Phage Hunters Spring 2016
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
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| unacceptable | HUMAN:HMOX1 | 2016-04-10 09:08:31 CDT | GO:0004392 heme oxygenase (decyclizing) activity (F) | PMID:27058954 | ECO:0000316 genetic interaction evidence used in manual assertion | A group of experimental scientists analyzed the global mRNa expression and the methylation profiles in APP to identify the genes involved to be able to treat Alzheimer's. They particularly focused on the functions of protein heme oxygenase 1 found in gene HMOX1. The group of researchers basically evaluated the how important the protein HMOX1 is in Alzheimer's. For this experiment, the scientists used human blood and lab mice. This was an extremely extensive project as plenty of processes were involved. The processes were: - RNA extraction (qRT), quantitative reverse-transcription polymerase chain reaction (PCR), Transcriptome sequential analysis, Western blot analysis, genomic DNA extraction, genomic DNA modification, Methylation microarray, Quantitative methylation-specific PCR (qMSP), bisulfite sequential analysis, deoxycytidine treatment, amyloid preparation and treatment and in the end Statistical Analysis.
Figure 1 shows the HMOX1 expression up-regulated in an APP-mutant cell line and transgenic mice.The effect of the protein is heavily evaluated by the virtue of its effects on the minds of mice. Alzheimer's is a disease that is becoming increasingly common in humans and therefore, this experiment is significant in understanding the pros and cons of this enzyme so that we can come up with better treatments for this amnesic disease.
The results of this experiment showed that heme oxygenase 1 is in fact directly correlated with Alzheimer's as shown from the results in Figures 1,2,3,4,5 and 6. The statistical analysis also convinced the researchers that HMOX1 is a key factor in cognitive impairment of Alzheimer's.
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| unacceptable | HUMAN:SAA1 | 2016-04-10 10:11:20 CDT | GO:0045087 innate immune response (P) | PMID:27058895 | ECO:0000317 genomic context evidence used in manual assertion | The acute-phase protein, Serum amyloid A (SAA1) is usually found in the liver and has been recently been proven to be found in cancer tissues. SAA1's content in breast cancer hadn't been described hence the researchers of this protein decided to study the protein's abundance. Immunohistochemistry was applied in this investigation to determine the quantity of SAA1 in tumor-associated macrophage (TAM). Fluorescent in situ hybridization (FISH) was performed to examine the expression and location of the mRNA of SAA1. The results of this investigation showed that TAM's may be the main source of SAA1's in breast cancer. Therefore presence of SAA1 in TAM's could correlate with the occurrence of breast cancer.
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| unacceptable | HUMAN:CXCR4 | 2016-04-10 11:14:35 CDT | GO:0016494 C-X-C chemokine receptor activity (F) | PMID:27058821 | ECO:0000316 genetic interaction evidence used in manual assertion | CXCR4 is a chemokine receptor that is recognized by C-X-C motif chemokine 12 (CXCL12) a.k.a stromal cell-divided factor 1 (SDF1). CXCL12 plays a big role in immune responses and metastatic cancer. Calculations and Virtual Screening with the help of the NMR complex structure was performed. This investigation proved that interfaces between proteins may often possess lead compounds for fragment-based optimization.
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| unacceptable | RAT:GLRA1 | 2016-04-10 11:44:14 CDT | GO:0060080 response to alcohol (P) | PMID:27058626 | ECO:0000250 sequence similarity evidence used in manual assertion | The graphical display figure in the paper describes and explains the effect of glycine in rat's brains. The figure is also indirectly an info-graphic that helps in understanding the protein's function.
Glycine receptors are ligand gated chloride channels that are found in a rat's brain. In this investigation, the researchers investigated the inhibitory potential of glycine against alcohol-induced oxidative stress, neuroinflammation and neurodegeneration in the rat brain. The researchers performed Gly co-treatment on the rat pups to investigate it's effects by injecting ethanol into the rat brains. They found that glycine reduced the alcohol induced stress and neuronal loss in the rat brain. Therefore with this finding, they concluded that glycine could be a potential treatment against alcohol-intoxication for newborns and infants.
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| updatedbyinstructor | HUMAN:AKAP8 | 2016-05-04 22:13:04 CDT | GO:0005730 nucleolus (C) | PMID:26683827 | ECO:0000314 direct assay evidence used in manual assertion | Figure 1. shows the intra-nuclear localization of AKAP95 is dependent on both RNA polymerase I and RNA polymerase II.
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