Cytosolic Extraction Protocol and Method

Cytosolic Extraction

Preparation of Cytosolic Extracts.

Specimens are snap-frozen in liquid nitrogen immediately after surgery and stored at –80 O C until extraction.

Frozen tissues (20 – 100 mg) are pulverized on dry ice to a fine powder and added to 10 volumes of extraction buffer (50 mM Tris, pH 8.0, 150 mM NaCl, 5 mM EDTA, 10 g/L of NP-40 surfactant, 1 mM phenylmethyl sulphonyl fluoride, 1 g/L of aprotinin, 1 g/L of leupeptin).

Suspensions are incubated on ice for 30 minutes, with repeated shaking and vortexing every 10 minutes.

Mixtures are then centrifuged at 14,000 rpm at 40 0 C for 30 minutes and the supernatant (cytosolic extract) is collected and stored at –80 0 C until further analysis. Protein concentration of the extracts is determined using the bicinchoninic acid bicinchoninic acid method, with albumin as standard (Pierce Chemical Co., Rockford , IL ).

The cytosol can then be used for numerous different analyses, by use in many protocols.

Total Cellular RNA Extraction Protocol

METHODS and MATERIALS: A Protocol for Total Cellular RNA Extraction

Total cellular RNA is isolated from 60-80% confluent cell monolayers using the RNeasy Midi Kit (QIAGEN Inc., Valencia , CA ) and following the manufacturer’s instructions. Total RNA concentration and its purity can and should be determined spectrophotometrically.

Bisulphite Treatment Methylight

This method is great for detecting minimal amounts of aberrant DNA methylation. Primers are designed that overlap with CpG dinucleotides, and the DNA is treated with sodium bisulphite as mentioned previsouly. The advantage of this method, is that there is no need for any steps after PCR, as it uses fluoresence-based real-time PCR, Taqman, technology.

2018 Healthcare Center Architecture Design that Will Make Your Jaw Drop

2018 Healthcare Center Architecture Design that Will Make Your Jaw Drop

This time, let’s discuss the healthcare center architecture design. Who says healthcare centers don’t really mind about their architectural? If you are someone assuming like that, this is where you are wrong. Contrary to many people believe, healthcare does mind about the architectural design. Just like how someone thinks it through when he wants to build the house. They would think about what kind of design is good for the future dwelling, and how comfortable the place should be. Well, the institutions will also consider the architecture design because they want people to feel comfortable when they are in the healthcare to make people feel like they are in their own home.

Now, we go straight to the topic, one the very best healthcare center architecture design is the one that Navyas has. Build in 2018, the original instruction that the designer receive is to design a naturopathy center—which has a yoga hall inside it—in a rather tight urban site. Obviously, to build a building with therapy and wellness purposes amidst a noisy, busy, and polluted environment was challenging. However, as the team found several characters on the site, eventually, they are able to point out what’s good for them to make.

The second one is princess maxima center for child oncology architectural design. Build in 2018, located in the Netherlands, the purpose of the building is to help and cure children with cancer. The center wants to offer them the optimum quality of life that they deserve. Using colorful and soft colors, the designers want to make the place as comfortable as they can. Moreover, the wide green field surrounds the main building is specifically designed for children to have a calm and serene environment.

The third one is an architectural design from UTHSC Center. Located in the US and build in 2018, this building is for healthcare improvement as well as patient simulation. In overall, you can say that the medical clinic architecture of this building is that aesthetically pleasing in the eyes. Even if one would say that the building is too simple for a well-known designer, you can’t judge a book by its cover only. The building is perfect in its own way without betraying the original purpose of the building. The color they used for each room and the overall interior of the building can be deemed as suitable and perfect for a healthcare center architecture design.

via Designestyle


Southern Blotting Method for DNA Methylation Detection

This method utilized methylation-sensitive restriction enzymes to digest DNA, cleaving at specific sites, which have been altered by DNA methylation, followed by Southern blot analysis of the DNA products. A very simple technique to analyze DNA methylation, however, it is very prone to numerous downfalls: poor sensitivity; very large amounts of DNA are required in order to receive a signal on blotting, and is only to detect methylated CpG’s that are recognized by the enzymes. Overall, there is little control of the sites/outcome of the test by the researcher, and a great deal of work and time must be spent in obtaining large amounts of DNA, and of good quality. Not recommended for any clinical samples/materials, such as biopsies and paraffin-embedded tissues because of this.

J.P.Issa, et al. Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon. Nat. Genet. (1994) 7: 536-540.

Combined Bisulfite Restriction Analysis COBRA Protocol

COBRA is a great, flexible, and easy method to quantitatively analyze CpG dinucleotides within DNA, at specific gene loci in small amount of DNA. It is a great method to use, as it can quantitatively assess CpG islands. Sodium bisulfite treatment of DNA is the initial step, followed by PCR. Subsequently, restriction digestion of the DNA is carried out. Methylation levels in the original DNA sample are revealed by the differing amounts of digested and undigested PCR products quantitatively. Overall, a great method, especially for paraffin sections, and clinical studies due to its ease and quantitative aspects.

Z. Xiong et al. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res (1997) 24: 5058-5059.

Restriction Endonuclease Enzymes

Restriction Endonuclease Enzymes to Study DNA Methylation and Epigenetic Changes

A few restriction enzymes are known to differential cleave methylated versus non-methylated DNA. These enzymes can be used to help you. When selecting these restriction enzymes, it is crucial to that they leave staggered ends, have a cut site that is different from the recognition site, and cannot be affected through potentially methylated target sequences.

C. Laird et al. Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc Nat Acad Sci (2004) 101: 204-209.

Chromatin Immunoprecipitation

Chromatin Immunoprecipitation Assay (ChIP)

Chromatin Immunoprecipitation Assay, also known as the ChIP assay allows one to determine the mechanism of trascriptional repression, by immunoprecipitating chromatin with antibodies. ChIP involves formaldehyde treatment of a cell population to cross-link proteins to their target DNA in vivo, cell lysis, sonication to fragment chromatin, and then immunoprecipitation of specific chromatin complexes using an antibody against the protein of interest. After removal of the cross-links, PCR amplification at a selected locus, or slot blot hybridization using a specific probe is performed.

Chromatin Immunoprecipitation Assay / ChIP Advantages

Chromatin Immunoprecipitation Assay / ChIP has the advantage of measuring protein DNA interactions of promoter regions with protein complexes in the natural genomic state. Moreover, the ChIP assay can directly provide information on the histone acetylase status of specific chromatin regions, and be used to study non-histone proteins, even ones that do not directly bind DNA. It also minimizes the chances of chromatin rearrangements during preparation and precipitation, and it can be used with gene-specific primers for increased sensitivity or with a specific probe, slot blot hybridization, for increased specificity.

Chromatin Immunoprecipitation Assay / ChIP Disadvantages

Dificulties with using ChIp will include, the danger that the cross-linking step may fix interactions that are of minor functional sugnificance, precipitation us often very inefficient, and purifying cross-linked DNA-protein usually requires isopycnic centrifugation, a prolonged and expensive procedure. A large number of cells are usually required and the data represents an average of potentially multiple functional states in the cell population. In addition, negative results do not necessarily mean that a given factor is not associated with the site. Certain antibodies are poor in immunoprecipitating crosslinked chromatin and lack of crosslinking can results from inaccessibility of factors in large complexes or biochemical properties of proteins that decrease cross-linking efficiency.

Chromatin Immunoprecipitation Assay / ChIP Success

The likelihood of success with the Chromatin Immunoprecipitation Assay / ChIP method is protein and antibody dependent, but the methods track record suggests that this technique is extremely versatile and widely applicable. Success will depend on the abundance of the desired protein-DNA adducts being studied, the quality and affinity of the antibodies being used, and on the size and complexity of the genetic loci studied.

Alternative Approaches Instead of Chromatin Immunoprecipitation Assay / ChIP

Alternative approaches include, studies using conventional methods such as transient transfection assays, electrophoretic mobility shift assays (EMSA) and coimmunoprecipitation.

ChIP References

Beatrice N et al. Location analysis of DNA-bound proteins at the whole genome level: untangling transcriptional regulatory networks. Bioassays 23, 472-476 (2001)

Weinmann AS et al. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26, 37-47 (2002)

Johnson KD et al. Dissecting long-range transcriptional mechanisms by chromatin immunoprecipitation. Methods 26, 27-36 (2002)

Kuo MH et al. In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods 19, 425-433 (1999)

Hairpin-Bisulfite Polymerase Chain Reaction PCR

Laird C. et al, published a great paper describing this method that they utilized to assess the fidelity of methylation transmission of CpG islands within the FMR1 gene of human lymphocytes. They generated a hairpin-linker with staggered ends (25 base pairs long), complementary to the targeted cut-site of the DNA, which was used after restriction enzyme digest of the DNA. The linker was attached to the DNA through the use of DNA ligase. The double-stranded target DNA was then subjected to sodium bisulfite treatment, and PCR amplification with designed primers that bound to the linker approximately 200 nucleotides away. The PCR products were then subsequently sequenced.

C. Laird et al. Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc Nat Acad Sci (2004) 101: 204-209.

Identification of CpG Islands Exhibiting Altered Methylation Patterns (ICEAMP)

This method allows for the identification of large regions of DNA with changes in methylation patterns through the use of methyl-CpG binding domain column which isolates methylated GC-rich sequences from both tumors and surrounding normal tissue. Subtractive hybridization is used subsequently, which removes sequences common to both, thereby leaving only methylated sequences unique to the tumor cells. Such a technique has numerous advantages and is easily one of the best methods to assess CpG islands for clinical studies.

S.Cross et al. Purification of CpG islands using a methylated DNA binding column. Nat. Genet. (1994) 6: 236-244.