Managing Gene Expression in Pseudomonas Simiae EGD-AQ6 for Chloroaromatic Compound Degradation

Abstract Pseudomonas simiae EGD-AQ6 showed utilization of chloroaromatic compound, 2-4-dichlorophenoxyacetic acid (2,4-D) efficiently in its biofilm phenotype. The differential rates of accumulation of intermediate metabolite 4-chlorocatechol (4-CCA) were significant in both planktonic and biofilm phenotypes; also increased number of biofilm cells were observed during 2,4-D utilization. Interestingly, response surface analysis demonstrated the combined positive effects of 2,4-D degradation and 4-CCA accumulations. Also, gene expression profiles showed significant up-regulation of degradative and biofilm genes (particularly pellicle forming genes) in the biofilm phenotypes than their planktonic counterparts, thereby confirming occurrence of phenotype variations of Pseudomonas simiae EGD-AQ6 during chloroaromatic degradation. Furthermore, the sequence similarity of the 2-4-D catabolic genes and biofilm forming proteins (pel ABCDEFG and pga ABCD) which are responsible for building carbohydrate rich extracellular matrix, were significant with the respective organisms as revealed through genome analysis. This is the first report, which endorses this Pseudomonas simiae species to be unique in chloro-aromatic degradation through phenotype variation, thereby proving as a potential candidate in the improvement of bioremediation technologies.

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Integrated bioinformatics analysis reveals ASPM and CENPF with prognostic value in lung cancer

10.21203/rs.2.13321/v2 ◽

2019 ◽

Author(s):

jinghang li ◽

Jing Zhang ◽

Lin Huang ◽

Sheng Zhao

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Cell Cycle ◽

Expression Profiles ◽

Mirna Gene ◽

Gene Expression Profiles ◽

Genetic Alterations ◽

Potential Candidate ◽

Expression Microarrays ◽

Regulation Of Cell Cycle

Abstract Lung cancer (LC) is the most frequent type of cancer in the world. But the mechanism of LC is still largely unknown. In this study, we analyzed three lung cancer gene expression microarrays of different pathologic types to explore the potential candidate genes in LC by Integrated bioinformatical methods. 459 overlapped differentially expressed genes (DEGs) were explored in three GEO gene expression profiles of different pathologic types of lung cancer and function annotation of DEGs were performed. The main biological process of DEGs was regulation of vasculature development and angiogenesis. The most significant molecular function of DEGs was TGF-β receptor activity. The most significant Reactome pathway of DEGs was cell cycle and extracellular matrix organization pathway. The PPI network of the DEGs was constructed and 23 candidate hub genes were identified in the network . Kaplan-Meier survival analysis show 21 genes were associated with the prognosis of LC. The genetic alterations analysis of these genes by using cBioPortal shown ASPM has the highest genetic alteration rate of 9% in main pathological types of 3191 LC patients , CENPF has the second highest alteration rate of 6% in LC patients. ASPM and CENPF also identified have a significant co-occurrence relationship in LC, and the GO analysis shown they both participate in the regulation of cell cycle. In the TF -miRNA-gene network of 21 genes shown CENPF have the most significant value in the network and the most relevant TF are NFYA, E2F1 and MYC.In conclusion, this study explored several key genes about LC and analyzed potential TF of those genes, provides possible therapeutic targets and biomarker for further clinical application.

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Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon

Physiological Genomics ◽

10.1152/physiolgenomics.00068.2007 ◽

2007 ◽

Vol 31 (1) ◽

pp. 126-138 ◽

Cited By ~ 47

Author(s):

Enrique de la Vega ◽

Michael R. Hall ◽

Kate J. Wilson ◽

Antonio Reverter ◽

Rick G. Woods ◽

...

Keyword(s):

Gene Expression ◽

Sequence Similarity ◽

Expression Profiles ◽

Penaeus Monodon ◽

Gene Expression Profiles ◽

Subtractive Hybridization ◽

Long Terminal Repeat Retrotransposons ◽

Differentially Expressed ◽

Specific Gene ◽

Immune Related Genes

Cultured shrimp are continuously exposed to variable environmental conditions that have been associated with stress and subsequent outbreaks of disease. To investigate the effect of environmental stress on Penaeus monodon gene expression, a 3,853 random cDNA microarray chip was generated with clones originating from six stress-enriched hemocyte libraries generated by suppression subtractive hybridization and a normal hemocyte cDNA library. Changes in temporal gene expression were analyzed from shrimp exposed to hypoxic, hyperthermic, and hypoosmotic conditions; 3.1% of the cDNAs were differentially expressed in response to at least one of the environmental stressors, and 72% of the differentially expressed clones had no significant sequence similarity to previously known genes. Among those genes with high identity to known sequences, the most common functional groups were immune-related genes and non-long terminal repeat retrotransposons. Hierarchical clustering revealed a set of cDNAs with temporal and stress-specific gene expression profiles as well as a set of cDNAs indicating a common stress response between stressors. Hypoxic and hyperthermic stressors induced the most severe short-term response in terms of gene regulation, and the osmotic stress had the least variation in expression profiles relative to the control. These expression data agree with observed differences in shrimp physical appearance and behavior following exposure to stress conditions.

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Identification of Candidate Biomarkers and Prognostic Analysis in Colorectal Cancer Liver Metastases

Frontiers in Oncology ◽

10.3389/fonc.2021.652354 ◽

2021 ◽

Vol 11 ◽

Author(s):

Tianhao Zhang ◽

Kaitao Yuan ◽

Yingzhao Wang ◽

Mingze Xu ◽

Shirong Cai ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Malignant Tumors ◽

Expression Profiles ◽

Gene Expression Profiles ◽

The Cancer Genome Atlas ◽

Coagulation Cascade ◽

Potential Candidate ◽

Colorectal Cancer Liver Metastases ◽

Targeting Therapy

BackgroundColorectal cancer (CRC), one of the most common malignant tumors worldwide, has a high mortality rate, especially for patients with CRC liver metastasis (CLM). However, CLM pathogenesis remains unclear.MethodsWe integrated multiple cohort datasets and databases to clarify and verify potential key candidate biomarkers and signal transduction pathways in CLM. GEO2R, DAVID 6.8, ImageGP, STRING, UALCAN, ONCOMINE, THE HUMAN PROTEIN ATLAS, GEPIA 2.0, cBioPortal, TIMER 2.0, DRUGSURV, CRN, GSEA 4.0.3, FUNRICH 3.1.3 and R 4.0.3 were utilized in this study.ResultsSixty-three pairs of matched colorectal primary cancer and liver metastatic gene expression profiles were screened from three gene expression profiles (GSE6988, GSE14297 and GSE81558). Thirty-one up-regulated genes and four down-regulated genes were identified from these three gene expression profiles and verified by another gene expression profiles (GSE 49355) and TCGA database. Two pathways (IGFBP-IGF signaling pathway and complement-coagulation cascade), eighteen key differentially expressed genes (DEGs), six hub genes (SPARCL1, CDH2, CP, HP, TF and SERPINA5) and two biomarkers (CDH2 and SPARCL1) with significantly prognostic values were screened by multi-omics data analysis and verified by Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) cohort.ConclusionsIn this study, we identified a robust set of potential candidate biomarkers in CLM, which would provide potential value for early diagnosis and prognosis, and would promote molecular targeting therapy for CRC and CLM.

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Gene expression profiles in Ciona intestinalis tailbud embryos

Development ◽

10.1242/dev.128.15.2893 ◽

2001 ◽

Vol 128 (15) ◽

pp. 2893-2904 ◽

Cited By ~ 9

Author(s):

Yutaka Satou ◽

Naohito Takatori ◽

Lixy Yamada ◽

Yasuaki Mochizuki ◽

Makoto Hamaguchi ◽

...

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Sequence Similarity ◽

Expression Profiles ◽

Expression Patterns ◽

Posterior Part ◽

Gene Expression Profiles ◽

Ciona Intestinalis ◽

Sequence Information ◽

Sufficient Information

A set of 3423 expressed sequence tags derived from the Ciona intestinalis tailbud embryos was categorized into 1213 independent clusters. When compared with DNA Data Bank of Japan database, 502 clusters of them showed significant matches to reported proteins with distinct function, whereas 184 lacked sufficient information to be categorized (including reported proteins with undefined function) and 527 had no significant similarities to known proteins. Sequence similarity analyses of the 502 clusters in relation to the biosynthetic function, as well as the structure of the message population at this stage, demonstrated that 390 of them were associated with functions that many kinds of cells use, 85 with cell-cell communication and 27 with transcription factors and other gene regulatory proteins. All of the 1213 clusters were subjected to whole-mount in situ hybridization to analyze the gene expression profiles at this stage. A total of 387 clusters showed expression specific to a certain tissue or organ; 149 showed epidermis-specific expression; 34 were specific to the nervous system; 29 to endoderm; 112 to mesenchyme; 32 to notochord; and 31 to muscle. Many genes were also specifically expressed in multiple tissues. The study also highlighted characteristic gene expression profiles dependent on the tissues. In addition, several genes showed intriguing expression patterns that have not been reported previously; for example, four genes were expressed specifically in the nerve cord cells and one gene was expressed only in the posterior part of muscle cells. This study provides molecular markers for each of the tissues and/or organs that constitutes the Ciona tailbud embryo. The sequence information will also be used for further genome scientific approach to explore molecular mechanisms involved in the formation of one of the most primitive chordate body plans.

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Network Pharmacology of Ginseng (Part II): The Differential Effects of Red Ginseng and Ginsenoside Rg5 in Cancer and Heart Diseases as Determined by Transcriptomics

10.20944/preprints202109.0258.v1 ◽

2021 ◽

Author(s):

Alexander Panossian ◽

Sara Abdelfatah ◽

Thomas Efferth

Keyword(s):

Gene Expression ◽

Heart Diseases ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ginseng Root ◽

Network Pharmacology ◽

Pharmacokinetic Studies ◽

Red Ginseng ◽

Positive Effects ◽

Wide Range

Panax ginseng C.A.Mey. is an adaptogenic plant traditionally used to enhance mental and physical capacities in cases of weakness, exhaustion, tiredness, loss of concentration, and during recovery. According to ancient records, Red Ginseng root preparations enhance longevity with long-term intake. Recent pharmacokinetic studies of ginsenosides in humans and our in vitro study in neuronal cells suggest that ginsenosides are effective when their level in blood is shallow - at concentrations from 10-6 to 10-18 M. In the present study, we compared the effects of Red Ginseng root preparation HRG80TM(HRG) at concentrations from 0.01 to 10,000 ng/ml with effects of White Ginseng (WG) and purified ginsenosides Rb1, Rg3, Rg5 and Rk1 on gene expression of isolated hippocampal neurons. The aim of this study was to predict the effects of differently expressed genes on cellular and physiological functions in organismal disorders and diseases. Gene expression profiling was performed by transcriptome-wide mRNA microarray analyses in murine HT22 cells after treatment with ginseng preparations. Ingenuity pathway downstream/upstream analysis (IPA) was performed with datasets of significantly up-or downregulated genes, and expected effects on cellular function and disease were identified by IPA software. Ginsenosides Rb1, Rg3, Rg5, and Rk1 have substantially various effects on gene expression profiles (signatures) and are different from signatures of HRG and WG. Furthermore, the signature of HRG is changed significantly with dilution from 10000 to 0.01 ng/ml. Network pharmacological analyses of gene expression profiles showed that HRG exhibits predictable positive effects in neuroinflammation, senescence, apoptosis, and immune response, suggesting beneficial soft-acting effects in cancer, gastrointestinal, and endocrine systems diseases and disorders in a wide range of low concentrations in blood.

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Network Pharmacology of Ginseng (Part II): The Differential Effects of Red Ginseng and Ginsenoside Rg5 in Cancer and Heart Diseases as Determined by Transcriptomics

Pharmaceuticals ◽

10.3390/ph14101010 ◽

2021 ◽

Vol 14 (10) ◽

pp. 1010

Author(s):

Alexander Panossian ◽

Sara Abdelfatah ◽

Thomas Efferth

Keyword(s):

Gene Expression ◽

Heart Diseases ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ginseng Root ◽

Network Pharmacology ◽

Pharmacokinetic Studies ◽

Red Ginseng ◽

Positive Effects ◽

Wide Range

Panax ginseng C.A.Mey. is an adaptogenic plant traditionally used to enhance mental and physical capacities in cases of weakness, exhaustion, tiredness, or loss of concentration, and during recovery. According to ancient records, red ginseng root preparations enhance longevity with long-term intake. Recent pharmacokinetic studies of ginsenosides in humans and our in vitro study in neuronal cells suggest that ginsenosides are effective when their levels in blood is low—at concentrations from 10−6 to 10−18 M. In the present study, we compared the effects of red ginseng root preparation HRG80TM(HRG) at concentrations from 0.01 to 10,000 ng/mL with effects of white ginseng (WG) and purified ginsenosides Rb1, Rg3, Rg5 and Rk1 on gene expression in isolated hippocampal neurons. The aim of this study was to predict the effects of differently expressed genes on cellular and physiological functions in organismal disorders and diseases. Gene expression profiling was performed by transcriptome-wide mRNA microarray analyses in murine HT22 cells after treatment with ginseng preparations. Ingenuity pathway downstream/upstream analysis (IPA) was performed with datasets of significantly up- or downregulated genes, and expected effects on cellular function and disease were identified by IPA software. Ginsenosides Rb1, Rg3, Rg5, and Rk1 have substantially varied effects on gene expression profiles (signatures) and are different from signatures of HRG and WG. Furthermore, the signature of HRG is changed significantly with dilution from 10,000 to 0.01 ng/mL. Network pharmacological analyses of gene expression profiles showed that HRG exhibits predictable positive effects in neuroinflammation, senescence, apoptosis, and immune response, suggesting beneficial soft-acting effects in cancer, gastrointestinal, and endocrine systems diseases and disorders in a wide range of low concentrations in blood.

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