Rna Seq Isoform Analysis Essays


Found 62563 essays.

Genes and Mechanisms in Colorectal Cancer (CRC)

However, further studies are still needed to confirm our results.Genes such as PTGS2, CXCL3, IL8, ABCG2, ATP1A2 and AQP8 may be potential therapeutic target genes for CRC.The functional enrichment analysis results showed that down-regulated genes were significantly enriched in cytokine-cytokine receptor interaction and TNF signaling pathways, while up-regulated genes were related to bile secretion function.In this study, the RNA-seq data of GSE29580 was downloaded from GEO database to identify DEGs between CRC and normal samples using bioinformatics analysis.Total 23 pathways were obtained in KEGG enrichment analysis.


2192 words (5.5 pages)
Transcript Expression Level of White Kelampayan

Expression analysis of samples will be observed and recorded.Using CLC Genomics Workbench 7.5 (Qiagen, Denmark), RNA-Seq analysis will be selected to run in a Batch mode.The preparation before analysis such as sample collection, RNA isolation, cDNA library construction, sequencing and mapping are done.Results of statistical analysis on transcript expression level will be visualized in volcano plots with CLC Genomics Workbench 7.5 (Qiagen, Denmark).Furthermore, there are several applications used in NGS technology such as transcriptome sequencing or RNA-Sequencing (RNA-Seq), genomic sequencing and epigenetic applications which use CHIP-Seq and methylation profiling to work out analysis on interaction in between proteins and DNA and analys...


1912 words (4.8 pages)
Prioritising Drug Targets for Antimalarial Drugs

As figure 4 shows, nine different stages during the development of P. falciparum 3D7 were assayed by oligonucleotide microarray analysis.According to the related research, ATP-binding contains biological processes including translocation of various substrates across membranes and non-transport-related processes such as translation of RNA and DNA repair, which need the energy of adenosine triphosphate (ATP).As figure 17 shows, nine different stages during the development of P. falciparum 3D7 were assayed by oligonucleotide microarray analysis.As figure 20 shows, nine different stages during the development of P. falciparum 3D7 were assayed by oligonucleotide microarray analysis.Beside, according to the analysis of the data of Life cycle e...


1902 words (4.8 pages)
Essay on The Cloning, Characterization, And Tissue

A representative experiment is shown in each case.Interestingly, a third protected band was detected with fat RNA indicating the possible existence of a third human PPARg isoform.Each experiment was repeated at least two times.The b-galactosidase expression plasmid pCH110 was used to normalize difference in transfection efficiencies.The presence of tissue-specific distribution of isoforms and the variable ratio of PPARg1 to PPARg2 raised the possibility that isoform expression may be modulated in disease states like non-insulin-dependent diabetes mellitus.


390 words (1.0 pages)
Report on RNA-seq Transcriptomics

Secondly, tophat was run for both tubule and wholefly samples followed by running Cuffdiff for the analysis of differential expression between these two types of tissue.In order to characterize small non-coding RNA, small RNA-SEQ or miRNA microarrays are used.In this report, analysis of the differential expression between two groups of samples corresponding to two Drosophila melanogaster tissues was implemented.No significant genes were excluded from further analysis.The prototype method, MPSS, applies four rounds of restriction enzyme digestion and ligation reactions to determine the nucleotide sequence of c DNA ends, generating a 17-20 bp sequence as the fingerprint of a corresponding RNA (Brenner et al., 2000).


2172 words (5.4 pages)
Comparison of Techniques for Diagnosis of Multiple Sclerosis

The A-allele is considered risky and the G-allele is protective, so those with the AA genotype in particular should be carefully monitored for evidence of disease activity Conversely, GG genotype may protect against increased disease activity.Results: Genotyping analysis of the OAS1 gene revealed a significant difference between RRMS patients and control group, with lower frequency of GG in patients (25%) compared to controls (65 %) (p = 0.0001).The G-allele conserves the splice site, generating a p46 enzyme isoform, whereas the A-allele ablates the splice site, resulting in a dual-function antiviral/proapoptotic p48 isoform and a novel p52 isoform.The p48 isoform has been shown to have proapoptotic activity, localized to a BH3 (Bcl-2 h...


1992 words (5.0 pages)
Genes of Calcium Transporters

The present investigation was carried out to identify potential candidate genes that may be responsible for the accumulation and storage of calcium in the developing grain in finger millet with the following objectives: .Such a study will enable us to understand and formulate effective strategies to increase the levels of calcium in grains.Molecular cloning and comparative analysis of calmodulin genes from cereals and millets were done for understanding the mechanism of differential calcium accumulation .Hence RNA-seq has provided a powerful tool for analysis of transcriptomes.Therefore, in the parallel studies on rice, sorghum, and finger millet (high & low calcium variety), have been studied to identify possible candidate genes o...


2307 words (5.8 pages)
Understanding an Unknown Protein Sequence

The query sequence was identified as predicted protein [Physcomitrella patens] >gi|162695322|gb|EDQ81666.1| Seq ID: gi|168001481|ref|XP_001753443.1.The full identification name given in the results page is the predicted protein [Physcomitrella patens] >gi|162695322|gb|EDQ81666.1| Seq ID: gi|168001481|ref|XP_001753443.1 .Figure 2: (A) PSI-BLAST shows similarity index to query sequence (B) ClustalW2 results showing alignment between predicted protein (Seq ID: gi|168001481|ref|XP_001753443.1) and predicted protein (Seq ID: gi|168035394|ref|XP_001770195.1).It may also be that the second protein in the similarity match, Seq ID: gi|168035394|ref|XP_001770195.1 may be distantly related to the query protein.Based on the bioinformatics meth...


2749 words (6.9 pages)
Controlling Pol II Pausing

Consistent with this, the majority of RNA associated with paused Pol II is capped (Nechaev et al., 2010).In 2008, our lab identified Zelda (Zld; Zinc-finger early Drosophila activator; also known as Vfl) to be the key activator of the early Drosophila zygotic genome (Liang et al., 2008).Third, short, capped RNA sequencing (scRNA-seq) detected 25-60 nt transcripts generated from paused Pol II in Drosophila (Nechaev et al., 2010).zld mRNA is maternally loaded from the nurse cells in the ovary, and is evenly distributed in the embryo excluding PGCs until cellularization, when maternally deposited zld is replaced by zygotically transcribed zld (Liang et al., 2008; Staudt et al., 2006).Therefore, pausing may function as a checkpoint for RNA p...


2262 words (5.7 pages)
Toxicity and Autoactivation of Baits Experiment

Small nuclear RNA can be of 5 important types U1, U2, U4, U5 and U6.For negative control the bait strain was L40 with bait pBTM116/GluR2 and the target was the same Y187[pGADT7-T] The negative control bait was obtained by the transformation of L40 with the plasmids isolated from provided E.Coli cultures.In evolutionary terms alternate splicing has a major role in the functional development of species right from the times of “RNA world”.Many different proteins are involved in splicing most importantly the spliceosome, a complex formed of small nuclear RNA (snRNA) and small nuclear ribonucleoproteins (Hagiwara et al, 2005 and Jurica et al, 2003)... A colony of Saccharomyces cerevisiae L40 yeast was inoculated into 10ml of YPAD media.


5242 words (13.1 pages)
CRM Prediction and CRM Validation Approaches

Another commonly used database website is the University of California Santa Cruz (UCSC) Genome Browser Database, which provide all aspects of information for CRM prediction including experimental (DNase hypersensitivity clusters, epigenetic marks of histone proteins, and binding of transcription factors from ChIP seq) as well as computational (conservation level among vertebrates from DNA sequence alignment) study[181].The miR-125b prevents cancer proliferation by activation of p21(WAF1/Cip1) G1/S cell cycle arrest as well as repression of SIRT7 gene induction[244].The overall functions of HCC-associated miRNAs are implicated in STAT3, by modulating Bcl-2 and Mcl-1 functions, and NF-κB inflammatory pathways, leading to hepatocacinogenes...


2745 words (6.9 pages)
Anti Cancer Activity of Some Novel Quinazoline Derivatives

The entire test Compounds which have lowest ligand energy compared to the Standard compounds ( ) All the test compounds are less potent than Standard compounds.The ligands with good ligand scores of The binding mode of the title compounds with the Fibroblast Growth Factor 4 (FGF4) inhibitor was clarified by flexible docking method.Thus based on ligand score, glide energy and interaction with residues in the active site of the FGF4, compound was found to be more potent inhibitor as they exhibit drug like activity.Thus based on ligand score, glide energy and interaction with residues in the active site of the TERT, compound was found to be more potent inhibitor as they exhibit drug like activity.The entire test Compounds which have hi...


1658 words (4.1 pages)
Rapamycin And Cisplatin In Breast Cancers

.. Drug combination analysis was performed by using the method as described by Chou and Talalay [14].To validate that the rapamycin and cisplatin synergism is mediated by p73, we generated isogenic MDA-MB-231 and MDA-MB-468 cells that were depleted for p73 using a lentiviral-shRNA that target specifically the transactivating isoform of p73 (TAp73).These compounds were subsequently tested at different concentrations to determine the mode of interaction by isobologram analysis.All PCR products were confirmed by the presence of a single peak upon melting curve analysis and by gel electrophoresis.The observed changes in p73 protein in MDA-MB-231 cells, however, were not due to parallel changes in p73 RNA levels, suggesting that inhibition o...


4002 words (10.0 pages)
Effect of Semecarpus Anacardium on Plasma Nitrates

RNA samples incubated with a mixture consisting of containing dNTPs, random primers, 10× RT mix, Quant Reverse Transcriptase, a reverse transcriptase and RNase-free water to a final volume of 10 μl at 37°C for 1 h. .Briefly, RNA (1 μg) pretreated with DNA-free DNase treatment and removal reagents.The quantitatively major source for NO in the CNS thus is the “neuronal” isoform NOS-I present in approximately 1% of all neurons.Groups of data were compared with the analysis of variance (ANOVA) followed by dunnett’s t-test values for statistical significance.Whether or not this isoform is also expressed in neural cells, is still a matter of debate but data arguing for this are only sparse.


2583 words (6.5 pages)
Analysis of GATA3 ChIP-seq in the Four Cells

In addition, the specific regulation of GATA3 in the four tumor cells need to be demonstrated in combination with experimental data.The GATA3 targets gene among the four tumor cells were further subjected to pathway enrichment analysis, Gene ontology (GO) enrichment analysis and motif identification.MACS (Model-based Analysis of ChIP-Seq) [19] and CisGenome [20] are two different peak detection algorithms in predicting transcription factor binding sites in ChIP-seq data.In this study, pathway enrichment analysis and GO enrichment analysis revealed that AKR1C1 was enriched in process related with xenobiotics metabolism.Pathway enrichment analysis revealed that the common GATA3 target genes were enriched in pathways related with cancer,...


2788 words (7.0 pages)
Eukaryotic Gene Regulation Transcription Factors

Briefly, recruitment of a coactivator by activators that bound to regulatory sequences of genes leads to the recruitment of RNA polymerase ΙΙ (Russell, 2010).The sigma factor that contacts the promoter directly at the -35 and -10 regions enables the proper orientation of the RNA polymerase so that transcription can be started at the correct nucleotide of the gene when the RNA polymerase is bound at -10 region (Russell, 2010).GTFs are needed for precise transcription initiation by assembling on the core promoter to form PIC which directs RNA polymerase ΙΙ to the site where transcription starts (Maston , 2006).RNA structure and the mechanisms of alternative splicing.Whereas, RNA polymerase ΙΙΙ synthesize transfer RNAs (tRNAs), 5S rRNA mol...


2516 words (6.3 pages)
Glucose Transporter 4 (GLUT4) and Diabetes

Epub 1995/08/15.Antonescu CN, Huang C, Niu W, Liu Z, Eyers PA, Heidenreich KA, et al.1995;213(2):533-40.In Liu L. Z. et al work, stimulation of insulin conferred a glucose uptake or translocation of surface glucose transporter 4 (GLUT4).Using specific inhibitors to key kinases of both pathways and PKCzeta small interference RNA, it was found that protein kinase C zeta (PKCzeta) the presence of berberine, PKCzeta controlled AMPK activation and AMPK blocked PKB activity in perinuclear region.Petersen S, Bahr M, Eckel J. Insulin-dependent regulation of Glut4 gene expression in ventricular cardiomyocytes: evidence for a direct effect on Glut4 transcription.


1972 words (4.9 pages)
Developing Antimicrobial Peptides Agents

Bioinformatic analysis was done to predict the secondary structure and three-dimensional structure of these seven gene fragments that may exist... pPICzαA/stomoxyn recombinant plasmid was extracted from DH5α with Mini Plasmid Purification Kit according to the instructions, restriction enzyme analysis was peformed as following ; 1 µg of recombinant plasmid ws digested by restriction enzyme EcoR I and Not I at 37°C, for 8h; 5 µl of digestion product was analysed with 1% agarose gel electrophoresis; colony PCR was conducted for Zeocin resistance transformants and the insert was sequenced to ensure that the coding sequence of H.illucens L stomoxyn was correct and inframe with the α-factor secretion signal the positive plasmid was sequenced...


2287 words (5.7 pages)
14-3-3 Protein Analysis | Essay

Although 14-3-3 σ is the isoform that has been most extensively studied for its association with human cancers, there are also several ongoing studies which attempt to establish a correlation between 14-3-3 γ expression and the development of tumours.[] The authors of this paper were however unable to comment on the functional relevance of the ATPase activity of 14-3-3 proteins.[] Interestingly, it was found that in case of the γ isoform, the mutation of the conserved Asp, found at position 129 to Ala (D129A) led to an over two-fold gain in ATPase function, reflecting that the binding of this mutant to ATP is probably either more energetically or sterically favourable.[] They also studied the putative residues essential to this activity ...


2654 words (6.6 pages)
Fibroblast Growth Factors (FGFs) in Neural Induction

In support of this model, consistent with the idea that BMP activity inhibits neural fates, animal caps which had been injected with RNA encoding effectors of BMP4 (Smad 1/5 or Msx1) neuralization did not occur.During these 5 hours, several genes become activated such as, ERNI (early response to neural induction) which becomes active after 1 hour (Streit et al., 2000) and Churchill (Chch) after about 4 hours (Sheng et al., 2003).In the chick, FGF8 is expressed in the hypoblast, prior to gastrulation before Hensen’s node appears (the chick equivalent to the organizer) indicating that neural induction is in fact able to begin before gastrulation.It is FGF8 which has been identified as the best candidate because it is expressed in the anter...


3251 words (8.1 pages)
Genes Encoding HLA Antigens

The sizes of the PCR products were confirmed by sequence analysis.To the contrary, low soluble HLA-G seems to be correlated with an adverse pregnancy outcome (20).The amplification was done using the forward primer 5´-GTGATGGGCTGTTTAAAGTGTCACC-3´ and the reverse primer 5´-GGAAGGAATGCAGTTCAGCATGA-3´ for the HLA-G 14 bp insertion/deletion polymorphism analysis.In the current study, higher frequencies of the 14-bpinsertion allele in RSA group may be a reflection of the association between the 14-bp insertion and the altered balance in HLA-G mRNA isoforms and probably the protein concentration.Taken together, our data indicated that the 14-bp insertion allele might have importance in the outcome of pregnancy.


1915 words (4.8 pages)
Case Brief – Del Monte Fresh Produce Company v. Dole Food Company, Inc

, 119 F.3d 935, 951 (11th Cir.Deceptive and unfair trade practices under the Florida Deceptive and Unfair Trade Practices Act, Florida Statutes § 501.204 et seq.Misappropriation of trade secrets under the Florida Trade Secret Act, Florida Statutes § 688.001 et seq.A two tier analysis must be made to determine whether a ., 330 U.S. 501, 508, 91 L. Ed.


1397 words (3.5 pages)
Gene Hox Essay

Another way to regulate Hox gene expression can be done through differential RNA treatments, either alternative splicing, alternative polyadenylation and / or the use of an alternative promoter .Differential treatments of RNA lead to the formation of various messenger RNAs (mRNAs) with different structures and / or genetic information.RNA differentials are a common process in the regulation of Hox genes in Drosophila.The primary results from this study are that first of all the Ptc expression pattern agrees with that of a reduced mite opisthosoma.The researchers conclude that the results obtained suggest that Ubx and Abd-B are expressed in a single segment of the opisthosoma.


3607 words (9.0 pages)
Electrophoresis Types and Applications

The application of zymograms can vary from analysing of ribonucleases using normal electrophoresis or isoelectri focusing, two-dimensional analysis of bacteria, fungal works, and also for detection and characterization of microbial proteases [25, 26, 27, and 28].[8] introduced the use of Tris media (Tris-acetate-EDTA (TAE) and Tris-borate-EDTA (TBE)) as the buffer solution for separation of RNA.The advantage of the higher resolving power of the isoelectric focusing and 2D electrophoresis techniques have enable rapid and more accurate analysis of proteins.The microchip electrophoresis system is also fully automated, from sample handling to data analysis, which allows minimal human handling and possible error [34].It involves the movement ...


3795 words (9.5 pages)
Character Analysis of Hester from The Scarlet Letter by Nathaniel Hawthorne

Because the letter "A" is a symbol of sin and awkwardness, or at least a means, it has a deeper meaning than affair.Hester's Personality Analysis in Nathaniel Hawthorne's Letter "In the eyes of man, there is nothing to lose now, there is no hope, I do not seem to want anything, be careful that it really came back (153) Nathaniel Hawthorne, his exact technical terms in his novel "Scarlet Letter", in the hero's Hester Prynne (Hester Prynne) and between the strict Puritan society around her There is a disagreement in opinion.Hawthorn novel "Red Letter", the hero, Hester Prinn is a true contemporary of the modern era cast in the Massachusetts 17th century Boston Puritan.As a result of adultery, Hester 's punishment is a clear symbol of her s...


457 words (1.1 pages)
Sippican Corporation Essay

Benefits: Better working atmosphere, satisfaction, higher motivation and a win-win situation for executives and a workers.Challenge: Hard to predict the right price increase detailed market analysis is necessary.Price volume compromise has to be respected by the price-volume compromise analysis made, for 1% of price increase, the volume should not decrease by more than 1.56% in order to achieve the same profitability at least.Flow controllers´ actual gross margin was negative (-4%) and pumps had a gross margin of 20% (15 percentage points more than with previous analysis) so there was still a space for price decrease in pumps if it becomes necessary to react to market pushing of prices.That could cause unhappiness among those who conside...


1847 words (4.6 pages)
The Polymerase Chain Reaction Pcr

The quantity of the isolated RNA was determined by nanodrop spectrophotometry (absorbance at 260 nm of a 40µg/ml solution of RNA is 1.0) using nuclease-free water as a blank.RT- qPCR can differentiate between messenger RNAs (mRNAs) with almost identical sequences and requires much less RNA template than other methods of gene expression analysis... A DNase digestion step was performed as a precaution using RQ1 RNase-free DNase kit although the TRIzol method generally results in RNA which is essentially free from genomic DNA (2).The quality of the isolated RNA was verified by agarose gel electrophoresis.RNA was isolated from cell pellets using Trizol procedure.


1090 words (2.7 pages)
Novel Sequential-presentation-only (SPO) Line-up Effects

Lindsay and Wells (1985) devised the sequential line-up (SEQ) procedure as a better alternative.The first hypothesis was partially supported as there were fewer hit rates but not false alarms in the SEQ condition.A post-hoc analysis using the Bonferroni correction for multiple comparisons showed significant difference in the hit rate between the SIM condition and the SEQ condition ( = 0.08, < .001) and between the SIM and SPO condition ( = 0.05, = .02), but not between the SEQ and the SPO condition ( = 0.04, = .10).The “superiority effect” stems from the enhanced overall accuracy as SEQ reduces false identifications(false alarms) when the target is absent(target-absent conditions), more than it reduces correct identifications (...


2683 words (6.7 pages)
Ricin: History, Origins, Toxicity and Properties

Necrotic changes were evident in the capillary endothelium and type I epithelial cells, accompanied by intraalveolar edema 12-15 h after exposure.Using transmission electron microscopy, Brown and White (1997) (see also Griffiths et al., 1995b, 2007) examined the histopathological changes in the lungs of rats upon ricin inhalation.The A chain has enzymatic properties (ribosomal RNA N-glycosidase, EC 3.2.2.22) responsible for the toxicity of ricin, while the B chain is a lectin binding to galactose-containing glycoproteins and glycolipids on the surface of target cell components.Ricin is highly toxic upon injection and inhalation.In the serum of animals treated with ricin, antibodies specific to ricin have repeatedly been detected (see, fo...


1525 words (3.8 pages)
Non Steroidal Anti Inflammatory Drugs (NSAID): Effects

Paracetamol has few adverse side effects as it is tolerated by the stomach because inhibition of prostaglandin in the periphery is weak; allergic reactions and skin rash sometimes occur.The mechanism of action of paracetamol is now thought to be via COX-3 inhibition.Prostaglandins derived from COX-2 can be generated at the ulcer margin and appear to play an important role in ulcer healing through triggering the cell proliferation, promotion of angiogenesis and restoration of mucosal integrity .This isoform is the primary target for anti-inflammatory drugs.This enzyme is present in the brain and spinal cord and is selectively inhibited by paracetamol.The central action of paracetamol explains it antipyretic effects and its lack of other p...


2090 words (5.2 pages)

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