Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid

Polyploidization is a universal phenomenon in plants and plays a crucial role in evolution. In this study, the transcriptomes of developing seeds of a synthetic Brassica hexaploid and its parents (B. rapa and B. carinata) were analyzed to find the gene expression changes in hexaploid seeds. There were 3166 and 3893 DEGs between the Brassica hexaploid and its parents at the full-size stage and mature stage, respectively, most of which were upregulated in hexaploid seeds compared to its parents. At the mature stage, the hexaploid seeds showed a greater difference from its parents. These DEGs had a wide range of functions, which may account for the physiological and morphological differences between the Brassica hexaploid and its parents. The KEGG pathway analysis revealed that hexaploid seeds had higher levels of expression of genes involved in metabolic pathways, RNA transport and biosynthesis of secondary metabolites, and the expression levels in the photosynthesis-related pathways were significantly higher than those in B. rapa. Transgressive expression was the main non-additive expression pattern of the Brassica hexaploid. The gene expression difference between the Brassica hexaploid and its paternal parent was more significant than that with its maternal parent, which may be due in part to the cytoplasmic and maternal effects. Moreover, transcription factor genes, such as G2-like, MYB and mTERF, were highly expressed in hexaploid seeds, possibly promoting their resistance to stress. Our results may provide valuable insights into the adaptation mechanisms of polyploid plants.

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Lokiarchaeon exhibits homoacetogenesis

10.1101/826495 ◽

2019 ◽

Author(s):

William D. Orsi ◽

Aurèle Vuillemin ◽

Paula Rodriguez ◽

Ömer K. Coskun ◽

Gonzalo V. Gomez-Saez ◽

...

Keyword(s):

Gene Expression ◽

Host Cell ◽

Extracellular Polymeric Substances ◽

Carbon Fixation ◽

Carbon Sources ◽

Stable Isotope Probing ◽

Organic Substrates ◽

Sugar Fermentation ◽

Expression Of Genes ◽

Wide Range

AbstractThe proposed Asgard superphylum of Archaea comprises the closest archaeal relatives of eukaryotes, whose genomes hold clues pertaining to the nature host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Genomes of the Asgard candidate Phylum ‘Candidatus Lokiarchaeota’ [Lokiarchaeon] suggest an acetogenic H2 –dependent lifestyle5 and mixotrophic capabilities6. However, data on the activity of Lokiarchaeon are currently lacking, and the ecology of the host cell that acquired the mitochondrion is debated4,7. Here, we show that in anoxic marine sediments underlying highly productive waters on the Namibian continental shelf Lokiarchaeon gene expression increases with depth below the seafloor, and was significantly different across a redox gradient spanning hypoxic to sulfidic conditions. Notably, Lokiarchaeon increased expression of genes involved in growth, carbohydrate metabolism, and the H2-dependent Wood-Ljungdahl (WLP) carbon fixation pathway under the most reducing (sulfidic) conditions. Quantitative stable isotope probing experiments revealed multiple populations of Lokiarchaeota utilizing both CO2 and diatomaceous extracellular polymeric substances (dEPS) as carbon sources over a 10-day incubation under anoxic conditions. This apparent anaerobic mixotrophic metabolism was consistent with the expression of Lokiarchaeon genes involved in transport and fermentation of sugars and amino acids. Remarkably, several Asgard populations were more enriched with 13C-dEPS compared to the community average, indicating a preference for dEPS as a growth substrate. The qSIP and gene expression data indicate a metabolism of “Candidatus Lokiarchaeota” similar to that of sugar fermenting homoacetogenic bacteria8, namely that Lokiarchaeon can couple fermentative H2 production from organic substrates with electron bifurcation and the autotrophic and H2-dependent WLP. Homoacetogenesis allows to access a wide range of substrates and relatively high ATP gain during acetogenic sugar fermentation8 thereby providing an ecological advantage for Lokiarchaeon in anoxic, energy limited settings.

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Gene Expression Profile in the CML Cell Line K562 Treated with SKI-606, a Dual Inhibitor of Src/Abl Kinase.

Blood ◽

10.1182/blood.v106.11.4870.4870 ◽

2005 ◽

Vol 106 (11) ◽

pp. 4870-4870

Author(s):

Matteo Renzulli ◽

Tiziana Grafone ◽

Cristian Taccioli ◽

Carolina Terragna ◽

Frank Boschelli ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Differential Expression ◽

Signalling Pathways ◽

Dual Inhibitor ◽

Imatinib Resistance ◽

Regulatory Pathways ◽

Abl Kinase ◽

Expression Of Genes ◽

Wide Range

Abstract Although Imatinib represents the drug of choice for the treatment of Chronic Myeloid Leukemia (CML), new approaches to the treatment of CML remain a high priority in view of the continuing problems of Imatinib resistance. Previously (ASH 2004), we reported on the anti-proliferative and pro-apoptotic effects of the new drug, SKI-606, a potent Src/Abl kinase inhibitor, in blast crisis cell lines in vitro. Here we describe results of a transcriptional profiling study of SKI-606 activity in CML cells. Oligonucleotide microarray analysis using the Human 1A (V2) Oligo Microarrays of Agilent, containing more than 20,000 different genes was performed with untreated K562 cells and compared to the profile obtained from the same cells treated with 10 nM SKI-606 over a 48 h period. We labelled the amplified aRNA of the untreated cells with green (Cy3) dye and that of the treated with red (Cy5) dye, and also performed the reverse labeling experiment to confirm our data. Our approach to design comparisons utilizes a Lowess normalization and a filter followed by an analysis of variance (ANOVA) models to identify the genes with the greatest differential expression in the treated cells. We found identified 121 genes whose expression was modified by treatment with SKI-606. BCR-ABL activity results in activation of several downstream signalling pathways, including RAS/MAPK, PI3K/AKT and STAT pathways, which are implicated in mutagenic signalling and enhancement of survival. Our study showed that the expression of some genes involved in these regulatory pathways was altered by SKI-606. The greatest transcriptional changes (decreases or increases in gene expression of 2-fold or greater) were observed after 24h, while between 24 and 48h, the gene expression pattern stabilized. Ontological information concerning the cellular function of these transcripts suggests differential expression of genes associated with a wide range of cellular processes, including transcriptional regulation (CHAF1B, MRPL1, FLI1, FLN29 and CIR) and signal transduction (HRAS, ELMO, P114-RHO-GEF), among other functions. SKI-606 also modulates the expression of genes involved in cell cycle regulation such as MLLT7, a transcription factor that regulates the cell cycle through transcriptional activation of p27kip1. Our data also provide the first evidence that SKI-606 treatment is down-regulates apoptotic suppressor genes, such as LAMR1, RAC1 and DDB2. Interestingly, the component of the ubiquitin/proteasome pathway, FLJ12673, a subunit of the ubiquitin protein ligase complex, is downregulated by SKI-606 treatment. Currently, we are analyzing the most interesting modified genes to validate our data by Real Time PCR. Genome-wide expression-level analysis combined with biochemical studies of altered signalling pathways with cultured leukemia cells is expected to be a useful functional-genomic approach to more completely characterize the mechanism of action of this compound.

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Generation and characterization of U937-TR: a platform cell line for inducible gene expression in human macrophages

Parasitology ◽

10.1017/s0031182020001110 ◽

2020 ◽

Vol 147 (13) ◽

pp. 1524-1531

Author(s):

Cristian Camilo Galindo ◽

Carlos Arturo Clavijo-Ramírez

Keyword(s):

Gene Expression ◽

Cell Line ◽

Molecular Mechanisms ◽

Expression System ◽

Precise Control ◽

Expression Of Genes ◽

Wide Range ◽

Monocytes And Macrophages

AbstractMonocytes and macrophages are involved in a wide range of biological processes and parasitic diseases. The characterization of the molecular mechanisms governing such processes usually requires precise control of the expression of genes of interest. We implemented a tetracycline-controlled gene expression system in the U937 cell line, one of the most used in vitro models for the research of human monocytes and macrophages. Here we characterized U937-derived cell lines in terms of phenotypic (morphology and marker expression) and functional (capacity for phagocytosis and for Leishmania parasite hosting) changes induced by phorbol-12-myristate-13-acetate (PMA). Finally, we provide evidence of tetracycline-inducible and reversible Lamin-A gene silencing of the PMA-differentiated U937-derived cells.

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Pasteurella multocida Gene Expression in Response to Iron Limitation

Infection and Immunity ◽

10.1128/iai.69.6.4109-4115.2001 ◽

2001 ◽

Vol 69 (6) ◽

pp. 4109-4115 ◽

Cited By ~ 67

Author(s):

Michael L. Paustian ◽

Barbara J. May ◽

Vivek Kapur

Keyword(s):

Gene Expression ◽

Pasteurella Multocida ◽

Molecular Mechanisms ◽

Iron Acquisition ◽

Expression Profiles ◽

Growth Conditions ◽

Whole Genome ◽

Altered Expression ◽

Expression Of Genes ◽

Wide Range

ABSTRACT Pasteurella multocida is the causative agent of a wide range of diseases in avian and mammalian hosts. Gene expression in response to low iron conditions was analyzed in P. multocida using whole-genome microarrays. The analysis shows that the expression of genes involved in energy metabolism and electron transport generally decreased 2.1- to 6-fold while that of genes used for iron binding and transport increased 2.1- to 7.7-fold in P. multocida during the first 2 h of growth under iron-limiting conditions compared with controls. Notably, 27% of the genes with significantly altered expression had no known function, illustrating the limitations of using publicly available databases to identify genes involved in microbial metabolism and pathogenesis. Taken together, the results of our investigations demonstrate the utility of whole-genome microarray analyses for the identification of genes with altered expression profiles during varying growth conditions and provide a framework for the detailed analysis of the molecular mechanisms of iron acquisition and metabolism in P. multocida and other gram-negative bacteria.

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Defining a rob Regulon in Escherichia coliby Using Transposon Mutagenesis

Journal of Bacteriology ◽

10.1128/jb.182.13.3794-3801.2000 ◽

2000 ◽

Vol 182 (13) ◽

pp. 3794-3801 ◽

Cited By ~ 38

Author(s):

Marjon H. J. Bennik ◽

Pablo J. Pomposiello ◽

Derek F. Thorne ◽

Bruce Demple

Keyword(s):

Gene Expression ◽

Organic Solvents ◽

Deletion Mutant ◽

Northern Analysis ◽

Promoter Regions ◽

Mobility Shift ◽

Basal Expression ◽

Transcription Cofactor ◽

Expression Of Genes ◽

Range Of Functions

ABSTRACT The Rob protein of Escherichia coli is a member of the AraC-XylS family of prokaryotic transcriptional regulators and is expressed constitutively. Deletion of the rob gene increases susceptibility to organic solvents, while overexpression of Rob increases tolerance to organic solvents and resistance to a variety of antibiotics and to the superoxide-generating compound phenazine methosulfate. To determine whether constitutive levels of Rob regulate basal gene expression, we performed a MudJ transposon screen in arob deletion mutant containing a plasmid that allows for controlled rob gene expression. We identified eight genes and confirmed that seven are transcriptionally activated by normal expression of Rob from the chromosomal rob gene (inaA, marR, aslB,ybaO, mdlA, yfhD, andybiS). One gene, galT, was repressed by Rob. We also demonstrated by Northern analysis that basal expression ofmicF is significantly higher in wild-type E. coli than in a rob deletion mutant. Rob binding to the promoter regions of most of these genes was substantiated in electrophoretic mobility shift assays. However, Mu insertions in individual Rob-regulated genes did not affect solvent sensitivity. This phenotype may depend on changes in the expression of several of these Rob-regulated genes or on other genes that were not identified. Rob clearly affects the basal expression of genes with a broad range of functions, including antibiotic resistance, acid adaptation, carbon metabolism, cell wall synthesis, central intermediary metabolism, and transport. The magnitudes of Rob's effects are modest, however, and the protein may thus play a role as a general transcription cofactor.

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Differential expression of genes during legume seed development

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1986.0059 ◽

1986 ◽

Vol 314 (1166) ◽

pp. 367-384 ◽

Cited By ~ 49

Keyword(s):

Gene Expression ◽

Seed Development ◽

Seed Protein ◽

Practical Significance ◽

Specific Expression ◽

Control Of Gene Expression ◽

Developing Seeds ◽

Expression Of Genes ◽

Seed Protein Genes ◽

Developmental Programme

The accumulation of certain proteins specific to those tissues in the developing seeds of legumes represents a system of academic and practical significance in the study of differential gene expression. Besides the simple distinction between ‘seed-specific’ and ‘non-seed-specific’ expression of genes, further controls are present in determining the level of expression of a particular gene, and the variations in its expression with cell type, developmental stage and environmental perturbation. There are also genetic factors that lead to variations in the expression of homologous genes between lines or species. Gene expression can be assayed at the levels of synthesis of specific proteins, level of mRNA species, and transcription of specific genes, and the results of all these assays lead to a broad correlation between events at the level of the gene and protein deposition in the developing seed. This correlation is strong at earlier stages of seed development, but is weaker at later stages. Evidence is presented that control of gene expression occurs both at transcription and by post-transcriptional processes. Seed protein genes have conserved sequences in their 5' flanking regions that are specific to gene families, and these are suggested to be involved in transcriptional control of the expression of these genes. Although such sequences are unlikely to be solely responsible for transcription control, there is no strong evidence for changes in DNA methylation or in chromatin conformation being causally related to expression of seed protein genes. Control of gene expression in developing seeds is considered in terms of a genetically determined, conserved developmental programme, the aim of which is to produce a viable embryo. This programme will allow considerable plasticity in gene expression within constraints prescribed by seed viability. Although it may be possible to understand the immediate controls of seed protein gene expression, present systems are not adequate to study the genes that control the developmental programme. More fundamental investigations will be assisted by mutants that possess altered seed development patterns.

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Differential Effects of Epinephrine, Norepinephrine, and Indole on Escherichia coli O157:H7 Chemotaxis, Colonization, and Gene Expression

Infection and Immunity ◽

10.1128/iai.00630-07 ◽

2007 ◽

Vol 75 (9) ◽

pp. 4597-4607 ◽

Cited By ~ 195

Author(s):

Tarun Bansal ◽

Derek Englert ◽

Jintae Lee ◽

Manjunath Hegde ◽

Thomas K. Wood ◽

...

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Biofilm Formation ◽

Signaling Molecules ◽

Signal Molecules ◽

Autoinducer 2 ◽

Expression Of Genes ◽

Wide Range ◽

Host Cell Surface

ABSTRACT During infection in the gastrointestinal tract, enterohemorrhagic Escherichia coli (EHEC) O157:H7 is exposed to a wide range of signaling molecules, including the eukaryotic hormones epinephrine and norepinephrine, and bacterial signal molecules such as indole. Since these signaling molecules have been shown to be involved in the regulation of phenotypes such as motility and virulence that are crucial for EHEC infections, we hypothesized that these molecules also govern the initial recognition of the large intestine environment and attachment to the host cell surface. Here, we report that, compared to indole, epinephrine and norepinephrine exert divergent effects on EHEC chemotaxis, motility, biofilm formation, gene expression, and colonization of HeLa cells. Using a novel two-fluorophore chemotaxis assay, it was found that EHEC is attracted to epinephrine and norepinephrine while it is repelled by indole. In addition, epinephrine and norepinephrine also increased EHEC motility and biofilm formation while indole attenuated these phenotypes. DNA microarray analysis of surface-associated EHEC indicated that epinephrine/norepinephrine up-regulated the expression of genes involved in surface colonization and virulence while exposure to indole decreased their expression. The gene expression data also suggested that autoinducer 2 uptake was repressed upon exposure to epinephrine/norepinephrine but not indole. In vitro adherence experiments confirmed that epinephrine and norepinephrine increased attachment to epithelial cells while indole decreased adherence. Taken together, these results suggest that epinephrine and norepinephrine increase EHEC infection while indole attenuates the process.

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Reverse Screening Bioinformatics Approach to Identify Potential Anti Breast Cancer Targets Using Thymoquinone from Neutraceuticals Black Cumin Oil

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520619666190124155359 ◽

2019 ◽

Vol 19 (5) ◽

pp. 599-609 ◽

Cited By ~ 1

Author(s):

Sumathi Sundaravadivelu ◽

Sonia K. Raj ◽

Banupriya S. Kumar ◽

Poornima Arumugamand ◽

Padma P. Ragunathan

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cell Cycle ◽

Cell Death ◽

In Silico ◽

Chemotherapeutic Agents ◽

Normal Cells ◽

Black Cumin ◽

In Silico Docking ◽

Wide Range

Background: Functional foods, neutraceuticals and natural antioxidants have established their potential roles in the protection of human health and diseases. Thymoquinone (TQ), the main bioactive component of Nigella sativa seeds (black cumin seeds), a plant derived neutraceutical was used by ancient Egyptians because of their ability to cure a variety of health conditions and used as a dietary food supplement. Owing to its multi targeting nature, TQ interferes with a wide range of tumorigenic processes and counteracts carcinogenesis, malignant growth, invasion, migration, and angiogenesis. Additionally, TQ can specifically sensitize tumor cells towards conventional cancer treatments (e.g., radiotherapy, chemotherapy, and immunotherapy) and simultaneously minimize therapy-associated toxic effects in normal cells besides being cost effective and safe. TQ was found to play a protective role when given along with chemotherapeutic agents to normal cells. Methods: In the present study, reverse in silico docking approach was used to search for potential molecular targets for cancer therapy. Various metastatic and apoptotic targets were docked with the target ligand. TQ was also tested for its anticancer activities for its ability to cause cell death, arrest cell cycle and ability to inhibit PARP gene expression. Results: In silico docking studies showed that TQ effectively docked metastatic targets MMPs and other apoptotic and cell proliferation targets EGFR. They were able to bring about cell death mediated by apoptosis, cell cycle arrest in the late apoptotic stage and induce DNA damage too. TQ effectively down regulated PARP gene expression which can lead to enhanced cancer cell death. Conclusion: Thymoquinone a neutraceutical can be employed as a new therapeutic agent to target triple negative breast cancer which is otherwise difficult to treat as there are no receptors on them. Can be employed along with standard chemotherapeutic drugs to treat breast cancer as a combinatorial therapy.

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Structure, Function and Interactions of Tau: Particular Focus on Potential Drug Targets for the Treatment of Tauopathies

CNS & Neurological Disorders - Drug Targets ◽

10.2174/1871527317666180525112008 ◽

2018 ◽

Vol 17 (5) ◽

pp. 325-337 ◽

Cited By ~ 2

Author(s):

Hojjat Borna ◽

Kasim Assadoulahei ◽

Gholamhossein Riazi ◽

Asghar Beigi Harchegani ◽

Alireza Shahriary

Keyword(s):

Tau Protein ◽

Drug Targets ◽

Brain Injuries ◽

Potential Drug ◽

Microtubule Network ◽

Wide Range ◽

Potential Risk Factors ◽

Range Of Functions ◽

Potential Drug Targets

Background & Objective: Neurodegenrative diseases are among the most widespread lifethreatening disorders around the world in elderly ages. The common feature of a group of neurodegenerative disorders, called tauopathies, is an accumulation of microtubule associated protein tau inside the neurons. The exact mechanism underlying tauopathies is not well-understood but several factors such as traumatic brain injuries and genetics are considered as potential risk factors. Although tau protein is well-known for its key role in stabilizing and organization of axonal microtubule network, it bears a broad range of functions including DNA protection and participation in signaling pathways. Moreover, the flexible unfolded structure of tau facilitates modification of tau by a wide range of intracellular enzymes which in turn broadens tau function and interaction spectrum. The distinctive properties of tau protein concomitant with the crucial role of tau interaction partners in the progression of neurodegeneration suggest tau and its binding partners as potential drug targets for the treatment of neurodegenerative diseases. Conclusion: This review aims to give a detailed description of structure, functions and interactions of tau protein in order to provide insight into potential therapeutic targets for treatment of tauopathies.

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The Differential Metabolomes in Cumulus and Mural Granulosa Cells from Human Preovulatory Follicles

Reproductive Sciences ◽

10.1007/s43032-021-00691-3 ◽

2021 ◽

Author(s):

Er-Meng Gao ◽

Bongkoch Turathum ◽

Ling Wang ◽

Di Zhang ◽

Yu-Bing Liu ◽

...

Keyword(s):

Oocyte Maturation ◽

Granulosa Cells ◽

Quantitative Polymerase Chain Reaction ◽

Cumulus Cells ◽

Cholesterol Transport ◽

Vitro Fertilization ◽

Expression Of Genes ◽

Preovulatory Follicles ◽

Morphological Differences

AbstractThis study evaluated the differences in metabolites between cumulus cells (CCs) and mural granulosa cells (MGCs) from human preovulatory follicles to understand the mechanism of oocyte maturation involving CCs and MGCs. CCs and MGCs were collected from women who were undergoing in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) treatment. The differences in morphology were determined by immunofluorescence. The metabolomics of CCs and MGCs was measured by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) followed by quantitative polymerase chain reaction (qPCR) and western blot analysis to further confirm the genes and proteins involved in oocyte maturation. CCs and MGCs were cultured for 48 h in vitro, and the medium was collected for detection of hormone levels. There were minor morphological differences between CCs and MGCs. LC-MS/MS analysis showed that there were differences in 101 metabolites between CCs and MGCs: 7 metabolites were upregulated in CCs, and 94 metabolites were upregulated in MGCs. The metabolites related to cholesterol transport and estradiol production were enriched in CCs, while metabolites related to antiapoptosis were enriched in MGCs. The expression of genes and proteins involved in cholesterol transport (ABCA1, LDLR, and SCARB1) and estradiol production (SULT2B1 and CYP19A1) was significantly higher in CCs, and the expression of genes and proteins involved in antiapoptosis (CRLS1, LPCAT3, and PLA2G4A) was significantly higher in MGCs. The level of estrogen in CCs was significantly higher than that in MGCs, while the progesterone level showed no significant differences. There are differences between the metabolomes of CCs and MGCs. These differences may be involved in the regulation of oocyte maturation.

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