽  
1993 ◽  
Vol 134 (1) ◽  
pp. 331-339 ◽  
Author(s):  
Y Horiuchi ◽  
H Kawaguchi ◽  
F Figueroa ◽  
C O'hUigin ◽  
J Klein
Keyword(s):  
World Monkey ◽  
Orthologous Genes ◽  
Pigtail Macaque ◽  
Single Chromosome ◽  
Old World ◽  
Histocompatibility Complex ◽  
Cyp21 Gene ◽  
Multiple Copies ◽  
Fourth Component ◽  
Flanking Regions

Abstract C4 and CYP21 are two adjacent, but functionally unrelated genes residing in the middle of the mammalian major histocompatibility complex (Mhc). The C4 gene codes for the fourth component of the complement cascade, whereas the CYP21 gene specifies an enzyme (cytochrome P450c21) of the glucocorticoid and mineralocorticoid pathways. The genes occur frequently in multiple copies on a single chromosome arranged in the order C4 ... CYP21 ... C4 ... CYP21. The unit of duplication (a module) is the C4-CYP21 gene pair. We sequenced the flanking regions of the C4-CYP21 modules and the intermodular regions of the chimpanzee, gorilla, and orangutan, as well as the intermodular region of an Old World monkey, the pigtail macaque. By aligning the sequences, we could identify the duplication breakpoints in these species. The breakpoint turned out to be at exactly the same position as that found previously in humans. The sequences flanking paralogous genes in the same species were found to be more similar to one another than sequences flanking orthologous genes in different species. We interpret these results as indicating that the original (primigenial) duplication occurred before the separation of apes from Old World monkeys more than 23 million years ago. The nature of the sequence at the breakpoint suggests that the duplication occurred by nonhomologous recombination. Since then, the C4-CYP21 haplotypes have been expanding and contracting by homologous crossing over which has homogenized the sequences in each species.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Genome-edited Camelina sativa with a unique fatty acid content and its potential impact on ecosystems

2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Katharina Kawall
Keyword(s):  
Fatty Acid ◽  
Genome Editing ◽  
Defense Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Fatty Acid Content ◽  
Camelina Sativa ◽  
Nutritional Composition ◽  
Oilseed Crop ◽  
Biotic And Abiotic Stress ◽  
Multiple Copies

Abstract‘Genome editing’ is intended to accelerate modern plant breeding enabling a much faster and more efficient development of crops with improved traits such as increased yield, altered nutritional composition, as well as resistance to factors of biotic and abiotic stress. These traits are often generated by site-directed nuclease-1 (SDN-1) applications that induce small, targeted changes in the plant genomes. These intended alterations can be combined in a way to generate plants with genomes that are altered on a larger scale than it is possible with conventional breeding techniques. The power and the potential of genome editing comes from its highly effective mode of action being able to generate different allelic combinations of genes, creating, at its most efficient, homozygous gene knockouts. Additionally, multiple copies of functional genes can be targeted all at once. This is especially relevant in polyploid plants such as Camelina sativa which contain complex genomes with multiple chromosome sets. Intended alterations induced by genome editing have potential to unintentionally alter the composition of a plant and/or interfere with its metabolism, e.g., with the biosynthesis of secondary metabolites such as phytohormones or other biomolecules. This could affect diverse defense mechanisms and inter-/intra-specific communication of plants having a direct impact on associated ecosystems. This review focuses on the intended alterations in crops mediated by SDN-1 applications, the generation of novel genotypes and the ecological effects emerging from these intended alterations. Genome editing applications in C. sativa are used to exemplify these issues in a crop with a complex genome. C. sativa is mainly altered in its fatty acid biosynthesis and used as an oilseed crop to produce biofuels.

scholarly journals Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1103-1115 ◽  
Author(s):  
Hongguang Shao ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analyses ◽  
Mosquito Species ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Wide Range ◽  
Multiple Copies ◽  
Catalytic Motif ◽  
Open The Doors ◽  
Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

scholarly journals Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy

2018 ◽  
Vol 115 (17) ◽  
pp. E3969-E3977 ◽  
Author(s):  
Sasikumar Rajoo ◽  
Pascal Vallotton ◽  
Evgeny Onischenko ◽  
Karsten Weis
Keyword(s):  
Nuclear Pore Complex ◽  
Yeast Cells ◽  
Nuclear Pore ◽  
Altered Expression ◽  
Copy Numbers ◽  
Quantitative Image ◽  
Multiple Copies ◽  
Almost All ◽  
High Degree

The nuclear pore complex (NPC) is an eightfold symmetrical channel providing selective transport of biomolecules across the nuclear envelope. Each NPC consists of ∼30 different nuclear pore proteins (Nups) all present in multiple copies per NPC. Significant progress has recently been made in the characterization of the vertebrate NPC structure. However, because of the estimated size differences between the vertebrate and yeast NPC, it has been unclear whether the NPC architecture is conserved between species. Here, we have developed a quantitative image analysis pipeline, termed nuclear rim intensity measurement (NuRIM), to precisely determine copy numbers for almost all Nups within native NPCs of budding yeast cells. Our analysis demonstrates that the majority of yeast Nups are present at most in 16 copies per NPC. This reveals a dramatic difference to the stoichiometry determined for the human NPC, suggesting that despite a high degree of individual Nup conservation, the yeast and human NPC architecture is significantly different. Furthermore, using NuRIM, we examined the effects of mutations on NPC stoichiometry. We demonstrate for two paralog pairs of key scaffold Nups, Nup170/Nup157 and Nup192/Nup188, that their altered expression leads to significant changes in the NPC stoichiometry inducing either voids in the NPC structure or substitution of one paralog by the other. Thus, our results not only provide accurate stoichiometry information for the intact yeast NPC but also reveal an intriguing compositional plasticity of the NPC architecture, which may explain how differences in NPC composition could arise in the course of evolution.

Transcription of multiple copies of the yeast GAL7 gene is limited by specific factors in addition to GAL4

1987 ◽  
Vol 208 (1-2) ◽  
pp. 127-134 ◽  
Author(s):  
S. M. Baker ◽  
S. A. Johnston ◽  
J. E. Hopper ◽  
J. A. Jaehning
Keyword(s):  
Multiple Copies ◽  
Specific Factors

scholarly journals Scaffolding proteins guide the evolution of algal light harvesting antennas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Harry W. Rathbone ◽  
Katharine A. Michie ◽  
Michael J. Landsberg ◽  
Beverley R. Green ◽  
Paul M. G. Curmi
Keyword(s):  
Hydrophobic Surface ◽  
Scaffolding Protein ◽  
Secondary Endosymbiosis ◽  
Scaffolding Proteins ◽  
Α Subunit ◽  
Binding Partner ◽  
Photosynthetic Organisms ◽  
New Family ◽  
Red Algal ◽  
Multiple Copies

AbstractPhotosynthetic organisms have developed diverse antennas composed of chromophorylated proteins to increase photon capture. Cryptophyte algae acquired their photosynthetic organelles (plastids) from a red alga by secondary endosymbiosis. Cryptophytes lost the primary red algal antenna, the red algal phycobilisome, replacing it with a unique antenna composed of αβ protomers, where the β subunit originates from the red algal phycobilisome. The origin of the cryptophyte antenna, particularly the unique α subunit, is unknown. Here we show that the cryptophyte antenna evolved from a complex between a red algal scaffolding protein and phycoerythrin β. Published cryo-EM maps for two red algal phycobilisomes contain clusters of unmodelled density homologous to the cryptophyte-αβ protomer. We modelled these densities, identifying a new family of scaffolding proteins related to red algal phycobilisome linker proteins that possess multiple copies of a cryptophyte-α-like domain. These domains bind to, and stabilise, a conserved hydrophobic surface on phycoerythrin β, which is the same binding site for its primary partner in the red algal phycobilisome, phycoerythrin α. We propose that after endosymbiosis these scaffolding proteins outcompeted the primary binding partner of phycoerythrin β, resulting in the demise of the red algal phycobilisome and emergence of the cryptophyte antenna.

scholarly journals Multiple copies of a novel amphipathic α-helix forming segment in Physcomitrella patens dehydrin play a key role in abiotic stress mitigation

2021 ◽  
pp. 100596
Author(s):  
Gouranga Upadhyaya ◽  
Arup Das ◽  
Chandradeep Basu ◽  
Tanushree Agarwal ◽  
Chandra Basak ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Physcomitrella Patens ◽  
Multiple Copies ◽  
Α Helix

scholarly journals Multivalent nanoparticle-based vaccines protect hamsters against SARS-CoV-2 after a single immunization

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Shiho Chiba ◽  
Steven J. Frey ◽  
Peter J. Halfmann ◽  
Makoto Kuroda ◽  
Tadashi Maemura ◽  
...  
Keyword(s):  
Coat Protein ◽  
Infectious Virus ◽  
Neutralizing Antibody ◽  
Vaccine Platform ◽  
Death Rates ◽  
Widespread Distribution ◽  
Syrian Hamsters ◽  
Vaccine Trials ◽  
Multiple Copies ◽  
Antibody Titers

AbstractThe COVID-19 pandemic continues to wreak havoc as worldwide SARS-CoV-2 infection, hospitalization, and death rates climb unabated. Effective vaccines remain the most promising approach to counter SARS-CoV-2. Yet, while promising results are emerging from COVID-19 vaccine trials, the need for multiple doses and the challenges associated with the widespread distribution and administration of vaccines remain concerns. Here, we engineered the coat protein of the MS2 bacteriophage and generated nanoparticles displaying multiple copies of the SARS-CoV-2 spike (S) protein. The use of these nanoparticles as vaccines generated high neutralizing antibody titers and protected Syrian hamsters from a challenge with SARS-CoV-2 after a single immunization with no infectious virus detected in the lungs. This nanoparticle-based vaccine platform thus provides protection after a single immunization and may be broadly applicable for protecting against SARS-CoV-2 and future pathogens with pandemic potential.

scholarly journals Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jose J. De Vega ◽  
Abel Teshome ◽  
Manfred Klaas ◽  
Jim Grant ◽  
John Finnan ◽  
...  
Keyword(s):  
Drought Stress ◽  
Water Supply ◽  
Biomass Yield ◽  
Transcriptional Response ◽  
Biomass Productivity ◽  
Differentially Expressed ◽  
Model Organisms ◽  
Drought Conditions ◽  
Multiple Copies ◽  
Response To Water

Abstract Background Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. Results A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. Conclusions Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.

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