The Primate Embryo Gene Expression Resource in embryology and stem cell biology

2006 ◽  
Vol 18 (8) ◽  
pp. 807 ◽  
Author(s):  
Keith E. Latham
Keyword(s):  
Gene Expression ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Embryonic Stem ◽  
Cdna Libraries ◽  
Human Embryos ◽  
Preimplantation Stage ◽  
Study Gene Expression ◽  
On Line ◽  
Legal Constraints

The analysis of temporal patterns of gene expression in embryos is an essential component of any research program seeking to understand molecular mechanisms that control development. Little is known of early regulatory mechanisms that operate in primate oocytes and preimplantation-stage embryos. Such studies have been hindered by the cost of obtaining, and limited availability of, non-human primate oocytes and embryos, and by ethical and legal constraints on studies of human embryos. Over the past 4 years we have established the Primate Embryo Gene Expression Resource (PREGER) to circumvent these limitations. A set of over 200 samples of rhesus monkey oocytes and embryos has been converted to cDNA libraries, which are, in turn, used for a variety of molecular analyses. Both the libraries and cDNA dot blots can be distributed free of charge to anyone wishing to study gene expression at these stages. This includes providing an inexpensive and rapid method for confirming and extending results of gene discovery approaches such as microarray analysis. PREGER includes an on-line resource with a database and other useful tools for embryologists. The resource is being expanded to incorporate samples from other species and from embryonic stem cells.

Gene Expression Analysis on the Early Development of Pig Embryos Exposed to Malathion

2007 ◽  
Vol 26 (2) ◽  
pp. 143-149 ◽  
Author(s):  
Zayil Salazar ◽  
Yvonne Ducolomb ◽  
Miguel Betancourt ◽  
Edmundo Bonilla ◽  
Leticia Cortés ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Hypothetical Protein ◽  
Cdna Libraries ◽  
Mhc I ◽  
Vitro Fertilization ◽  
Embryo Cells ◽  
Gene Expression Alterations

Malathion is a widely used pesticide and there is evidence that it could alter mammal’s germ and somatic cells, as well as cell lines. There are not enough studies showing how the nonacute malathion doses affect gene expression. This study analyzes gene expression alterations in pig morular embryos exposed in vitro , for 96 h, to several malathion concentrations after in vitro fertilization. cDNA libraries of isolated morular embryos were created and differential screenings performed to identify target genes. Seven clones were certainly identified. Genes related to mitochondrial metabolism as cytochrome c subunits I and III, nuclear genes such as major histocompatibility complex I (MHC I), and a hypothetical protein related with a splicing factor were the target of malathion’s deregulation effect. The widespread use of malathion as a pesticide should be regarded with reproductive implications and more detailed analysis would yield more about molecular mechanisms of malathion injury on embryo cells.

scholarly journals Pluripotency and nuclear reprogramming

2008 ◽  
Vol 363 (1500) ◽  
pp. 2079-2087 ◽  
Author(s):  
Shinya Yamanaka
Keyword(s):  
Stem Cells ◽  
Molecular Mechanisms ◽  
Potential Problem ◽  
Somatic Cells ◽  
Embryonic Stem ◽  
Donor Cell ◽  
Human Embryos ◽  
Cell Sources ◽  
Cell Transplantation Therapy ◽  
Transplantation Therapy

Embryonic stem cells are promising donor cell sources for cell transplantation therapy, which may in the future be used to treat various diseases and injuries. However, as is the case for organ transplantation, immune rejection after transplantation is a potential problem with this type of therapy. Moreover, the use of human embryos presents serious ethical difficulties. These issues may be overcome if pluripotent stem cells are generated from patients' somatic cells. Here, we review the molecular mechanisms underlying pluripotency and the currently known methods of inducing pluripotency in somatic cells.

scholarly journals Study of Cold Tolerance in Blueberry Using EST Libraries, cDNA Microarrays, and Subtractive Hybridization

HortScience ◽  
2008 ◽  
Vol 43 (7) ◽  
pp. 1975-1981 ◽  
Author(s):  
Lisa J. Rowland ◽  
Anik L. Dhanaraj ◽  
Dhananjay Naik ◽  
Nadim Alkharouf ◽  
Ben Matthews ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cold Acclimation ◽  
Subtractive Hybridization ◽  
Vaccinium Corymbosum ◽  
Cdna Libraries ◽  
Woody Perennial ◽  
Floral Buds ◽  
Cold Room ◽  
Study Gene Expression ◽  
Low Temperature Exposure

To gain a better understanding of changes in gene expression associated with cold acclimation in the woody perennial blueberry (Vaccinium corymbosum L.) and ultimately use this information to develop more freeze-tolerant cultivars, a genomics approach based on the analysis of expressed sequence tags (ESTs) and microarrays was undertaken. Initially, two standard cDNA libraries, constructed using RNA from cold-acclimated (CA) and nonacclimated (NA) floral buds of the blueberry cultivar Bluecrop, were used for the generation of ≈2400 ESTs, half from each library. Putative functions were assigned to cDNAs based on homology to other genes/ESTs from GenBank. From contig analyses, 796 and 865 unique transcripts were identified from the CA and NA libraries, respectively. The most highly abundant cDNAs, that were picked many more times from one library than from the other, were identified as representing potentially differentially expressed transcripts. A cDNA microarray was constructed and used to study gene expression under cold-acclimating conditions in the field and cold room. Results indicated that the abundance of transcripts of numerous blueberry genes change during cold acclimation, including genes not found previously to be cold-responsive in Arabidopsis, and, interestingly, more transcripts were found to be upregulated under cold room conditions than under field conditions. Finally, forward and reverse subtracted cDNA libraries were prepared from ‘Bluecrop’ RNA to enrich for transcripts that are expressed at higher levels in floral buds at 400 h and at 0 h of low-temperature exposure, respectively. Many genes encoding putative transcription factors and other proteins related to signal transduction were identified from both libraries.

scholarly journals Ferritin Light Chain (FTL) competes with long noncoding RNA Linc00467 for miR-133b binding site to regulate chemoresistance and metastasis of colorectal cancer

2019 ◽  
Vol 41 (4) ◽  
pp. 467-477 ◽  
Author(s):  
Zengyao Li ◽  
Jing Liu ◽  
Hang Chen ◽  
Ye Zhang ◽  
Haoze Shi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Light Chain ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Luciferase Reporter ◽  
Migration And Invasion ◽  
Cell Resistance ◽  
Biological Functions ◽  
Study Gene Expression

Abstract Although the colorectal cancer (CRC) mortality rates are decreasing in virtue of CRC screening and improved therapeutic methods, CRC is still a leading cause of cancer deaths. One of the main causes is chemoresistance occurrence in CRC. Understanding of the molecular mechanisms of chemoresistance benefits to CRC diagnosis and treatment. In this study, gene expression was determined by western blot and qRT-PCR. The biological functions of genes in CRC cells were studied by knocking down or overexpressing the gene in CRC cells and then analyzing cell sensitivity to 5-Fu by the MTT assay and the flow cytometry, and analyzing cell migration and invasion by transwell assays. The luciferase reporter assay was used to examine microRNA regulation of target gene expression, and biotin pull-down assay was performed to detect interaction between RNA molecules. This study found that ferritin light chain (FTL) and long intergenic noncoding RNA Linc00467 were both upregulated in CRC tissues and cell lines, and inversely correlated to CRC patient survival. FTL and Linc00467 promoted CRC cells abilities to resistance against 5-fluor-ouracil (5-Fu), migration and invasion. These effects were compromised by miR-133b which targeted both FTL and Linc00467. miR-133b interacted with Linc00467 and miR-133b inhibitor prevented Linc00467 knockdown-induced alternations of FTL expression and biological functions. Both FTL and Linc00467 are oncogenes in CRC. FTL expression upregulated in CRC via Linc00467/ miR-133b axis, and leads to CRC cell resistance against 5-FU treatment and promotes CRC metastasis. FTL expression upregulated in CRC via Linc00467/miR-133b axis, and leads to CRC cell resistance to 5-FU treatment and promotes CRC metastasis.

scholarly journals Evaluation of drought resistance and transcriptome analysis for the identification of drought-responsive genes in Iris germanica

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jingwei Zhang ◽  
Dazhuang Huang ◽  
Xiaojie Zhao ◽  
Man Zhang
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Drought Resistance ◽  
Molecular Mechanisms ◽  
Cdna Libraries ◽  
Sequencing Analysis ◽  
Peg 6000 ◽  
Sequencing Platform ◽  
Iris Germanica ◽  
Drought Resistant

AbstractIris germanica, a species with very high ornamental value, exhibits the strongest drought resistance among the species in the genus Iris, but the molecular mechanism underlying its drought resistance has not been evaluated. To investigate the gene expression profile changes exhibited by high-drought-resistant I. germanica under drought stress, 10 cultivars with excellent characteristics were included in pot experiments under drought stress conditions, and the changes in the chlorophyll (Chl) content, plasma membrane relative permeability (RP), and superoxide dismutase (SOD), malondialdehyde (MDA), free proline (Pro), and soluble protein (SP) levels in leaves were compared among these cultivars. Based on their drought-resistance performance, the 10 cultivars were ordered as follows: ‘Little Dream’ > ‘Music Box’ > ‘X’Brassie’ > ‘Blood Stone’ > ‘Cherry Garden’ > ‘Memory of Harvest’ > ‘Immortality’ > ‘White and Gold’ > ‘Tantara’ > ‘Clarence’. Using the high-drought-resistant cultivar ‘Little Dream’ as the experimental material, cDNA libraries from leaves and rhizomes treated for 0, 6, 12, 24, and 48 h with 20% polyethylene glycol (PEG)-6000 to simulate a drought environment were sequenced using the Illumina sequencing platform. We obtained 1, 976, 033 transcripts and 743, 982 unigenes (mean length of 716 bp) through a hierarchical clustering analysis of the resulting transcriptome data. The unigenes were compared against the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and gene ontology (GO) databases for functional annotation, and the gene expression levels in leaves and rhizomes were compared between the 20% PEG-6000 stress treated (6, 12, 24, and 48 h) and control (0 h) groups using DESeq2. 7849 and 24,127 differentially expressed genes (DEGs) were obtained from leaves and rhizomes, respectively. GO and KEGG enrichment analyses of the DEGs revealed significantly enriched KEGG pathways, including ribosome, photosynthesis, hormone signal transduction, starch and sucrose metabolism, synthesis of secondary metabolites, and related genes, such as heat shock proteins (HSPs), transcription factors (TFs), and active oxygen scavengers. In conclusion, we conducted the first transcriptome sequencing analysis of the I. germanica cultivar ‘Little Dream’ under drought stress and generated a large amount of genetic information. This study lays the foundation for further exploration of the molecular mechanisms underlying the responses of I. germanica to drought stress and provides valuable genetic resources for the breeding of drought-resistant plants.

scholarly journals MMP14 Contributes to HDAC Inhibition-Induced Radiosensitization of Glioblastoma

2021 ◽  
Vol 22 (19) ◽  
pp. 10403
Author(s):  
Yuchuan Zhou ◽  
Hongxia Liu ◽  
Wang Zheng ◽  
Qianping Chen ◽  
Songling Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Quantitative Polymerase Chain Reaction ◽  
Treatment Method ◽  
Gene Expression Omnibus ◽  
Primary Brain Tumor ◽  
Study Gene Expression ◽  
Radiation Induced ◽  
Human Gbm

Glioblastoma (GBM) is the most common and malignant primary brain tumor in adults. Radiotherapy has long been an important treatment method of GBM. However, the intrinsic radioresistance of GBM cells is a key reason of poor therapeutic efficiency. Recently, many studies have shown that using the histone deacetylase (HDAC) inhibitor suberoylanilide hydroxamic acid (SAHA) in radiotherapy may improve the prognosis of GBM patients, but the underlying molecular mechanisms remain unclear. In this study, Gene Expression Omnibus (GEO) datasets GSE153982 and GSE131956 were analyzed to evaluate radiation-induced changes of gene expression in GBM without or with SAHA treatment, respectively. Additionally, the survival-associated genes of GBM patients were screened using the Chinese Glioma Genome Atlas (CGGA) database. Taking the intersection of these three datasets, 11 survival-associated genes were discovered to be activated by irradiation and regulated by SAHA. The expressions of these genes were further verified in human GBM cell lines U251, T98G, and U251 homologous radioresistant cells (U251R) by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). It was found that MMP14 mRNA was considerably highly expressed in the radioresistant cell lines and was reduced by SAHA treatment. Transfection of MMP14 siRNA (siMMP14) suppressed cell survivals of these GBM cells after irradiation. Taken together, our results reveal for the first time that the MMP14 gene contributed to SAHA-induced radiosensitization of GBM.

Parthenogenesis in mammals: pros and cons in pluripotent cell derivation

2011 ◽  
Vol 6 (5) ◽  
pp. 770-775
Author(s):  
Georgia Pennarossa ◽  
Alessio Paffoni ◽  
Guido Ragni ◽  
Fulvio Gandolfi ◽  
Tiziana Brevini
Keyword(s):  
Cell Biology ◽  
Ad Hoc ◽  
Embryonic Stem ◽  
Telomerase Activity ◽  
Human Embryos ◽  
In Vitro Production ◽  
Alternative Source ◽  
Depth Analysis ◽  
Mature Cell Type

AbstractEmbryonic stem cells (ESCs) represent a useful tool for cell therapy studies, however the use of embryos for their derivation give rise to ethical, religious and legal problems when applied to the human. During the last years parthenogenesis has been proposed as an alternative source to obtain ESCs. Based on the fact that parthenotes avoid many concerns surrounding the “ad hoc” in vitro production and following destruction of viable human embryos. Unfortunately many aspects related to parthenogenetic cell biology are not fully understood and still need to be elucidated. In this review we describe advantages and limits of these cells. We discuss their typical ESC morphology and high telomerase activity, which disappears after differentiation. We examine the pluripotency signature that they share with bi-parental ESCs. We review their high differentiation plasticity that allow for the derivation of several mature cell type populations when we expose these cells to adequate conditions. On the other hand, in-depth analysis demonstrated chromosome mal-segregation and altered mechanisms controlling centriole arrangement and mitotic spindle formation in these cells. We hypothesize their monoparental origin as one of the possible cause of these anomalies and suggest a great caution if a therapeutic use is considered.

Factor XII gene expression in endometrial stromal cells during decidualisation

2009 ◽  
Vol 21 (7) ◽  
pp. 840 ◽  
Author(s):  
Hiroaki Kawato ◽  
Tsutomu Tabata ◽  
Hiroyuki Minoura ◽  
Nao Murabayashi ◽  
Ning Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stromal Cells ◽  
Molecular Mechanisms ◽  
Human Embryos ◽  
Factor Xii ◽  
Kinin System ◽  
Endometrial Stromal Cells ◽  
Weak Expression ◽  
Secretory Endometrium

Decidualisation of endometrial stromal cells (ESC) is a prerequisite for the implantation of human embryos. Identification of genes that are upregulated or downregulated during decidualisation could lead to a better understanding of the molecular mechanisms involved in this process. In the present study, we examined differences in gene expression between decidualised and non-decidualised cells using microarray analysis and found that Factor XII (FXII) gene expression was upregulated during decidualisation. Furthermore, we also examined the expression of FXII by human ESC before and during pregnancy, as well as its expression by cells that had undergone decidualisation in vitro. Weak expression of FXII mRNA was detected in the non-pregnant endometrium that increased gradually from the proliferative to the secretory endometrium. During pregnancy, FXII mRNA expression was markedly increased in decidualised endometrium. When sex steroids (200 pg mL–1 of 17β-oestradiol and 100 ng mL–1 of progesterone) were used to induce in vitro decidualisation of ESC, the expression of FXII mRNA increased by approximately 25.3-fold compared with that in non-decidualised ESC. Using western blotting, we confirmed the presence of FXII protein (80 kDa) in ESC after in vitro decidualisation. Increased expression of FXII in ESC during decidualisation suggests that the kallikrein–kininogen–kinin system may be activated during the implantation of human embryos.

scholarly journals Full-Length Enrich c-DNA Libraries-Clear Cell-Renal Cell Carcinoma

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Sai-Wen Tang ◽  
Jung-Yaw Lin
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Molecular Mechanisms ◽  
Clear Cell ◽  
Expression Profiles ◽  
Full Length ◽  
Cdna Libraries ◽  
Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC), the most common subtype of RCC, is characterized by high metastasis potential and strong resistance to traditional therapies, resulting in a poor five-year survival rate of patients. Several therapies targeted to VEGF pathway for advanced RCC have been developed, however, it still needs to discover new therapeutic targets for treating RCC. Genome-wide gene expression analyses have been broadly used to identify unknown molecular mechanisms of cancer progression. Recently, we applied the oligo-capping method to construct the full-length cDNA libraries of ccRCC and adjacent normal kidney, and analyzed the gene expression profiles by high-throughput sequencing. This paper presents a review for recent findings on therapeutic potential of MYC pathway and nicotinamide N-methyltransferase for the treatment of RCC.

scholarly journals Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2578 ◽  
Author(s):  
Pedro Morgado ◽  
Dipak Manna ◽  
Upinder Singh
Keyword(s):  
Gene Expression ◽  
Drug Discovery ◽  
Rna Interference ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Global Impact ◽  
Human Parasite ◽  
Recent Advances ◽  
Substantial Progress ◽  
Made In

In recent years, substantial progress has been made in understanding the molecular and cell biology of the human parasite Entamoeba histolytica, an important pathogen with significant global impact. This review outlines some recent advances in the Entamoeba field in the last five years, focusing on areas that have not recently been discussed in detail: (i) molecular mechanisms regulating parasite gene expression, (ii) new efforts at drug discovery using high-throughput drug screens, and (iii) the effect of gut microbiota on amoebiasis.

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