scholarly journals Evidence in support of gene regulatory hypothesis: Gene expression profiling manifests homeopathy effect as more than placebo

2021 ◽  
Vol 12 (45) ◽  
pp. 162-167
Author(s):  
Anisur Rahman Khuda-Bukhsh ◽  
Santu Kumar Saha ◽  
Sourav Roy
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Gene Expressions ◽  
Microarray Gene Expression ◽  
Hydrastis Canadensis ◽  
Modulation Of Gene Expression ◽  
Homeopathic Remedies

Background: Use of ultra-high diluted remedies in homeopathy and their claimed efficacy in curing diseases has been challenged time and again by non-believers despite many evidence-based positive results published in favor of their efficacy in curing/ameliorating disease symptoms. Aims: To test the ability of ultra-high diluted homeopathic remedies beyond Avogadro’s limit, if any, in manifesting gene modulating effects in controlled in vitro experimental model. Methods: Since cancer cells manifest aberrant epigenetic gene expressions, we conducted global microarray gene expression profiling of HeLa cells (an established epigenetic model of HPV18 positive cell line) treated with two different potentized homeopathic remedies, namely, Condurango 30c and Hydrastis canadensis 30C (used in the treatment of cancer), as compared to that of placebo (succussed alcohol 30c). Results: Data revealed distinctly different expression patterns of over 100 genes as a consequence of treatment with both homeopathc remedies compared to placebo. Conclusion: Results indicate that action of the potentized drugs was “more than placebo” and these ultra-highly diluted drugs acted primarily through modulation of gene expression.

scholarly journals What can we learn from gene expression profiling of mouse oocytes?

Reproduction ◽  
2008 ◽  
Vol 135 (5) ◽  
pp. 581-592 ◽  
Author(s):  
Toshio Hamatani ◽  
Mitsutoshi Yamada ◽  
Hidenori Akutsu ◽  
Naoaki Kuji ◽  
Yoshiyuki Mochimaru ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Oocyte Quality ◽  
Preimplantation Development ◽  
Preimplantation Embryos ◽  
Gene Expressions ◽  
Oocyte Competence

Mammalian ooplasm supports the preimplantation development and reprograms the introduced nucleus transferred from a somatic cell to confer pluripotency in a cloning experiment. However, the underlying molecular mechanisms of oocyte competence remain unknown. Recent advances in microarray technologies have allowed gene expression profiling of such tiny specimens as oocytes and preimplantation embryos, generating a flood of information about gene expressions. So, what can we learn from it? Here, we review the initiative global gene expression studies of mouse and/or human oocytes, focusing on the lists of maternal transcripts and their expression patterns during oogenesis and preimplantation development. Especially, the genes expressed exclusively in oocytes should contribute to the uniqueness of oocyte competence, driving mammalian development systems of oocytes and preimplantation embryos. Furthermore, we discuss future directions for oocyte gene expression profiling, including discovering biomarkers of oocyte quality and exploiting the microarray data for ‘making oocytes’.

Gene expression profiling reveals the profound upregulation of hypoxia-responsive genes in primary human astrocytes

2006 ◽  
Vol 25 (3) ◽  
pp. 435-449 ◽  
Author(s):  
S. M. Mense ◽  
A. Sengupta ◽  
M. Zhou ◽  
C. Lan ◽  
G. Bentsman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Hela Cells ◽  
Expression Profiling ◽  
Target Genes ◽  
Expression Patterns ◽  
Angiogenic Growth Factors ◽  
Microarray Gene Expression ◽  
Human Astrocytes ◽  
The Brain

Oxygen is vital for the development and survival of mammals. In response to hypoxia, the brain initiates numerous adaptive responses at the organ level as well as at the molecular and cellular levels, including the alteration of gene expression. Astrocytes play critical roles in the proper functioning of the brain; thus the manner in which astrocytes respond to hypoxia is likely important in determining the outcome of brain hypoxia. Here, we used microarray gene expression profiling and data-analysis algorithms to identify and analyze hypoxia-responsive genes in primary human astrocytes. We also compared gene expression patterns in astrocytes with those in human HeLa cells and pulmonary artery endothelial cells (ECs). Remarkably, in astrocytes, five times as many genes were induced as suppressed, whereas in HeLa and pulmonary ECs, as many as or more genes were suppressed than induced. More genes encoding hypoxia-inducible functions, such as glycolytic enzymes and angiogenic growth factors, were strongly induced in astrocytes compared with HeLa cells. Furthermore, gene ontology and computational algorithms revealed that many target genes of the EGF and insulin signaling pathways and the transcriptional regulators Myc, Jun, and p53 were selectively altered by hypoxia in astrocytes. Indeed, Western blot analysis confirmed that two major signal transducers mediating insulin and EGF action, Akt and MEK1/2, were activated by hypoxia in astrocytes. These results provide a global view of the signaling and regulatory network mediating oxygen regulation in human astrocytes.

scholarly journals Gene-expression profiling elucidates molecular signaling networks that can be therapeutically targeted in vestibular schwannoma

2014 ◽  
Vol 121 (6) ◽  
pp. 1434-1445 ◽  
Author(s):  
Sameer Agnihotri ◽  
Isabel Gugel ◽  
Marc Remke ◽  
Antje Bornemann ◽  
Georgios Pantazis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Cell Line ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Mtor Pathway ◽  
Signaling Networks ◽  
Benign Tumors ◽  
Specific Gene

ObjectVestibular schwannomas (VS) are common benign tumors of the vestibular nerve that cause significant morbidity. The current treatment strategies for VS include surgery or radiation, with each treatment option having associated complications and side effects. The transcriptional landscape of schwannoma remains largely unknown.MethodsIn this study the authors performed gene-expression profiling of 49 schwannomas and 7 normal control vestibular nerves to identify tumor-specific gene-expression patterns. They also interrogated whether schwannomas comprise several molecular subtypes using several transcription-based clustering strategies. The authors also performed in vitro experiments testing therapeutic inhibitors of over-activated pathways in a schwannoma cell line, namely the PI3K/AKT/mTOR pathway.ResultsThe authors identified over 4000 differentially expressed genes between controls and schwannomas with network analysis, uncovering proliferation and anti-apoptotic pathways previously not implicated in VS. Furthermore, using several distinct clustering technologies, they could not reproducibly identify distinct VS subtypes or significant differences between sporadic and germline NF2–associated schwannomas, suggesting that they are highly similar entities. The authors identified overexpression of PI3K/AKT/mTOR signaling networks in their geneexpression study and evaluated this pathway for therapeutic targeting. Testing the compounds BEZ235 and PKI-587, both novel dual inhibitors of PI3K and mTOR, attenuated tumor growth in a preclinical cell line model of schwannoma (HEI-293). In vitro findings demonstrated that pharmacological inhibition of the PI3K/AKT/mTOR pathway with next-generation compounds led to decreased cell viability and increased cell death.ConclusionsThese findings implicate aberrant activation of the PI3K/AKT/mTOR pathway as a molecular mechanism of pathogenesis in VS and suggest inhibition of this pathway as a potential treatment strategy.

scholarly journals 256CONSTRUCTION OF A BOVINE CDNA ARRAY TO MONITOR GENE EXPRESSION PROFILES IN BOVINE PREIMPLANTATION EMBRYOS

2004 ◽  
Vol 16 (2) ◽  
pp. 248
Author(s):  
C. Wrenzycki ◽  
T. Brambrink ◽  
D. Herrmann ◽  
J.W. Carnwath ◽  
H. Niemann
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Expression Profiles ◽  
Cdna Array ◽  
Preimplantation Embryos ◽  
Average Insert Size ◽  
Rt Pcr ◽  
Public Data

Array technology is a widely used tool for gene expression profiling, providing the possibility to monitor expression levels of an unlimited number of genes in various biological systems including preimplantation embryos. The objective of the present study was to develop and validate a bovine cDNA array and to compare expression profiles of embryos derived from different origins. A bovine blastocyst cDNA library was generated. Poly(A+)RNA was extracted from in vitro-produced embryos using a Dynabead mRNA purification kit. First-strand synthesis was performed with SacIT21 primer followed by randomly primed second-strand synthesis with a DOP primer mix (Roche) and a global PCR with 35 cycles using SacIT21 and DOP primers. Complementary DNA fragments from 300 to 1500bp were extracted from the gel and normalized via reassoziation and hydroxyapatite chromatography. Resulting cDNAs were digested with SacI and XhoI, ligated into a pBKs vector, and transfected into competent bacteria (Stratagene). After blue/white colony selection, plasmids were extracted and the inserts were subjected to PCR using vector specific primers. Average insert size was determined by size idenfication on agarose gels stained with ethidium bromide. After purification via precipitation and denaturation, 192 cDNA probes were double-spotted onto a nylon membrane and bound to the membrane by UV cross linking. Amplified RNA (aRNA) probes from pools of three or single blastocysts were generated as described recently (Brambrink et al., 2002 BioTechniques, 33, 3–9) and hybridized to the membranes. Expression profiles of in vitro-produced blastocysts cultured in either SOF plus BSA or TCM plus serum were compared with those of diploid parthenogenetic ones generated by chemical activation. Thirty-three probes have been sequenced and, after comparison with public data bases, 26 were identified as cDNAs or genes. Twelve out of 192 (6%) seem to be differentially expressed within the three groups;; 7/12 (58%) were down-regulated, 3/12 (25%) were up-regulated in SOF-derived embryos, and 2/12 (20%) were up-regulated in parthenogenetic blastocysts compared to their in vitro-generated counterparts. Three of these genes involved in calcium signaling (calmodulin, calreticulin) and regulation of actin cytoskeleton (destrin) were validated by semi-quantitative RT-PCR (Wrenzycki et al., 2001 Biol. Reprod. 65, 309–317) employing poly(A+) RNA from a single blastocyst as starting material. No differences were detected in the relative abundance of the analysed gene transcripts within the different groups. These findings were confirmed employing the aRNA used for hybridization in RT-PCR and showed a good representativity of the selected transcripts. Results indicate that it is possible to construct a homologous cDNA array which could be used for gene expression profiling of bovine preimplantation embryos. Supported by the Deutsche Forschungsgemeinschaft (DFG Ni 256/18-1).

scholarly journals Three Years Follow-Up Study Showed Prenatal Methamphetamine Exposure May Cause Chronic Abnormalities In Transcriptomic Pattern

2021 ◽  
Author(s):  
Arvin Haghighatfard ◽  
Soha Seifollahi ◽  
Pegah Rajabi ◽  
Niloofar Rahmani ◽  
Rojin Ghannadzadeh
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Rna Extraction ◽  
Childbearing Age ◽  
Methamphetamine Use ◽  
Methamphetamine Use Disorder

Abstract Background: The high rate of methamphetamine use disorder among young adults and women of childbearing age makes it imperative to clarify the long-term effects of Methamphetamine exposure on the offspring. Behavioral and cognitive problems had been reported in children with parental Methamphetamine exposure (PME). The present study aimed to assess the acute and chronic effects of PME in molecular regulations and gene expression profiles of children during their first years of life.Methods: All subjects were recruited before birth, and sampling was conducted from the first ten days of birth, twelve months, twenty months, and thirty-six months of age. Finally, 2658 children with PME and 3573 normal children had been finished the follow-up. RNA extraction was operated from blood samples and gene expression profiling was conducted by using the Affymetrix GeneChip Human Genome U133 plus 2.0 Array Platform. Gene expression data were confirmed by Real-time PCR. Results: Gene expression profiling during thirty-six months showed several constant mRNA level alterations in children with PME compared with normal. These genes are involved in several gene ontologies and pathways involved with the immune system, neuronal functions, and bioenergetic metabolism. It seems that Methamphetamine use disorder before and during the pregnancy period may affect the expression profile of children, and these changes could remain years after birth. Affected genes have some similarities with the gene expression patterns of addiction, psychiatric disorders, neurodevelopmental disabilities, and immune deficiencies. Conclusion: Findings may shed light on the molecular effects of prenatal methamphetamine exposure and may lead to new psychological and somatic caring protocols for these children based on their potential abnormalities.

Biological Image Analysis via Matrix Approximation

2011 ◽  
pp. 166-170
Author(s):  
Jieping Ye ◽  
Ravi Janardan ◽  
Sudhir Kumar
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Controlled Vocabulary ◽  
Gene Expression Patterns ◽  
Image Content ◽  
Gene Expressions ◽  
Microarray Gene Expression ◽  
Individual Gene

Understanding the roles of genes and their interactions is one of the central challenges in genome research. One popular approach is based on the analysis of microarray gene expression data (Golub et al., 1999; White, et al., 1999; Oshlack et al., 2007). By their very nature, these data often do not capture spatial patterns of individual gene expressions, which is accomplished by direct visualization of the presence or absence of gene products (mRNA or protein) (e.g., Tomancak et al., 2002; Christiansen et al., 2006). For instance, the gene expression pattern images of a Drosophila melanogaster embryo capture the spatial and temporal distribution of gene expression patterns at a given developmental stage (Bownes, 1975; Tsai et al., 1998; Myasnikova et al., 2002; Harmon et al., 2007). The identification of genes showing spatial overlaps in their expression patterns is fundamentally important to formulating and testing gene interaction hypotheses (Kumar et al., 2002; Tomancak et al., 2002; Gurunathan et al., 2004; Peng & Myers, 2004; Pan et al., 2006). Recent high-throughput experiments of Drosophila have produced over fifty thousand images (http://www. fruitfly.org/cgi-bin/ex/insitu.pl). It is thus desirable to design efficient computational approaches that can automatically retrieve images with overlapping expression patterns. There are two primary ways of accomplishing this task. In one approach, gene expression patterns are described using a controlled vocabulary, and images containing overlapping patterns are found based on the similarity of textual annotations. In the second approach, the most similar expression patterns are identified by a direct comparison of image content, emulating the visual inspection carried out by biologists [(Kumar et al., 2002); see also www.flyexpress.net]. The direct comparison of image content is expected to be complementary to, and more powerful than, the controlled vocabulary approach, because it is unlikely that all attributes of an expression pattern can be completely captured via textual descriptions. Hence, to facilitate the efficient and widespread use of such datasets, there is a significant need for sophisticated, high-performance, informatics-based solutions for the analysis of large collections of biological images.

Study of Basic Concepts on the Development of Protein Microarray - Gene Expression Profiling

2016 ◽  
pp. 263-295
Author(s):  
P. Sivashanmugam ◽  
Arun C. ◽  
Selvakumar P.
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Protein Microarray ◽  
Microarray Technology ◽  
Microarray Gene Expression ◽  
High Throughput Technology ◽  
Multiple Cell ◽  
Stressed Cell ◽  
Microarray Gene

The physical and biological activity of any organisms is mainly depended on the genetic information which stored in DNA. A process at which a gene gives rise to a phenotype is called as gene expression. Analysis of gene expression can be used to interpret the changes that occur at biological level of a stressed cell or tissue. Hybridization technology helps to study the gene expression of multiple cell at a same time. Among them microarray technology is a high- throughput technology to study the gene expression at transcription level (DNA) or translation level (Protein). Analysis the protein only can predict the accurate changes that happens in a tissue, when they are infected by a disease causing organisms. Protein microarray mainly used to identify the interactions and activities of proteins with other molecules, and to determine their function for a system at normal state and stressed state. The scope of this chapter is to outline a detail description on the fabrication, types, data analysis, and application of protein microarray technology towards gene expression profiling.

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