An MF alpha 1-SUC2 (alpha-factor-invertase) gene fusion for study of protein localization and gene expression in yeast.

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.

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The Human Carotid Body

Anesthesiology ◽

10.1097/aln.0b013e3181fac061 ◽

2010 ◽

Vol 113 (6) ◽

pp. 1270-1279 ◽

Cited By ~ 37

Author(s):

Malin Jonsson Fagerlund ◽

Jessica Kåhlin ◽

Anette Ebberyd ◽

Gunnar Schulte ◽

Souren Mkrtchian ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Nicotinic Acetylcholine Receptors ◽

Carotid Body ◽

Protein Localization ◽

Oxygen Sensing ◽

Radical Neck Dissection ◽

K Channel ◽

General Anesthetics ◽

Anesthetic Drugs

Background Hypoxia is a common cause of adverse events in the postoperative period, where respiratory depression due to residual effects of drugs used in anesthesia is an important underlying factor. General anesthetics and neuromuscular blocking agents reduce the human ventilatory response to hypoxia. Although the carotid body (CB) is the major oxygen sensor in humans, critical oxygen sensing and signaling pathways have been investigated only in animals so far. Thus, the aim of this study was to characterize the expression of key genes and localization of their products involved in the human oxygen sensing and signaling pathways with a focus on receptor systems and ion channels of relevance in anesthesia. Methods Six CBs were removed unilaterally from patients undergoing radical neck dissection. The gene expression and cell-specific protein localization in the CBs were investigated with DNA microarrays, real-time polymerase chain reaction, and immunohistochemistry. Results We found gene expression of the oxygen-sensing pathway, heme oxygenase 2, and the K channels TASK (TWIK-related acid sensitive K channel)-1 and BK (large-conductance potassium channel). In addition, we show the expression of critical receptor subunits such as γ-aminobutyric acid A (α2, β3, and γ2), nicotinic acetylcholine receptors (α3, α7, and β2), purinoceptors (A2A and P2X2), and the dopamine D2 receptor. Conclusions In unique samples of the human CB, we here demonstrate presence of critical proteins in the oxygen-sensing and signaling cascade. Our findings demonstrate similarities to, but also important differences from, established animal models. In addition, our work establishes an essential platform for studying the interaction between anesthetic drugs and human CB chemoreception.

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Influence of yeast-derived invertase gene expression in potato plants on membrane lipid peroxidation at low temperature

Journal of Thermal Biology ◽

10.1016/j.jtherbio.2004.07.002 ◽

2005 ◽

Vol 30 (1) ◽

pp. 73-77 ◽

Cited By ~ 18

Author(s):

A.N. Deryabin ◽

I.M. Dubinina ◽

E.A. Burakhanova ◽

N.V. Astakhova ◽

E.P. Sabel’nikova ◽

...

Keyword(s):

Gene Expression ◽

Lipid Peroxidation ◽

Low Temperature ◽

Membrane Lipid ◽

Membrane Lipid Peroxidation ◽

Potato Plants ◽

Invertase Gene

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Induction of yeast histone genes by stimulation of stationary-phase cells

Molecular and Cellular Biology ◽

10.1128/mcb.10.12.6356-6361.1990 ◽

1990 ◽

Vol 10 (12) ◽

pp. 6356-6361

Author(s):

M A Drebot ◽

L M Veinot-Drebot ◽

R A Singer ◽

G C Johnston

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Stationary Phase ◽

Mitotic Cell ◽

Specific Gene ◽

Mitotic Cell Cycle ◽

Histone Genes ◽

Yeast Saccharomyces Cerevisiae ◽

Alpha Factor ◽

Stimulation Of

In the cell cycle of the budding yeast Saccharomyces cerevisiae, expression of the histone genes H2A and H2B of the TRT1 and TRT2 loci is regulated by the performance of "start," the step that also regulates the cell cycle. Here we show that histone production is also subject to an additional form of regulation that is unrelated to the mitotic cell cycle. Expression of histone genes, as assessed by Northern (RNA) analysis, was shown to increase promptly after the stimulation, brought about by fresh medium, that activates stationary-phase cells to reenter the mitotic cell cycle. The use of a yeast mutant that is conditionally blocked in the resumption of proliferation at a step that is not part of the mitotic cell cycle (M.A. Drebot, G.C. Johnston, and R.A. Singer, Proc. Natl. Acad. Sci. 84:7948, 1987) showed that this increased gene expression that occurs upon stimulation of stationary-phase cells took place in the absence of DNA synthesis and without the performance of start. This stimulation-specific gene expression was blocked by the mating pheromone alpha-factor, indicating that alpha-factor directly inhibits expression of these histone genes, independently of start.

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Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications

Journal of Molecular Cell Biology ◽

10.1093/jmcb/mjz080 ◽

2019 ◽

Vol 11 (10) ◽

pp. 886-898 ◽

Cited By ~ 1

Author(s):

Cai Han ◽

Lin-Yu Sun ◽

Wen-Tao Wang ◽

Yu-Meng Sun ◽

Yue-Qin Chen

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Fusion Proteins ◽

Gene Fusion ◽

Chromosomal Rearrangements ◽

Chromosomal Translocation ◽

Chromosomal Translocations ◽

Rna Molecules ◽

Non Coding Rnas ◽

The Relationship

Abstract Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.

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A combined gene expression tool for parallel histological prediction and gene fusion detection in non-small cell lung cancer

Scientific Reports ◽

10.1038/s41598-019-41585-4 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Anna Karlsson ◽

Helena Cirenajwis ◽

Kajsa Ericson-Lindquist ◽

Hans Brunnström ◽

Christel Reuterswärd ◽

...

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Small Cell Lung Cancer ◽

Cell Lung Cancer ◽

Gene Fusion ◽

Small Cell ◽

Small Cell Lung ◽

Fusion Detection

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Granulosa-Lutein Cell Sirtuin Gene Expression Profiles Differ between Normal Donors and Infertile Women

International Journal of Molecular Sciences ◽

10.3390/ijms21010295 ◽

2019 ◽

Vol 21 (1) ◽

pp. 295

Author(s):

Rebeca González-Fernández ◽

Rita Martín-Ramírez ◽

Deborah Rotoli ◽

Jairo Hernández ◽

Frederick Naftolin ◽

...

Keyword(s):

Gene Expression ◽

Protein Localization ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cellular Protein ◽

Control Group ◽

Poor Responders ◽

Male Factor ◽

Expression Levels ◽

Genes Expression

Sirtuins are a family of deacetylases that modify structural proteins, metabolic enzymes, and histones to change cellular protein localization and function. In mammals, there are seven sirtuins involved in processes like oxidative stress or metabolic homeostasis associated with aging, degeneration or cancer. We studied gene expression of sirtuins by qRT-PCR in human mural granulosa-lutein cells (hGL) from IVF patients in different infertility diagnostic groups and in oocyte donors (OD; control group). Study 1: sirtuins genes’ expression levels and correlations with age and IVF parameters in women with no ovarian factor. We found significantly higher expression levels of SIRT1, SIRT2 and SIRT5 in patients ≥40 years old than in OD and in women between 27 and 39 years old with tubal or male factor, and no ovarian factor (NOF). Only SIRT2, SIRT5 and SIRT7 expression correlated with age. Study 2: sirtuin genes’ expression in women poor responders (PR), endometriosis (EM) and polycystic ovarian syndrome. Compared to NOF controls, we found higher SIRT2 gene expression in all diagnostic groups while SIRT3, SIRT5, SIRT6 and SIRT7 expression were higher only in PR. Related to clinical parameters SIRT1, SIRT6 and SIRT7 correlate positively with FSH and LH doses administered in EM patients. The number of mature oocytes retrieved in PR is positively correlated with the expression levels of SIRT3, SIRT4 and SIRT5. These data suggest that cellular physiopathology in PR’s follicle may be associated with cumulative DNA damage, indicating that further studies are necessary.

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A reporter for noninvasively monitoring gene expression and plant transformation

Horticulture Research ◽

10.1038/s41438-020-00390-1 ◽

2020 ◽

Vol 7 (1) ◽

Cited By ~ 1

Author(s):

Yubing He ◽

Tao Zhang ◽

Hui Sun ◽

Huadong Zhan ◽

Yunde Zhao

Keyword(s):

Gene Expression ◽

Plant Transformation ◽

Protein Localization ◽

Fruit Tree ◽

Selection Marker ◽

Special Equipment ◽

Chemical Treatments ◽

Effective Selection ◽

Monitoring Gene Expression ◽

Large Crop

Abstract Reporters have been widely used to visualize gene expression, protein localization, and other cellular activities, but the commonly used reporters require special equipment, expensive chemicals, or invasive treatments. Here, we construct a new reporter RUBY that converts tyrosine to vividly red betalain, which is clearly visible to naked eyes without the need of using special equipment or chemical treatments. We show that RUBY can be used to noninvasively monitor gene expression in plants. Furthermore, we show that RUBY is an effective selection marker for transformation events in both rice and Arabidopsis. The new reporter will be especially useful for monitoring cellular activities in large crop plants such as a fruit tree under field conditions and for observing transformation and gene expression in tissue culture under sterile conditions.

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Gene expression within the periaqueductal gray is linked to vocal behavior and early-onset parkinsonism in Pink1 knockout rats

BMC Genomics ◽

10.1186/s12864-020-07037-4 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Cynthia A. Kelm-Nelson ◽

Stephen Gammie

Keyword(s):

Gene Expression ◽

Early Onset ◽

Early Stage ◽

Protein Localization ◽

Periaqueductal Gray ◽

Female Rats ◽

Vocal Behavior ◽

Metabotropic Receptors ◽

Male And Female ◽

Male And Female Rats

Abstract Background Parkinson’s disease (PD) is a degenerative disease with early-stage pathology hypothesized to manifest in brainstem regions. Vocal deficits, including soft, monotone speech, result in significant clinical and quality of life issues and are present in 90% of PD patients; yet the underlying pathology mediating these significant voice deficits is unknown. The Pink1−/− rat is a valid model of early-onset PD that presents with analogous vocal communication deficits. Previous work shows abnormal α-synuclein protein aggregation in the periaqueductal gray (PAG), a brain region critical and necessary to the modulation of mammalian vocal behavior. In this study, we used high-throughput RNA sequencing to examine gene expression within the PAG of both male and female Pink1−/− rats as compared to age-matched wildtype controls. We used a bioinformatic approach to (1) test the hypothesis that loss of Pink1 in the PAG will influence the differential expression of genes that interact with Pink1, (2) highlight other key genes that relate to this type of Mendelian PD, and (3) catalog molecular targets that may be important for the production of rat vocalizations. Results Knockout of the Pink1 gene resulted in differentially expressed genes for both male and female rats that also mapped to human PD datasets. Pathway analysis highlighted several significant metabolic pathways. Weighted gene co-expression network analysis (WGCNA) was used to identify gene nodes and their interactions in (A) males, (B) females, and (C) combined-sexes datasets. For each analysis, within the module containing the Pink1 gene, Pink1 itself was the central node with the highest number of interactions with other genes including solute carriers, glutamate metabotropic receptors, and genes associated with protein localization. Strong connections between Pink1 and Krt2 and Hfe were found in both males and female datasets. In females a number of modules were significantly correlated with vocalization traits. Conclusions Overall, this work supports the premise that gene expression changes in the PAG may contribute to the vocal deficits observed in this PD rat model. Additionally, this dataset identifies genes that represent new therapeutic targets for PD voice disorders.

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