scholarly journals Generation of white-eyed Daphnia magna mutants lacking scarlet function

2018 ◽  
Author(s):  
Nur Izzatur Binti Ismail ◽  
Yasuhiko Kato ◽  
Tomoaki Matsuura ◽  
Hajime Watanabe
Keyword(s):  
Genetic Transformation ◽  
Daphnia Magna ◽  
Compound Eye ◽  
Marker Gene ◽  
Draft Genome ◽  
Evolutionary Developmental Biology ◽  
Eye Color ◽  
A Genome ◽  
Screenable Marker ◽  
Mutant Lines

ABSTRACTThe crustacean Daphnia magna is an important model in multi-disciplinary scientific fields such as genetics, evolutionary developmental biology, toxicology, and ecology. Recently, draft genome sequence and transcriptome data became publicly available for this species. Genetic transformation by introduction of plasmid DNA into a genome has been achieved. To further advance D. magna functional genomics, identification of a screenable marker gene and generation of its mutant are indispensable. Because Daphnia is more closely related to insects among crustaceans, we hypothesized that eye color-related genes can function as a marker gene as used in Drosophila genetics. We searched orthologs of Drosophila eye pigment transporters White, Scarlet, and Brown in the genome of D. magna. Amino acid sequence alignment and phylogenetic analysis suggested that D. magna has six white and one scarlet orthologs, but lacks the brown ortholog. Due to a multiplicity of white orthologs, we analyzed function of the scarlet ortholog, DapmaSt, using RNA interference. DapmaSt RNAi embryos showed disappearance of black pigments both in the compound eye and in the ocellus, suggesting that DapmaSt is necessary for black pigmentation in Daphnia eyes. To disrupt DapmaSt by using the Crispr/Cas9 system, we co-injected DapmaSt-targeting gRNAs with Cas9 mRNAs into eggs and established white-eyed DapmaSt mutant lines that lack eye pigments throughout their lifespan. Our results suggest that DapmaSt can be used as a transformation marker in D. magng+a and the DapmaSt mutants would be an important resource for genetic transformation of this species in the future.

scholarly journals In Planta Genetic Transformation of Mungbean (Vigna radiata (L.) Wilczek) with Marker Gene

2019 ◽  
Vol 29 (2) ◽  
pp. 245-255
Author(s):  
Mohammad Mahmood Hasan ◽  
Sujay Kumar Bhajan ◽  
M. Imdadul Hoque ◽  
R.H. Sarker ◽  
Mohammad Nurul Islam
Keyword(s):  
Genetic Transformation ◽  
Genetic Improvement ◽  
In Vitro Regeneration ◽  
Marker Gene ◽  
Gus Expression ◽  
In Planta ◽  
Leaf Tissues ◽  
Gus Gene Expression ◽  
Screenable Marker

In genetic improvement of mungbean much success has not been achieved due to its recalcitrant nature towards in vitro regeneration. An attempt was made to develop an Agrobacterium-mediated in planta genetic transformation protocol for a locally grown mungbean variety BARI Mung-3 using a screenable marker gene. Two minutes of vacuum infiltration followed by 60 minutes of incubation period in Agrobacterium suspension of Winans’ AB medium containing wounded tobacco leaf extract was found most suitable towards genetic transformation in pricked de-coated half seed explants. An optical density (OD600) of 0.7 was found most effective for transient gus gene expression. Chimeric GUS expression was observed in the root and leaf tissues from the successfully transformed plantlets obtained through in planta transformation. This methodology of genetic transformation was found more suitable, easier and less time consuming than tissue culture based genetic transformation, which may be used for the genetic improvement of mungbean.

Computer Reconstruction of the Cellular Architecture of the Daphnia Magna Optic Ganglion

1975 ◽  
Vol 33 ◽  
pp. 284-285
Author(s):  
E. R. Macagno ◽  
C. Levinthal
Keyword(s):  
Daphnia Magna ◽  
Genetic Background ◽  
Compound Eye ◽  
Synaptic Connectivity ◽  
Serial Sections ◽  
Cross Sectional ◽  
Small Crustacean ◽  
Optic Ganglion ◽  
Structural Invariance ◽  
High Degree

The optic ganglion of Daphnia Magna, a small crustacean that reproduces parthenogenetically contains about three hundred neurons: 110 neurons in the Lamina or anterior region and about 190 neurons in the Medulla or posterior region. The ganglion lies in the midplane of the organism and shows a high degree of left-right symmetry in its structures. The Lamina neurons form the first projection of the visual output from 176 retinula cells in the compound eye. In order to answer questions about structural invariance under constant genetic background, we have begun to reconstruct in detail the morphology and synaptic connectivity of various neurons in this ganglion from electron micrographs of serial sections (1). The ganglion is sectioned in a dorso-ventra1 direction so as to minimize the cross-sectional area photographed in each section. This area is about 60 μm x 120 μm, and hence most of the ganglion fit in a single 70 mm micrograph at the lowest magnification (685x) available on our Zeiss EM9-S.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress

Cells ◽  
2018 ◽  
Vol 7 (12) ◽  
pp. 269 ◽  
Author(s):  
Meenakshi Agarwal ◽  
Ashish Pathak ◽  
Rajesh Rathore ◽  
Om Prakash ◽  
Rakesh Singh ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Stress Response ◽  
Proteomic Analysis ◽  
Protein Biosynthesis ◽  
Draft Genome ◽  
Department Of Energy ◽  
Coding Sequences ◽  
Total Rna ◽  
A Genome ◽  
Rna Genes

Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis. Both strains showed a rapid depletion of U; draft genome sequences revealed SRS-25 genome to be of approximately 8,152,324 bp, a G + C content of 66.5, containing a total 7604 coding sequences with 77 total RNA genes. Similarly, strain SRS-46 contained a genome size of 8,587,429 bp with a G + C content of 67.1, 7895 coding sequences, with 73 total RNA genes, respectively. An in-depth, genome-wide comparisons between strains 25, 46 and a previously isolated strain from our research (Burkholderia sp. strain SRS-W-2-2016), revealed a common pool of 3128 genes; many were found to be homologues to previously characterized metal resistance genes (e.g., for cadmium, cobalt, and zinc), as well as for transporter, stress/detoxification, cytochromes, and drug resistance functions. Furthermore, proteomic analysis of strains with or without U stress, revealed the increased expression of 34 proteins from strain SRS-25 and 52 proteins from strain SRS-46; similar to the genomic analyses, many of these proteins have previously been shown to function in stress response, DNA repair, protein biosynthesis and metabolism. Overall, this comparative proteogenomics study confirms the repertoire of metabolic and stress response functions likely rendering the ecological competitiveness to the isolated strains for colonization and survival in the heavy metals contaminated SRS soil habitat.

scholarly journals Efficiency of Genetic Transformation via Pollen-Tube Pathway of Jatropha (Jatropha curcas L.) Based on Histochemical and Molecular Analysis

2018 ◽  
Vol 45 (3) ◽  
pp. 316
Author(s):  
Agus Zainudin ◽  
Bambang Sapta Purwoko ◽  
Tri Joko Santoso ◽  
Sintho Wahyuning Ardie ◽  
And Trikoesoemaningtyas
Keyword(s):  
Pollen Tube ◽  
Genetic Transformation ◽  
Molecular Analysis ◽  
Plasmid Dna ◽  
Jatropha Curcas ◽  
Marker Gene ◽  
Pcr Analysis ◽  
Jatropha Curcas L ◽  
Gus Reporter ◽  
Combination Treatments

The genetic transformation via pollen-tube pathway is an alternative method to overcome the constraints imposed by genotype specificity in transformation and regeneration in jatropha (Jatropha curcas L.) tissue culture. Therefore, it is necessary to establish important parameters for efficient genetic transformation of jatropha via pollen-tube pathway. The objective of the research was to study the efficiency of direct transformation of jatropha via pollen-tube pathway based on histochemical and molecular analysis. Solution of purified pCAMBIA1301 DNA plasmid carrying a hptII marker gene and a gus reporter gene with concentration level of 0.05, 0.25, 0.50 µg µl-1 were applied to stigma of flowers at 1, 2, 4, 7, 10 h after pollination. Seedling of IP3A, IP3P and JcUMM18 jatropha’s genotypes derived from 15 combination treatments of plasmid DNA concentration and application time, also wild type was subjected to histochemical and molecular analyses. Based on those analyses, the efficiency of transformation via pollen-tube pathway of three jatropha genotypes ranged from 1.5-16.7%. PCR analysis showed that a number of positive plants were identified by using specific primers hptII and gus, i.e. 1-3 and 3-7 plants of the 15 combined treatments, respectively. It indicated that the transformation efficiency via the pollen-tube pathway varied in each jatropha genotype.<br /><br />Keywords: Jatropha curcas L., pCAMBIA1301, plasmid DNA, stigma-drip<br /><br />

scholarly journals A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

2019 ◽  
Vol 7 (6) ◽  
pp. 161 ◽  
Author(s):  
Ming-Hsin Tsai ◽  
Yen-Yi Liu ◽  
Von-Wun Soo ◽  
Chih-Chieh Chen
Keyword(s):  
Microbial Diversity ◽  
Large Scale ◽  
Gene Selection ◽  
Marker Gene ◽  
Genome Comparison ◽  
Marker Genes ◽  
Species Classification ◽  
Genome Wide ◽  
A Genome ◽  
Comparison Approach

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

scholarly journals Genome Sequence of Pseudomonas sp. Strain AN3A02, Isolated from Rhizosphere of Deschampsia antarctica Desv., with Antagonism against Botrytis cinerea

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Matías Poblete-Morales ◽  
Claudia Rabert ◽  
Andrés F. Olea ◽  
Héctor Carrasco ◽  
Raúl Calderón ◽  
...  
Keyword(s):  
Botrytis Cinerea ◽  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Deschampsia Antarctica ◽  
Dual Culture ◽  
Content Type ◽  
A Genome ◽  
Antarctic Continent

ABSTRACT Here, we announce the draft genome sequence of Pseudomonas sp. strain AN3A02, isolated from the rhizosphere of one of the only two species of vascular plants existing in the Antarctic continent, Deschampsia antarctica Desv. This isolate, which inhibited the mycelial growth of Botrytis cinerea in dual culture, has a genome sequence of 6,778,644 bp, with a G+C content of 60.4%. These draft genome sequence data provide insight into the genetics underpinning the antifungal activity of this strain.

scholarly journals Draft Genome Sequence of Lactobacillus rhamnosus OSU-PECh-69, a Cheese Isolate with Antibacterial Activity

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Israel García-Cano ◽  
Walaa E. Hussein ◽  
Diana Rocha-Mendoza ◽  
Ahmed E. Yousef ◽  
Rafael Jiménez-Flores
Keyword(s):  
Genome Sequence ◽  
Antimicrobial Agents ◽  
Draft Genome ◽  
Lactobacillus Rhamnosus ◽  
Gc Content ◽  
Gene Clusters ◽  
Gram Negative Bacteria ◽  
The Novel ◽  
Content Type ◽  
A Genome

ABSTRACT The novel strain Lactobacillus rhamnosus OSU-PECh-69 was isolated from provolone cheese. It produces antimicrobial agents having a molecular mass of 5 to 10 kDa that are active against Gram-positive and Gram-negative bacteria. The strain has a genome sequence of 3,057,669 bp, a GC content of 46.6%, and up to two gene clusters encoding bacteriocins.

scholarly journals Draft Genome Sequence of Flavobacterium succinicans Strain DD5b

2017 ◽  
Vol 5 (2) ◽  
Author(s):  
Anja Poehlein ◽  
Hristo Najdenski ◽  
Diliana D. Simeonova
Keyword(s):  
Daphnia Magna ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type

ABSTRACT We present the first 3.315-Mbp assembled draft genome sequence of Flavobacterium succinicans strain DD5b. This bacterium is a phosphite-assimilating representative of the genus Flavobacterium isolated from guts of the zooplankton Daphnia magna.

scholarly journals Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice

2020 ◽  
Vol 21 (15) ◽  
pp. 5492 ◽  
Author(s):  
Yu Jin Jung ◽  
Jong Hee Kim ◽  
Hyo Ju Lee ◽  
Dong Hyun Kim ◽  
Jihyeon Yu ◽  
...  
Keyword(s):  
Gene Expression Analysis ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Loss Of Function ◽  
Amino Acid Motif ◽  
Dwarf Phenotype ◽  
Genome Wide ◽  
A Genome ◽  
Mutant Lines ◽  
Genome Wide Gene Expression

The rice SLR1 gene encodes the DELLA protein (protein with DELLA amino acid motif), and a loss-of-function mutation is dwarfed by inhibiting plant growth. We generate slr1-d mutants with a semi-dominant dwarf phenotype to target mutations of the DELLA/TVHYNP domain using CRISPR/Cas9 genome editing in rice. Sixteen genetic edited lines out of 31 transgenic plants were generated. Deep sequencing results showed that the mutants had six different mutation types at the target site of the TVHYNP domain of the SLR1 gene. The homo-edited plants selected individuals without DNA (T-DNA) transcribed by segregation in the T1 generation. The slr1-d7 and slr1-d8 plants caused a gibberellin (GA)-insensitive dwarf phenotype with shrunken leaves and shortened internodes. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two GA-related genes, GA20OX2 (Gibberellin oxidase) and GA3OX2, were increased in the edited mutant plants, suggesting that GA20OX2 acts as a convert of GA12 signaling. These mutant plants are required by altering GA responses, at least partially by a defect in the phytohormone signaling system process and prevented cell elongation. The new mutants, namely, the slr1-d7 and slr1-d8 lines, are valuable semi-dominant dwarf alleles with potential application value for molecule breeding using the CRISPR/Cas9 system in rice.

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