Decreased sink/source ratio enhances hexose transport in the fruits of greenhouse tomatoes: integration of gene expression and biochemical analyses

2020 ◽  
Vol 170 (1) ◽  
pp. 120-131
Author(s):  
Leila Aslani ◽  
Mahdiyeh Gholami ◽  
Mostafa Mobli ◽  
Parviz Ehsanzadeh ◽  
Nadia Bertin
Keyword(s):  
Gene Expression ◽  
Hexose Transport ◽  
Biochemical Analyses ◽  
Greenhouse Tomatoes

scholarly journals Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer’s disease

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Angela M. Crist ◽  
Kelly M. Hinkle ◽  
Xue Wang ◽  
Christina M. Moloney ◽  
Billie J. Matchett ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Digital Pathology ◽  
Selective Vulnerability ◽  
Brain Regions ◽  
Biochemical Analyses ◽  
The Brain ◽  
Relevant Gene ◽  
Tau Expression

AbstractSelective vulnerability of different brain regions is seen in many neurodegenerative disorders. The hippocampus and cortex are selectively vulnerable in Alzheimer’s disease (AD), however the degree of involvement of the different brain regions differs among patients. We classified corticolimbic patterns of neurofibrillary tangles in postmortem tissue to capture extreme and representative phenotypes. We combined bulk RNA sequencing with digital pathology to examine hippocampal vulnerability in AD. We identified hippocampal gene expression changes associated with hippocampal vulnerability and used machine learning to identify genes that were associated with AD neuropathology, including SERPINA5, RYBP, SLC38A2, FEM1B, and PYDC1. Further histologic and biochemical analyses suggested SERPINA5 expression is associated with tau expression in the brain. Our study highlights the importance of embracing heterogeneity of the human brain in disease to identify disease-relevant gene expression.

scholarly journals Transactivation by the E2 Protein of Oncogenic Human Papillomavirus Type 31 Is Not Essential for Early and Late Viral Functions

1998 ◽  
Vol 72 (10) ◽  
pp. 8115-8123 ◽  
Author(s):  
Frank Stubenrauch ◽  
Angela M. E. Colbert ◽  
Laimonis A. Laimins
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Human Keratinocytes ◽  
Viral Life Cycle ◽  
Human Papillomaviruses ◽  
Late Gene ◽  
Late Gene Expression ◽  
Positive Role ◽  
E2 Protein ◽  
Biochemical Analyses

ABSTRACT The activation of transcription and of DNA replication are, in some cases, mediated by the same proteins. A prime example is the E2 protein of human papillomaviruses (HPVs), which binds ACCN6GGT sequences and activates heterologous promoters from multimerized binding sites. The E2 protein also has functions in replication, where it complexes with the virally encoded origin recognition protein, E1. Much of the information on these activities is based on transient-transfection assays as well as biochemical analyses; however, their importance in the productive life cycle of oncogenic HPVs remains unclear. To determine the contributions of these E2 functions to the HPV life cycle, a genetic analysis was performed by using an organotypic tissue culture model. HPV type 31 (HPV31) genomes that contained mutations in the N terminus of E2 (amino acid 73) were constructed; these mutants retained replication activities but were transactivation defective. Following transfection of normal human keratinocytes, these mutant genomes were established as stable episomes and expressed early viral transcripts at levels similar to those of wild-type HPV31. Upon differentiation in organotypic raft cultures, the induction of late gene expression and amplification of viral DNA were detected in cell lines harboring mutant genomes. Interestingly, only a modest reduction in late gene expression was observed in the mutant lines. We conclude that the transactivation function of E2 is not essential for the viral life cycle of oncogenic HPVs, although it may act to moderately augment late expression. Our studies suggest that the primary positive role of E2 in the viral life cycle is as a replication factor.

scholarly journals BES1 is activated by EMS1-TPD1-SERK1/2-mediated signaling to control tapetum development in Arabidopsis thaliana

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Weiyue Chen ◽  
Minghui Lv ◽  
Yanze Wang ◽  
Ping-An Wang ◽  
Yanwei Cui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Plant Development ◽  
Family Members ◽  
Ectopic Expression ◽  
Null Mutant ◽  
Male Sterile ◽  
Receptor Like Kinase ◽  
Biochemical Analyses

Abstract BES1 and BZR1 were originally identified as two key transcription factors specifically regulating brassinosteroid (BR)-mediated gene expression. They belong to a family consisting of six members, BES1, BZR1, BEH1, BEH2, BEH3, and BEH4. bes1 and bzr1 single mutants do not exhibit any characteristic BR phenotypes, suggesting functional redundancy of these proteins. Here, by generating higher order mutants, we show that a quintuple mutant is male sterile due to defects in tapetum and microsporocyte development in anthers. Our genetic and biochemical analyses demonstrate that BES1 family members also act as downstream transcription factors in the EMS1-TPD1-SERK1/2 pathway. Ectopic expression of both TPD1 and EMS1 in bri1-116, a BR receptor null mutant, leads to the accumulation of non-phosphorylated, active BES1, similar to activation of BES1 by BRI1-BR-BAK1 signaling. These data suggest that two distinctive receptor-like kinase-mediated signaling pathways share BES1 family members as downstream transcription factors to regulate different aspects of plant development.

Splicing of plant pre-mRNAs

1992 ◽  
Vol 99 (3-4) ◽  
pp. 31-50 ◽  
Author(s):  
Craig G. Simpson ◽  
Gordon G. Simpson ◽  
Gillian Clark ◽  
David J. Leader ◽  
Petra Vaux ◽  
...  
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
Genetic Manipulation ◽  
Mrna Splicing ◽  
Mrna Transcripts ◽  
Dicotyledonous Plants ◽  
Intron Recognition ◽  
The Difference ◽  
Biochemical Analyses ◽  
Regulated Gene Expression

SynopsisPre-messenger RNA (pre-mRNA) splicing or the removal of introns from pre-mRNA transcripts is a key process in the maturation of mRNA. This process requires the assembly of a large complex of RNA and protein molecules, called the splicosome, on the pre-mRNA transcripts. Molecular and biochemical analyses of plant intron sequence and structure and of the components of the plant spliceosome are providing information on the mechanism of intron recognition and splice site selection in both monocoty-ledonous and dicotyledonous plants. This knowledge will help in gaining an understanding of phenomena such as the difference in splicing between monocotyledonous and dictoyledonous plants, the enhancement of gene expression brought about by the presence of some introns and alternative splicing. The importance of introns and pre-mRNA splicing to accurate and regulated gene expression, therefore, is of direct relevance to transgene expression and genetic manipulation.

Effect of 300 mT static and 50 Hz 0.1 mT extremely low frequency magnetic fields on Tuber borchii mycelium

2012 ◽  
Vol 58 (10) ◽  
pp. 1174-1182 ◽  
Author(s):  
Lucia Potenza ◽  
Roberta Saltarelli ◽  
Emanuela Polidori ◽  
Paola Ceccaroli ◽  
Antonella Amicucci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Magnetic Field ◽  
Low Frequency ◽  
Hyphal Growth ◽  
In Vitro Cultivation ◽  
Tuber Borchii ◽  
Extremely Low Frequency ◽  
Biochemical Analyses ◽  
Set Up

The present work aimed to investigate whether exposure to static magnetic field (SMF) and extremely low frequency magnetic field (ELF-MF) can induce biomolecular changes on Tuber borchii hyphal growth. Tuber borchii mycelium was exposed for 1 h for 3 consecutive days to a SMF of 300 mT or an ELF-MF of 0.1 mT 50 Hz. Gene expression and biochemical analyses were performed. In mycelia exposed to ELF-MF, some genes involved in hyphal growth, investigated using quantitative real-time polymerase chain reaction, were upregulated, and the activity of many glycolytic enzymes was increased. On the contrary, no differences were observed in gene expression after exposure to SMF treatment, and only the activities of glucose 6-phosphate dehydrogenase and hexokinase increased. The data herein presented suggest that the electromagnetic field can act as an environmental factor in promoting hyphal growth and can be used for applicative purposes, such as the set up of new in vitro cultivation techniques.

scholarly journals The Gene for the Embryonic Stem Cell Coactivator UTF1 Carries a Regulatory Element Which Selectively Interacts with a Complex Composed of Oct-3/4 and Sox-2

1999 ◽  
Vol 19 (8) ◽  
pp. 5453-5465 ◽  
Author(s):  
Masazumi Nishimoto ◽  
Akiko Fukushima ◽  
Akihiko Okuda ◽  
Masami Muramatsu
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Es Cells ◽  
Regulatory Element ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
General Mechanism ◽  
Octamer Motif ◽  
Biochemical Analyses ◽  
Binding Sequence

ABSTRACT UTF1 is a transcriptional coactivator which has recently been isolated and found to be expressed mainly in pluripotent embryonic stem (ES) cells (A. Okuda, A. Fukushima, M. Nishimoto, et al., EMBO J. 17:2019–2032, 1998). To gain insight into the regulatory network of gene expression in ES cells, we have characterized the regulatory elements governing UTF1 gene expression. The results indicate that the UTF1 gene is one of the target genes of an embryonic octamer binding transcription factor, Oct-3/4. UTF1 expression is, like the FGF-4 gene, regulated by the synergistic action of Oct-3/4 and another embryonic factor, Sox-2, implying that the requirement for Sox-2 by Oct-3/4 is not limited to the FGF-4 enhancer but is rather a general mechanism of activation for Oct-3/4. Our biochemical analyses, however, also reveal one distinct difference between these two regulatory elements: unlike the FGF-4 enhancer, the UTF1 regulatory element can, by its one-base difference from the canonical octamer-binding sequence, selectively recruit the complex comprising Oct-3/4 and Sox-2 and preclude the binding of the transcriptionally inactive complex containing Oct-1 or Oct-6. Furthermore, our analyses reveal that these properties are dictated by the unique ability of the Oct-3/4 POU-homeodomain that recognizes a variant of the Octamer motif in the UTF1 regulatory element.

scholarly journals Negative Regulation of the Keap1-Nrf2 Pathway by a p62/Sqstm1 Splicing Variant

2018 ◽  
Vol 38 (7) ◽  
Author(s):  
Shun Kageyama ◽  
Tetsuya Saito ◽  
Miki Obata ◽  
Ryo-hei Koide ◽  
Yoshinobu Ichimura ◽  
...  
Keyword(s):  
Gene Expression ◽  
Posttranslational Modifications ◽  
Negative Regulation ◽  
Full Length ◽  
Ensembl Database ◽  
Nrf2 Pathway ◽  
Splicing Variant ◽  
Autophagic Degradation ◽  
Response To Stress ◽  
Biochemical Analyses

ABSTRACT A key antioxidant pathway, the Keap1-Nrf2 system, is regulated by p62/Sqstm1 via multiple mechanisms, including gene expression, posttranslational modifications (such as ubiquitination and phosphorylation), and autophagic degradation of p62/Sqstm1 and Keap1. Here we demonstrate a novel mode of regulation of the Keap1-Nrf2 system, mediated by a splicing variant of p62/Sqstm1 pre-mRNA. Ensembl database searches and subsequent biochemical analyses of mice revealed the presence of an mRNA that encodes a p62/Sqstm1 protein lacking the Keap1-interacting region (KIR), which is essential for the interaction with Keap1. Like full-length p62, the variant was induced under conditions in which Nrf2 was activated (e.g., impairment of autophagy), formed oligomers with itself and/or the full-length protein, and was degraded by autophagy. However, the variant failed to interact with Keap1 and sequester it in variant-positive aggregates. Remarkably, while full-length p62 stabilized Nrf2 and induced the gene expression of Nrf2 targets, the variant increased the amount of Keap1 and enhanced ubiquitination of Nrf2, thereby suppressing the induction of Nrf2 targets. Hepatocytes isolated from genetically modified mice that express full-length p62, but not the variant, were susceptible to activation of Nrf2 in response to stress. Collectively, our results suggest that splicing of p62/Sqstm1 pre-mRNA negatively regulates the Keap1-Nrf2 pathway.

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