The main goal of this study is the development of a method to associate gene expression changes in response to perturbations with alterations in cell morphological features. The proposed approach for cell morphology enrichment analysis is composed of five main steps which we briefly describe here, illustrate in Figure 1, and discuss in detail in the rest of the Materials and Methods section.
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\includegraphics[width=0.8\textwidth]{Figure1.png}
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\caption{Overview of the proposed approach for cell morphology enrichment analysis. The input data are collected from the LINCS database to yield database transcriptomic and cell morphological profiles in \textit{Step I}. In \textit{Step II}, we find
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Step V: Applications of method. A set of cell morphological gene sets and related transcriptomic profiles can be used to suit many applications, such as identification of gene-gene interactions, pathway analysis, and model to reveal most significant morphological changes in response to treatment with a compound.
\subsection{LINCS database}
The Library of Integrated Network-Based Cellular Signatures (LINCS) is a comprehensive public resource of gene expression signatures and other cellular processes in responses to a variety of perturbing agents, including 847 approved drugs and 30455 small compound molecules ($http://www.lincsproject.org/$). LINCS database is divided into the 11 category based on the biological processes, and 314 subcategories based on the type of experimental assays. The category of \textit{Cellular component organization} includes morphological features extracted from the cell-painting assay, representing changes in shape, texture, and intensity of major cellular components upon treatment with perturbing agents \cite{4}. Cell-painting assay is a fluorescence imaging multiplex cytological profiling assay that uses fluorescent dyes followed by automatic image in order to investigate the effects that compound treatments have on cells \cite{4}. LINCS project for \textit{Gene expression} profiling is divided to
[1] – Molecular Cell Biology, 7th edition 2012, Harvey Lodish, Chris A. Kaiser, Anthony Bretscher, et al. Macmillian Higher Education.
P1: Outline the function of the main cells of the body. Cells are the main structure of the body as they all come together to form one cell. They are very important because without them, we wouldn’t be able to live. The cells carry out numerous of chemical reaction that we wouldn’t have heard of or even felt and it is simply done it on its own. Cells make up all the organs in the body.
There are many parts of a cell, they all have specific duties, and are all
Purpose: The purpose of this lab was to calculate the amount of time that was spent by a cell in each of the phases of mitosis. Also, it is used to be able to compare the process of mitosis between plant and animal cells.
3. Explain your prediction for the effect Na+ Cl- might have on glucose transport. In other words, explain why you picked the choice that you did. How well did the results compare with your prediction?
You are a nurse who works in a busy A&E department in a city hospital. Because you are experienced and highly regarded your manager has asked you to mentor some new nurses who have just qualified.
National Center for Biotechnology Information, U.S. National Library of Medicine. (n.d.). PubMed Central, Table 1: Plast Reconstr Surg. 2010 Aug; 126(2): 619–625. doi: 10.1097/PRS.0b013e3181de24bc. Retrieved from
Working as a Research Assistant at the Piano Laboratory, I have an interest in developmental biology. At the Piano Lab, I assist my mentor, Patricia Giselle Cipriani, and her project on using RNAi on ovary-expressed genes and time-lapse microscopy in order to understand a comprehensive molecular description of the genetic and evolutionary mechanisms behind early embryogenesis in C. elegans. From the data obtained from the RNAi tests, gene clusters based on the phenotypic analysis are created in order to investigate the functional analysis
this research would be to identify the factors that are involved in the cell making process that determines cell specialization. A few of our extreme medical conditions, like birth defects and cancer, are a direct result of abnormal cell specialization. If researchers obtain a better understanding of the normal cellular process, they can isolate the causes of these deadly illnesses. The most exciting potential use for stem cells is the generation of tissues and cells. Many diseases are a direct result from complications of cellular functions or destruction of tissues in the body. Many people donate organs and tissues to replace failing or destroyed tissues. Unfortunately, there are many more people suffering from these disorders than there are organs to transplant. That is where stem cells step in. They will give humans a chance to have a renewable source of cells and tissues that will treat a slue of diseases, and disabilities such as, Parkinson’s, stroke, burns, Alzheimer’s, spinal cord injury, diabetes, rheumatoid arthritis, and
A 24-well plate was used to perform this experiment. For the start of the experiment, the 24-well plate had 12 wells that contained our HepG2 cells. A cell suspension was created, that contained 0.5-1.0x10⁶ cells/ml containing 10% fetal bovine serum. 500µl of the cell suspension was then added to each well in use. The well plate contained both the HepG2 cells, and cell suspension was then incubated in a cell culture incubator for 24 hours; this allowed for a monolayer to be formed in the wells. After the incubation period elapsed, the well plate was removed and placed inside a tissue culture hood. We then carefully removed all the media from the wells with the use of a P1000 pipette; making sure not to touch the bottom of the well plate, and
"Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 01 May 2016.
The cancer specific genes can be identified by Differential display. This is a powerful technique for analyzing differences in gene expression. This technique used to compare mRNA expression patterns of tumor and adjacent non neoplastic tissue in radical prostate ectomy specimens. This can be useful in identifying novel genes and gene functions.
3. Tortora GJ. Functional Anatomy of Prokaryotic and Eukaryotic Cells. In: Microbiology an Introduction. 9th ed. San Francisco, CA: Pearson Education, Inc; 2007: 77-113.
LD50 or the lethal dose of 50%, is the amount of a chemical which kills 50% of the population of a test species (used in toxicity evaluations) exposed to that. The EPA study used IC50 toxicity data of selected chemicals towards HeLa cell lines to predict their in-vivo (LD50) toxicity values. IC50 is an index of the toxicity of a substance defined as the concentration of that chemical which have inhibitory effects on the growth of the 50% of the test population. HeLa cell used in this study is an immortal cell line, which is the oldest yet most commonly used human cell line for scientific research.21 In the next step, we explain how LD50 data predicted from the EPA’s correlative model can be further used to estimate the human health impacts
Proteins in this pathway communicate by the addition of phosphate groups to adjacent proteins. A signaling molecule binds to the cell's surface receptor ( typically mitogen) allowing the GTPase, RAS, to exchange GDP and GTP. The tyrosine kinase EGFR, binds with EGF (epidermal growth factor), leading to phosphorylation. Docking proteins bind to SOS, then to the phosphorylated EGFR, activating SOS and removing the GDP. The GTP and Ras bind leading to activation. Proteins along this pathway can become mutated. When this occurs, the proteins are lodged in an or off position. The MAPK pathway has been discovered in cancer cells. A malfunction occurs in this pathway causing uncontrolled growth and components that inhibit this pathway, reversing the on and off effect, may be utilized as cancer