Cancer - Science topic

I am looking for collaboration with microbiologist globally.

If you interested we can do it.

With regards.

Thank you

To increase CD107a and IFN-γ release, set the E ratio to 5:1 or 10:1, resulting in more NK cells per A375 target. Higher E ratios often increase NK cell activation and cytokine release.

Hello Ajay,

You may use in vitro assays to identify anticancer properties of the phytochemical in cultured murine or human tumor cell lines. However, there are cell-free systems as well, which you may use that include assays which measure enzyme inhibition, receptor binding, protein–small molecule interactions, or interference with components of important signal transduction pathways.

If you have a cell culture facility, then the simplest and commonly used in vitro cell-based assay would be the cytotoxicity assay such as the MTT assay.

You would need a cancer cell line (preferably derived from the tumor

tissue of the cancer of your interest. For instance, if you are aware that your phytochemical is effective against breast cancer, you may use breast cancer cell line such as MDA-MB-231 or MCF-7 cell line) to test various concentrations of the phytochemical on the cells.

You may follow the MTT protocol as provided below.

1. Plate the cancer cells of interest in a 96-well plate format at a desired cell density such that they are 80% confluent on the day of readout. If cells are overconfluent on the final day of the assay, you may end up with inaccurate results.

2. After 24 hours, when the cells have attached to the substratum, treat the cells with the phytochemical by changing the media with the treatment media at various concentration ranging from 5ug/ml to 500ug/ml (at least 5 concentrations).

3. Incubate the cells with the treatment media for 24, 48 and 72 hours.

4. After the treatment period, aspirate the treatment media and add MTT reagent to a final concentration of 0.2 to 0.5mg/ml and incubate in the dark for 1 to 4 hours for the formation of formazan crystals.

5. After incubation, solubilize the crystals into a colored solution with the solubilizing solution which may include either dimethyl

sulfoxide or acidified isopropanol solution, or a solution of 10% SDSin 0.01M hydrochloric acid.

6. Measure the absorbance at a wavelength of 570 nm.

7. IC50 value may be calculated from the graph constructed by plotting cell survival versus extract concentration.

Please note that IC50 stands for half-maximal inhibitory concentration, and it's a measure of how much of a drug or herbal extract is needed to inhibit a biological process by half. It's a widely used and informative way to measure a drug's efficacy and potency.

Good Luck!

@Seraphina Anderson good point

Thanks. My work involves studying the expression of CD8 T cells after cancer induction. Is immunodeficient mice a good option for this?

I personally received Mtt assay

if you are interested in learning about the basic Of this assay you can read this article

(( Proinsulin C-Peptide Enhances Cell Survival and Protects against Simvastatin-Induced Myotoxicity in L6 Rat Myoblasts))

Best Wishes.

With atovaquone you're out there on the bleeding edge. Good luck!

Can you please share the link and is it good?

Hello, I prefer to resuspend with a micropipette.

Hi Nurul Nurul Ashikin Mohamed Shahrehan ,

Thank you so much for your suggestions! I didn't think about the position of syringe before, and I think your suggestion would help me a lot!

Do you think that different gauge needles could make a difference? Why do you choose 26G?

We don't have matrix gel, so the cells were resuspended in the PBS.

When I took out the tumor, I found there were more like fat tissue in the tumor, and in some tumors, there's a lot of blood, eventhough I injected the same cells.

Best wishes,

Tingting

Hello Rafli, your micrograph does appear to illustrate apoptosis in your cultures. I can's see any serum in your DMEM usulaly ~10%FBS? I would also suggest that you remove the amphotericin and titrate the cobalt, as I would anticipate both reagent are stressing/killing the cultures.

best wishes

Yes Sandeep Jaiswal

We can no longer rely on the philosophy of determinism (control) of classical science.They only apply to invariant properties of physics; not to society/biology/ecology.The models of classical science become deadly if used on medicine (health care).

Our participation in creation operates in our body, as human AND humanity. Science is incapable to describe that; the same is the case for any religion. But we can all experience it in our body: it is based on this uniVersal dynamic.

Integral Health Care makes use of all the healing arts of the whole Earth. East & West, Far-East & Far-West therein logically complement each other. Together they define and form Integral Health Care.

Together they can prevent, early-detect/correct, cure and palliate.

The essence is simple:

Maybe use an anticoagulant in you culture medium like heparin?

If you are interested in this topic, you might wish to investigate the International Association for Near Death Studies (IANDS.org). or delve into Consciousness Studies.

Hi Glauco,

Are you aware of the Xena browser (https://xenabrowser.net/)? There are at least gene expression, mutation and methylation data per patient for the TCGA cohorts. Unfortunately I am not sure about the TE data, since I am not working with that but I think that Xena would be your best bet.

Received glass slide mounted tumors tissues form OT

ips institute upm university Malaysia

As you have stated gut microbiome and cancer relations are maybe the most complex issue of all medicine as within the scope of gastrointestinal oncology. The secrets of this utmost complex issue with so many unsolved neoplastic mechanisms are hidden as if rooted in darkest unknown ocean deeps. I recommend you to read the links below...

I am NOT a doctor but my research with an AI tool provided following info:

1. In the context of drug resistance, the bystander effect suggests that the presence of mutated cells can influence the surrounding non-mutated cells, leading to the development of resistance mechanisms. This can occur through the transfer of signaling molecules, genetic material, or other factors that mediate cellular communication.

2. A few reasons. Firstly, understanding the specific mutations responsible for resistance helps in the development of targeted therapies that can overcome or prevent resistance mechanisms. Secondly, monitoring these mutations allows for the early detection of emerging resistance, enabling timely treatment adjustments to improve patient outcomes. Lastly, studying gene mutations and their effects contributes to a deeper understanding of the underlying mechanisms of drug resistance, aiding in the development of more effective treatment strategies.

3. The most effective in vitro setting to demonstrate the bystander effect and resistance development depends on the specific research question and the cell type being studied. Co-culture experiments, where mutated and non-mutated cells are cultured together, can mimic the cellular interactions that occur in vivo and provide insights into the bystander effect. Additionally, organoid models or three-dimensional cell cultures that closely resemble the tumor microenvironment may offer more physiologically relevant settings to investigate the bystander effect.

4. To measure the direct and bystander effects of gene mutations causing chemotherapy resistance in cancer cell lines, several parameters can be assessed. These include:

- Cell viability and proliferation assays: Assessing the growth and survival of cancer cells in the presence of chemotherapy drugs can provide insights into their sensitivity or resistance.

- Gene expression analysis: Comparing gene expression patterns between drug-sensitive and drug-resistant cell lines can identify key genes or pathways involved in resistance development.

- Protein expression and activity: Analyzing protein levels and activities associated with drug resistance mechanisms, such as drug efflux pumps or DNA repair enzymes, can shed light on their contribution to resistance.

- Signaling pathway analysis: Investigating signaling pathways involved in resistance development, such as those related to cell survival or apoptosis, can provide mechanistic insights.

- Transfer experiments: Conducting experiments where media or conditioned media from drug-resistant cells are transferred to drug-sensitive cells can help assess the transferability of resistance and the bystander effect.

5. The clinical implications of measuring the bystander effect in drug resistance are significant. By understanding the mechanisms underlying resistance development, clinicians can make informed decisions regarding treatment strategies. This knowledge can guide the selection of appropriate therapies, the optimization of treatment regimens, and the identification of potential combination therapies to overcome drug resistance. Additionally, measuring the bystander effect can aid in the development of predictive biomarkers for resistance, allowing for personalized medicine approaches and improved patient outcomes.

Hope it helps

I am NOT a doctor but as compter science professional, little more AI provided detail:

In cases where there is nodular peritoneal thickening, ovarian cancer, and ascites, the source of ascites can be the result of various factors, including the presence of cancer cells in the peritoneal cavity.

CA-125 is a tumor marker that is often elevated in cases of ovarian cancer, although it can also be elevated in other conditions. The presence of high CA-125 levels, along with the imaging findings of nodular peritoneal thickening, suggests the possibility of peritoneal serosal carcinoma, which is a type of cancer that affects the lining of the abdominal cavity (peritoneum). Ovarian cancer can sometimes spread to the peritoneum, leading to peritoneal serosal carcinoma.

Ascites refers to the accumulation of fluid in the abdominal cavity. In the context of ovarian cancer, ascites can occur due to several reasons, including:

1. Peritoneal involvement: Cancer cells can spread to the peritoneum, leading to inflammation and the production of fluid.

2. Impaired lymphatic drainage: The presence of cancer can disrupt the normal flow of lymphatic fluid, leading to its accumulation in the abdomen.

3. Liver involvement: Advanced ovarian cancer can involve the liver, leading to impaired liver function and fluid accumulation.

Surgery, as you mentioned, is often a crucial component of the treatment plan for ovarian cancer. The specific surgical procedures performed can vary depending on the individual case, but they may include removal of the ovaries (oophorectomy), peritoneal biopsy, and collection of various samples for histological examination. These procedures aim to obtain a definitive diagnosis, determine the extent of the disease, and guide further treatment decisions.

Please consult qualified healthcare professionals who can provide personalized advice and guidance based on the specific details of your best friend's mother's case. They will be able to provide the most accurate information and help determine the most appropriate course of action.

Hope it helps

Although sugar is not directly labeled a carcinogen, recent research has unveiled the link between sugar consumption and cancer risk. Sugar, primarily sucrose and high-fructose corn syrup is commonly found in processed foods, sugary beverages, and sweet treats. Excessive sugar intake has long been associated with various health issues, such as obesity, diabetes, and heart disease. However, the emerging connection between sugar and cancer has garnered recent attention. High sugar consumption can lead to chronic inflammation, insulin resistance, and the promotion of obesity, creating an environment conducive to certain types of cancer. While sugar itself does not directly induce cancer, it can contribute by fueling the rapid division and growth of cancer cells, particularly in breast and lung cancer cases. Some research suggests that reducing sugar intake could be an effective strategy for cancer prevention and improving the outcomes of cancer treatments. It is crucial to note that the relationship between sugar and cancer is complex and not entirely understood. Several factors, including genetics and overall diet, contribute to an individual's cancer risk. Therefore, the main message is not to demonize sugar but to stress the importance of moderation and a well-balanced diet. Simultaneously, sugar is not classified as a direct carcinogen, but a growing body of evidence indicates that excessive sugar consumption can contribute to the risk of developing cancer. Maintaining a healthy, well-balanced diet with limited sugar intake is advisable for overall health and potentially reduces cancer risk.

Because older adults are under-represented in clinical trials, doctors can’t be certain that approved cancer drugs will work as intended in this age group. In the absence of high-quality evidence, researchers are looking for ways to improve medical decision-making and better predict outcomes based on age...

Q1. The KB cell line (CVCL_0372) is derived from a cell line called HeLa, but it is not considered a HeLa cross-contamination cell line. Instead, KB cells are classified as HeLa derivatives. The term "HeLa derivative" refers to cell lines that have been derived from the original HeLa cell line through various means, such as mutation or viral transfection. These derivatives can acquire different characteristics and properties while still retaining some similarities to the parent HeLa cells.

Q2. KB cells are commonly described as an oral carcinoma cell line, rather than a cervical carcinoma cell line. While both oral carcinoma and cervical carcinoma are types of cancer, it is important to accurately define the cell line being used in your research. In this case, KB cells are derived from HeLa cells, which are originally derived from cervical cancer cells.

When writing your thesis, it is crucial to provide accurate and specific information about the cell line you are using. You can mention that KB cells are derived from HeLa cells, which were derived from cervical cancer cells. However, it is generally recommended to refer to KB cells as an oral carcinoma cell line, as that is the most commonly accepted designation for this specific cell line.

All the best

Hi..Rather than establishing the resistance cell line,I've found some published articles compared the resistance of various cell lines (from the same cancer type) following drug treatment. Cells with greater survival rate following drug treatment were selected as a resistance model

Alendronate:

Paclitaxel:

Thiophene:

Thiophene can be dissolved in various solvents including ethanol, ether, benzene, and toluene. The solubility of thiophene in water is very low (0.052 g/L at room temperature) and it is generally not recommended to dissolve it in water. To dissolve thiophene, it can be added to the solvent slowly with stirring and heating may also be necessary to increase solubility. It is important to handle thiophene with care as it is flammable and toxic.

Following two papers should be helpful:

Wang, F., Deng, Y., Yu, L., Zhou, A., Wang, J., Jia, J., ... & Lin, X. (2022). A Macrophage Membrane–Polymer Hybrid Biomimetic Nanoplatform for Therapeutic Delivery of Somatostatin Peptide to Chronic Pancreatitis. Pharmaceutics, 14(11), 2341.

Zhu, S., Li, Z., Zheng, D., Yu, Y., Xiang, J., Ma, X., ... & Ren, Q. (2023). A cancer cell membrane coated, doxorubicin and microRNA co-encapsulated nanoplatform for colorectal cancer theranostics. Molecular Therapy-Oncolytics, 28, 182-196.

Of course, time is a significant factor for spheroids' size and viability of cells, due to when you seed the cells to the generation of spheroids after the cells are in the proliferative stage. More time (days) can lead to the big size of spheroids, in addition, the cells located in the core zone are suffered from nutrients, oxygen, and ...

I suggest you set up the best time to achieve reliable results too

Antonis Tsintarakis thank you for your reply! I will look into the BEST tool you have suggested.

Vahid Rakhshan I will definitely spread the word about this amazing initiative. It's great to know that we can contribute to such a noble cause by simply utilizing our excess computer power. Thank you for bringing this opportunity to my attention. Let's join hands in making a difference in the fight against diseases.

Hi,

C26 cells are from Balb/c background.

If you want to study cachexia in C57 background. You can use KPC model (intraspleenic or intrapancreatic models).

Hereby attached is a system of three Ordinary Differential Equations (ODE). We have to use numerical methods such as RK4 and Euler to obtain the results using Java. I think RK4 is better for this kind of problem. In this thread, Dudley J Benton has already mentioned C programming for this. It is really amazing.

For the parameter values, you can use your own values for your convenience.

Hello Muhammad Habiburrahman

You should make sure that your research proposal in cancer is created meticulously, if you have to make it more appealing to prospective professors. The panel of experts should get convinced with regards to the significance of your research. The research proposal that you put forward should clearly project that you will be able to justify your research and that you will execute it as per the required standards.

In your introduction you should exemplify your problem which you will be attempting to resolve and emphasize its significance. You should prove to the panel of experts that you have a command on research in your field by providing them with an extensive review of existing literature. The research methodology should be chosen carefully, and you should justify why have you made such a choice so that the reader is convinced.

Effective management of time plays a crucial role, and therefore you should provide a realistic timeframe and the resources that you would require to complete your research. The research question should be very much clear to the panel of experts.

So, before you begin writing the PhD research proposal in cancer you need to have a detailed meeting with your guide to select the topic of research and the research methodology, both of which are of utmost importance. Plan your proposal and create a proper outline before you start writing. Extensive work must be done in reviewing the literature in your domain of research to understand the current gaps. This will help you to choose a unique topic, and you will not end up with a topic that has already being researched.

Good Luck!

Hello Ariza Yandwiputra Besari

IC50 and LC50, both are similar in relation to their measurement.

If you are planning to study the anti-cancer activity of the candidate compound on mammalian cells (invitro study), then you need to consider IC50. IC50 gives the informative measure of a drug's efficacy. It indicates how much drug is needed to inhibit a biological process by half, thus providing a measure of potency.

On the other hand, LC stands for lethal concentration usually referring to the concentration of a chemical which is used in environmental studies that involves groups of animals exposed to a concentration (or a series of concentrations) for a period of time (usually 4 hours). The animals are then clinically observed for up to 14 days.

The concentration of the chemical that kills 50% of the test animals during the observation period is the LC50 value. When an LC50 value is reported, it should also state the kind of test animal studied and the duration of exposure. For instance, LC50 (mouse) 5mg/m^3/2hr.

The killing effect of the candidate drug has a sigmoidal relationship with drug concentration, and this sigmoidal model would be a proper way to measure the effectiveness of a compound in inhibiting biological/biochemical function.

So, use IC50 for the cytotoxicity assay.

Best.

DNA repair pathways are involved in maintaining genetic stability and, in this respect, repair factors are to be considered as tumor suppressors. This applies to the BRCA1/2 genes, for which inherited mutations in one allele predispose to cancer. There is no paradox in the fact that PARP inactivation leads to the death of BRCA-deficient tumor cells. In this case where homologous recombination is impaired, cell survival relies on PARP-dependent backup repair processes. Apparently, here, PARP promotes tumor development but even in non-tumor HR-deficient cells, survival would depend on PARP. We just take advantage of this synthetic lethality phenomenon due to HR deficiency to kill cancer cells.

Anyway PARP functions are not restricted to DNA repair and it is possible that in some peculiar circumstances PARP may rather promote tumorigenesis.

Also, see the RG link below.

Try the STITCH protein network and KEGG to get a better decision. Let me collaborate with you computationally.

It is increased due to alter body immune system by virus and drugs taken during infection

It's only one.

Good question . I thought it is 1. I hope following article will help you

Information regarding OS, DFI, DSS and PFI and their time ...

https://www.biostars.org › ...

Aqeel Kadhim Al Hamaidah

سلام عقیل عزیز

ایمیل بنده در قسمت نام کاربری موجود است

آرزوی موفقیت

Dear Doaa Yamani,

you could try to do immunoprecipitation experiments with, e.g., anti-phospho-Y or anti-phospho-S antibodies, to pull down all phosphorylated proteins in your samples. Then do western blotting and use your antibodies for the nonphosphorylated proteins to detect any enrichment after compound treatment of your cells.

There are several commercial kits available, but in principle it comes down to incubate your cell lysate with the first antibody that will bind to all phopsphorylated proteins in your sample (PY-20 detects phosphorylated tyrosine). Then you capture that complex with, e.g., Immunoglobulin binding Protein A or G coupled to either beads or agarose. After washing the pellet, resuspend your sample in sample buffer for western blotting, the bound proteins are released and loaded on the SDS gel. Detection is done with your antibodies for the nonphosphorylated proteins you mentioned in your question.

You have to be careful though during the detection step, since the Immunoglobulins (the heavy and light chains) used for the pull-down experiment can cause problems during the second detection step (check the species your antibodies are derived from to minimize cross-reactivity!).

Good luck with your experiments,

Christian

First of all, thank you for your reply. I'm going to do research on that. It took me so long to respond because of some health issues. Thanks for helping. Yuning Hou

If you use the absorbance differences (the absorbance of the sample minus the absorbance of the control) at each wavelength, you would require a different equation to calculate the % reduced. The equation you showed earlier includes the control absorbances, so you should enter them into the equation.

As for the protocol used by your supervisor, I don't think any calculation of % reduced is involved. It simply uses the change in the absorbance measurement at 570 nm (minus the background from the culture medium, measured at 600 nm) to represent the degree of reduction. The extinction coefficient at 570 nm of reduced Alamar Blue is higher than that of oxidized Alamar Blue by almost 2-fold, so the more reduction occurs, the more the absorbance at 570 nm increases. To be honest, I don't understand why the background from the culture medium measured at 570 nm instead of 600 nm isn't subtracted in this method.

If you want to, it would actually be pretty easy to derive equations for the concentrations of oxidized and reduced Alamar Blue from absorbance measurements at 570 and 600 nm and the provided extinction coefficients if you first subtract the background from the culture medium at each wavelength (in other words the ∆absorbances.) It just involves a pair of equations and high school algebra for dealing with simultaneous equations.

∆A570 = (E_570,ox)C_ox + (E_570,red)C_red

∆A600 = (E_600,ox)C_ox + (E_600,red)C_red

where C stands for concentration and E stands for extinction coefficient.

To solve for C_red, for example_:

C_ox = [∆A570 - (E_570,red)C_red]/(E_570,ox)

C_ox = [∆A600 - (E_600,red)C_red]/(E_600,ox)

[∆A570 - (E_570,red)C_red]/(E_570,ox) = [∆A600 - (E_600,red)C_red]/(E_600,ox)

C_red = [∆A570(E_600,ox) - ∆A600(E_570,ox)]/[(E_570,red)(E_600,ox) - (E_570,ox)(E_600,red)]

The denominator is a constant, with the value 1.706 x 10¹⁰ in whatever units the given extinction coefficients are in, presumably M^-1cm^-1. Putting in all the constants gives:

C_red = (6.896 x 10^-6)∆A570 - (4.739 x 10^-6)∆A600

Convert from molar to micromolar to get rid of the 10^-6s, and

C_red = (6.896)∆A570 - (4.739)∆A600.

Hello Hossein Shaki

You may refer to the article attached below wherein the investigators presented an ex vivo culture system for precision-cut slices of human pancreatic cancer. They have tried to establish conditions that allow successful culturing of pancreatic ductal adenocarcinoma with good tissue viability in a reproducible manner.

Best.

Antony Ieva When you add your cells to a hydrogel, the 3D internal structure will provide multiple points of contact for the cell to adhere unlike a 2D monolayer where the cell is stretched out and has contact with the one side of the TC plate.

If your cell density is low, initially the cells will appear as spheres similar to cells when they are trypsinised and in suspension. To visualize cells stretching out into their original shape, you will have to culture them for long time for example, 2-3 weeks. The cells will form clusters (high cell density) or remain in spherical form (low to medium cell density) in the first week.

Another consideration in the stiffness of your gel. Since A549 are lung epithelial cells, you may find references to native lung tissue ECM stiffness (compression modulus) and make your gels in a similar stiffness range.

As long as your cells do not die and not crawl out of your gel, they are fine and have adhered to the gel. if your gels are translucent enough, you can stain your cells with Rhodamin-phalloidin/DAPI and perform confocal /multiphoton imaging (after 2 weeks) to check the actual cytoskeleton to give you better understanding.

Hope this helps

All the best.

There are two, very different, ways to model an LQ model. The first assumes that the fractionated curve continues along the single dose curve. The second assumes that there is full recovery from each fraction and therefore the initial curve is repeated from the previous dose SF. The area between these curves is called the "envelope of additivity". See G.G. Steel or Peckham and Steel for more on this addition of survival curves for multifractionated doses. Interestingly, ionizing radiations (with shouldered survival curves) tend to repeat the initial portion of the curve (so-called repair of sublethal damage, but actually split-dose recovery), while some alkalizing agents, such as Bleomycin, have their curve continue along the single-dose curve (no split-dose recovery).

Hi,

Check the references below:

HCMV UL83/pp65 (NLVPMVATV)

Reference: UNIPROT https://www.uniprot.org/uniprotkb/P04439/entry

CMV pp65 peptide NLVPMVATV (HLA-A*0201) is a single peptide for stimulation of T cells. The peptide from human cytomegalovirus (CMV) phosphoprotein (pp65) is synthesized as it is presented by the MHC class I HLA-A*0201 allele and can be used for targeted in vitro generation and expansion of antigen-specific CD8+ T cells.

Reference:

"Although the anti-pp65 antibodies and the pp65 antigens are detected in immune-depressed patients with active viral infection [16], the antibody response to the pp65 antigen in normal infected individuals is not always detectable by immunoblotting [17]. It has been reported that the pp65 antigen is targeted by a cell-mediated immune response and that its vaccination can induce a pp65-specific CTL response"

Reference:

or https://academic.oup.com/cei/article/143/1/167/6440089

Hope it helps,

Best regards

Tomasz

No, there are essentially 3 major types of immune response to infection: an antiviral response which illicits interferon, a pro inflammatory response that makes il1, il6, tnfalpha etc wich is normally directed against bacterial and fungal infections ( and can lead to cytokine storm) and then the allergic response directed against allergens like ova that generates il4, il10, il13.

In mouse models, balb/c mice are typically used to study allergic responses as thy are inherently more allergic and c57bl/6 are used to study proinflammatory responses and diseases because they are inherently more prone to this type of immune reaction.

Benzo[a]pyrene (BP) is one of several ring-shaped chemicals called polycyclic aromatic hydrocarbons that are produced when organic matter, such as a tobacco leaf, is burnt. When it enters the body, BP becomes a powerful DNA disruptor, producing mutations that can lead to cancer.

Fortis Life Sciences (Bethyl Labs antibodies) has Rabbit pAb anti-BRCA2 where they describe the immunogen as "between 3350 and C-term": http://www.fortislife.com/p/A300-005A

Is best to prevention also to treatment.

The best test option for screening of CRC is FIT test and consecutively colonoscopy.

In some previous work I did with paclitaxel, we dissolved it in DMSO (5 mg/mL). Dissolving drugs directly into media is the most ideal method as you have less controls to deal with. However, if you choose to use a solvent like DMSO or ethanol which provide better solubility for many drugs, just be sure to include a control that contains the same percentage of DMSO/ethanol dissolved directly into media alone (without drug) to account for any background noise when running plates, etc. Yes, you will eventually have to dilute your working stock solution in media in order to actually treat the cells. Hope that clarifies things. All the best!

Microbiota influence many aspects of our health including our cancer risk. Since both microbes and cancer cells rely on incoming resources for their survival and replication, excess energy and nutrient input from the host can play a role in cancer initiation and progression.

Metastasis, in this view, is a secondary disease that affects the initial tumor cell. The original cell's cell cycle is disrupted, yet it has no desire to leave its source. According to the fusion theory, a healthy migratory leukocyte merges with a primary tumor cell, resulting in the acquisition of a metastatic phenotype. The resulting hybrid, like the original cancer cell, has the ability to travel across the body of a white blood cell while dividing uncontrollably

Also, I found these links that may helpful in related to this thread:

Hello Jose,

I usually use Graphpad prism 6, however, I hope the latest version does not vary that much.

I used to calculate the % of viability by using an excel template first, then I paste the viability% values in prism.

Please find the steps below from my lab book that may help you how to plot the dose-response curve and how to calculate IC50.

gOOD lUCK

Entire models ogf glycolysis and TCA cycle are created by figment of imagination of lactate production and ATP are the products of glucose catbolism. The models were initially developed by Canbridge school of thought on lactic acid and CO2 production, later Usurped by Warburg. Ironically protagonists and antagonists of lactic acid theory of energy and lactate production became prisoner's of this misguided notion. The models were based on the assumption that stress induced phosphate uptake promotes glycolysis and fermentation, a misinterpretation of his own experiments by Harden. Neither glucose, nor glucose polymers are the source of alcohol production. Th errors were was extrapolated by Warburg's discover of DPN and TPN as thermostable cofactors. It's the fructose which is the source of alcohol. Harden's work was also taken as model for glycolysis, both by experimental scientists and mathematical modellers. These models assumed that glucose is the energy source, and devided glucose catabolism into two blocks: Sugar ---(Block 1)---- FbisP ---( Block 2)----CO2 by Meyerhof, hill, Cories, and Warburg in experimental models, and Fell and Martin Brand and co-workers in Mathematical models. (See Keith manchester's article in TIBS 25 – FEBRUARY 2000). In the name of refining the unanswered qustions in Harden's work, they created a simplistic view of metabolism and created irrepairable confusions in basic science of cell metabolism.In fact, Fructose, Phosphate and Lipolysis (autophagy) devide the glycogen resrves into four blocks, which converge on alcohol priduction on one hand, and Glyceraldehyde-3phosphate on the other. Somatic cells activate RNA synthesis to remodel metabolism to incorporate nutrient metabolites into biomass. Inhibition of Nucleic acid synthesis promotes, gluconeogenesis, lipogenesis, and protein synthesis, which promotes cell differentiation and homeostasis. The puzzles of Covid Vaccines and the delta variant and O-micron variants emerge, as ROS generated are likely to induce alterations in viral genome during RNA synthesis, which manifests in altered viral capid phenotype!

Although Meyerhof, Hill and Cori couple altered their opinions on the role of aldolase, and pyruvate kinase, cancer Biologists are still struggling with "understanding Warburg effect"," reversible Warburg effect". and "Hall marks of cancer still emerging". These workers generate extensive data try to look to their results through Warburg lens not through their own eys and Brain. Unless this attitude is altered, the basic science will be on a wrong path, we face more tortuous Pandemics in future, with aggressive markets chasing for alibies to .make money

Hello Mohammed Fatih Rasul

The limitations of Real-Time PCR are as follows:

1. High false-negative due to presence of amplification inhibitors. This holds true for pathogen detection particularly, for new emerging or highly variable pathogen.

2. The multiplexing is still limited in Real-time PCR.

3. The variation increases with the number of cycles.

4. The overlap of emission spectra.

5. The occurrence of non-specific binding particularly, when carrying out SYBR green analysis.

6. The PCR product increases exponentially but one cannot monitor the amplicon size.

7. Kits are not available for all kinds of genes and disorders.

8. It needs specialized laboratories, operated by highly trained technicians for developing novel qPCR assays, which makes it too costly and difficult to scale up.

You could use other techniques that could be performed in the laboratory.

1) Fluorescence In Situ Hybridization (FISH), also known as molecular cytogenetic testing, is a way to visualize and document the location of genetic material, including specific genes or DNA sequences within genes. FISH is used to look for the presence, absence, relative positioning, and/or number of specific DNA segments under a fluorescence microscope. FISH is particularly helpful in identifying copy number variations, especially translocation and amplifications.

2) Comparative genomic hybridization (CGH) is a special FISH technique (dual probes) which is applied for detecting all genomic imbalances. CGH is used to determine copy number alterations of genome in cancer and those cells whose karyotype is hard or impossible to prepare or analyze.

3) Single Strand Conformational Polymorphism (SSCP) is one of the simplest screening techniques used for detecting unknown mutations (microlesions) such as unknown single-base substitutions, small deletions, small insertions, or micro inversions. A DNA variation causes alterations in the conformation of denatured DNA fragments during migration within gel electrophoresis. The logic is comparison of the altered migration of denatured wild-type and mutant fragments during gel electrophoresis.

4) Heteroduplex analysis in which a mixture of wild-type and mutant DNA molecules is denatured and renatured to produce heteroduplices. Homoduplices and heteroduplices show different electrophoretic mobilities through nondenaturing polyacrylamide gels.

5) Denaturing Gradient Gel Electrophoresis (DGGE) has been used for screening of unknown point mutations. It is based on differences in the melting behavior of small DNA fragments (200-700 bp); even a single base substitution can cause such a difference.

6) DNA microarrays can detect thousands of genes at once. DNA “chips” or microarrays can be used to test for multiple mutations. In this technology, single DNA strands including sequences of different targets are fixed to a solid support in an array format. On the other hand, the sample DNA or cDNA labeled with fluorescent dyes is hybridized to the chip. Then using a laser system, the presence of fluorescence is checked; the sequences and their quantities in the sample are determined.

7) Use of Next Generation Sequencing (NGS) allows comprehensive description of germ-line DNA, analysis of somatic mutations and RNA profiles in naturally occurring tumors, systematic analysis of microbiomes, etc. The resulting data can help in the identification of novel hereditary syndromes, molecular targets for cancer therapy, tumor-specific diagnostic markers, etc. But this technique would be expensive to work with.

Best Wishes.

Run the vcf-isec command along with the -c option. For example, to get the variants present only within your tumour samples, try inputting "vcf-isec -c marked_I_tumor-pe.vcf marked_I_normal-pe.vcf > tumor_only_variants.vcf", and for normal variants only, just swap the order of the input vcf files. Hope the above helps.

Check https://davetang.org/muse/2019/09/02/comparing-vcf-files/

Hello Giammarco Nebbioso

Wash the cells with PBS without Ca2+/Mg2+ at the time of trypsinization and preferably use trypsin with EDTA. Clumps form because of the presence of free DNA in cell suspension which are released from dead cells. Free DNA attracts cells which bind altogether forming clusters.

You can use DNase I at concentrations from 20-100µg/ml to avoid formation of clusters. For each cell type, the working concentration must be determined individually.

Hope this is helpful.

Best.

Hi Amrit,

The most commonly mutated gene in people with cancer is p53 or TP53. More than 50% of cancers involve a missing or damaged p53 gene. Most p53 gene mutations are acquired. Among most active carcinogenic mutagens the championship title belongs to polycyclic aromatic hydrocarbons (PAHs). These are the most abundant indirect-acting carcinogens to which humans are exposed to on a daily basis. Exposure has been associated with the development of breast, skin or lung cancer. Bioactivation of PAHs is required in order for these agents to exhibit mutagenic properties, which is primarily mediated by cytochrome P450 enzymes (among many others, our data on this subject - in http://www.xenobiovir.com/). Bioactivated metabolites target multiple genomic sites, including guanine and adenine bases via PAH diol epoxides. This results in the generation of bulky BPdG chemical DNA adducts; examples include quinone-mediated cross-linking of N7 position of guanine and N3 of adenine.

All the best,

Ilya

One paper that I can recommend on this particular study is this one:

Especially, the molecular simulation part. You can try it

Hello, Dear Geoff.

We continue to work on the subject you mentioned. There are methods that can analyze this.

thank you for answring my quesion dear Dr Erum Zafar

If you got your miRNA of interest based on data from a previous study, and want to know if it corresponds to 5p/3p in the current miRBase relase, you can do the following: first, lookup the old miRNA ID in older miRBase releases and retrieve its sequence; then, do a search in miRBase using the retrieved sequence, and see to which mature miRNA it corresponds to.

In your case, mir-204 (from e.g. miRBase v.17) corresponds to mir-204-5p (miRBase v.22).

thank you, dear Shin Murakami for your sugession

With time, tumor growth produces major tissue disruption that hematoxylin/eosin or trichrome staining will show clearly in comparison with controls and non-tumor implanted samples. 40 um sections may be a bit too thick for high mag, high resolution imaging, however. The attached paper reference shows examples of the disruption.

A mismatch repair deficiency in an advanced tumor does not necessarily mean a Lynch syndrome. It can just be a late mutation. Some authors consider this under the name of mutator mutations. As a Karolin Heinze says above you need to test the patient for germline mutations.