scholarly journals Reproductive switching analysis of Daphnia similoides between sexual female and parthenogenetic female by transcriptome comparison

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Ya-Nan Zhang ◽  
Xiu-Yun Zhu ◽  
Wen-Ping Wang ◽  
Yi Wang ◽  
Lu Wang ◽  
...  
Keyword(s):  
Parthenogenetic Female ◽  
Transcriptome Comparison

scholarly journals Utilizing MIKC-type MADS-box protein SOC1 for yield potential enhancement in maize

2021 ◽  
Author(s):  
Guo-qing Song ◽  
Xue Han ◽  
John T. Ryner ◽  
Addie Thompson ◽  
Kan Wang
Keyword(s):  
Transgenic Plants ◽  
Plant Height ◽  
No Reduction ◽  
Planting Density ◽  
Yield Potential ◽  
Grain Production ◽  
Mads Box ◽  
Young Leaves ◽  
Mads Box Gene ◽  
Transcriptome Comparison

Abstract Key message Overexpression of Zea mays SOC gene promotes flowering, reduces plant height, and leads to no reduction in grain production per plant, suggesting enhanced yield potential, at least, through increasing planting density. Abstract MIKC-type MADS-box gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) is an integrator conserved in the plant flowering pathway. In this study, the maize SOC1 (ZmSOC1) gene was cloned and overexpressed in transgenic maize Hi-II genotype. The T0 plants were backcrossed with nontransgenic inbred B73 to produce first generation backcross (BC1) seeds. Phenotyping of both transgenic and null segregant (NT) BC1 plants was conducted in three independent experiments. The BC1 transgenic plants showed new attributes such as increased vegetative growth, accelerated flowering time, reduced overall plant height, and increased grain weight. Second generation backcross (BC2) plants were evaluated in the field using two planting densities. Compared to BC2 NT plants, BC2 transgenic plants, were 12–18% shorter, flowered 5 days earlier, and showed no reduction in grain production per plant and an increase in fat, starch, and simple sugars in the grain. Transcriptome comparison in young leaves of 56-day-old BC1 plants revealed that the overexpressed ZmSOC1 resulted in 107 differentially expressed genes. The upregulated transcription factor DNA BINDING WITH ONE FINGER 5.4 (DOF5.4) was among the genes responsible for the reduced plant height. Modulating expression of SOC1 opens a new and effective approach to promote flowering and reduce plant height, which may have potential to enhance crop yield and improve grain quality.

The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate

Microbiology ◽  
2003 ◽  
Vol 149 (9) ◽  
pp. 2331-2343 ◽  
Author(s):  
Thierry Doan ◽  
Pascale Servant ◽  
Shigeo Tojo ◽  
Hirotake Yamaguchi ◽  
Guillaume Lerondel ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Malic Enzyme ◽  
Northern Analysis ◽  
Two Component System ◽  
Extracellular Medium ◽  
Component System ◽  
Two Component ◽  
Transcriptome Comparison ◽  
Physiological Tests

A transcriptome comparison of a wild-type Bacillus subtilis strain growing under glycolytic or gluconeogenic conditions was performed. In particular, it revealed that the ywkA gene, one of the four paralogues putatively encoding a malic enzyme, was more transcribed during gluconeogenesis. Using a lacZ reporter fusion to the ywkA promoter, it was shown that ywkA was specifically induced by external malate and not subject to glucose catabolite repression. Northern analysis confirmed this expression pattern and demonstrated that ywkA is cotranscribed with the downstream ywkB gene. The ywkA gene product was purified and biochemical studies demonstrated its malic enzyme activity, which was 10-fold higher with NAD than with NADP (k cat/K m 102 and 10 s−1 mM−1, respectively). However, physiological tests with single and multiple mutant strains affected in ywkA and/or in ywkA paralogues showed that ywkA does not contribute to efficient utilization of malate for growth. Transposon mutagenesis allowed the identification of the uncharacterized YufL/YufM two-component system as being responsible for the control of ywkA expression. Genetic analysis and in vitro studies with purified YufM protein showed that YufM binds just upstream of ywkA promoter and activates ywkA transcription in response to the presence of malate in the extracellular medium, transmitted by YufL. ywkA and yufL/yufM could thus be renamed maeA for malic enzyme and malK/malR for malate kinase sensor/malate response regulator, respectively.

Developmental deformities in the parthenogenetic lizard Cnemidophorus uniparens (Teiidae) and the "anomalous male" phenomenon

1986 ◽  
Vol 64 (11) ◽  
pp. 2418-2424 ◽  
Author(s):  
Allen J. Billy
Keyword(s):  
Sexual Differentiation ◽  
Vertebral Column ◽  
Female Offspring ◽  
Bisexual Species ◽  
Developmental Defects ◽  
Unresolved Problem ◽  
Parthenogenetic Species ◽  
Parthenogenetic Female ◽  
Lower Jaw ◽  
Cnemidophorus Uniparens

Parthenogenetic species of lizard occasionally produce male progeny characterized by developmental defects and low viability. Production of anomalous males is an unresolved problem in sexual differentiation as parthenogenetic female lizards are expected to produce female offspring. The "anomalous male" phenomenon was examined by sexing nonviable embryos produced by the parthenogenetic whiptail lizard Cnemidophorus uniparens. Twenty-six deformed embryos were obtained; all were female except for three which did not possess gonads. Male embryos were not detected. Developmental deformities found in Cnemidophorus embryos included anophthalmia, micropthalmia, encephalocoele, hypoplasia of the lower jaw, head foreshortening, gastroschisis, and malformations of the vertebral column. Several embryos possessed a combination of defects. Four hypotheses are presented to account for production of anomalous males by reptilian parthenoforms. Three hypotheses involve production of sex-reversed males (genetic females). A fourth hypothesis asserts that anomalous males are derived from hybridization events between a female from a unisexual species and a male from a bisexual species. Of the four hypotheses, the hybridization hypothesis has the greatest utility in explaining production of anomalous males by parthenogenetic lizards.

scholarly journals Characterization of gossypol biosynthetic pathway

2018 ◽  
Vol 115 (23) ◽  
pp. E5410-E5418 ◽  
Author(s):  
Xiu Tian ◽  
Ju-Xin Ruan ◽  
Jin-Quan Huang ◽  
Chang-Qing Yang ◽  
Xin Fang ◽  
...  
Keyword(s):  
Plant Disease Resistance ◽  
Biosynthetic Pathway ◽  
Virus Induced Gene Silencing ◽  
Defense Compounds ◽  
Oxidative Reactions ◽  
Substrate Conversion ◽  
Transcriptome Comparison ◽  
Tight Correlation

Gossypol and related sesquiterpene aldehydes in cotton function as defense compounds but are antinutritional in cottonseed products. By transcriptome comparison and coexpression analyses, we identified 146 candidates linked to gossypol biosynthesis. Analysis of metabolites accumulated in plants subjected to virus-induced gene silencing (VIGS) led to the identification of four enzymes and their supposed substrates. In vitro enzymatic assay and reconstitution in tobacco leaves elucidated a series of oxidative reactions of the gossypol biosynthesis pathway. The four functionally characterized enzymes, together with (+)-δ-cadinene synthase and the P450 involved in 7-hydroxy-(+)-δ-cadinene formation, convert farnesyl diphosphate (FPP) to hemigossypol, with two gaps left that each involves aromatization. Of six intermediates identified from the VIGS-treated leaves, 8-hydroxy-7-keto-δ-cadinene exerted a deleterious effect in dampening plant disease resistance if accumulated. Notably, CYP71BE79, the enzyme responsible for converting this phytotoxic intermediate, exhibited the highest catalytic activity among the five enzymes of the pathway assayed. In addition, despite their dispersed distribution in the cotton genome, all of the enzyme genes identified show a tight correlation of expression. Our data suggest that the enzymatic steps in the gossypol pathway are highly coordinated to ensure efficient substrate conversion.

A transcriptome comparison of time-matched developing human, mouse and rat neural progenitor cells reveals human uniqueness

2018 ◽  
Vol 354 ◽  
pp. 40-55 ◽  
Author(s):  
Stefan Masjosthusmann ◽  
Daniel Becker ◽  
Barbara Petzuch ◽  
Jördis Klose ◽  
Clara Siebert ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Neural Progenitor Cells ◽  
Neural Progenitor ◽  
Human Uniqueness ◽  
Transcriptome Comparison

scholarly journals Visualization of circular RNAs and their internal splicing events from transcriptomic data

2020 ◽  
Vol 36 (9) ◽  
pp. 2934-2935 ◽  
Author(s):  
Yi Zheng ◽  
Fangqing Zhao
Keyword(s):  
Supplementary Information ◽  
Circular Rnas ◽  
Visualization Tool ◽  
Command Line ◽  
Supplementary Data ◽  
Transcriptomic Data ◽  
Command Line Tool ◽  
Transcriptome Comparison ◽  
Multiple Samples ◽  
Splicing Patterns

Abstract Summary Circular RNAs (circRNAs) are proved to have unique compositions and splicing events distinct from canonical mRNAs. However, there is no visualization tool designed for the exploration of complex splicing patterns in circRNA transcriptomes. Here, we present CIRI-vis, a Java command-line tool for quantifying and visualizing circRNAs by integrating the alignments and junctions of circular transcripts. CIRI-vis can be applied to visualize the internal structure and isoform abundance of circRNAs and perform circRNA transcriptome comparison across multiple samples. Availability and implementation https://sourceforge.net/projects/ciri/files/CIRI-vis. Supplementary information Supplementary data are available at Bioinformatics online.

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