Science topic

Immunity - Science topic

Immunity is a nonsusceptibility to the invasive or pathogenic effects of foreign microorganisms or to the toxic effect of antigenic substances.
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Thinking of better way to obtain restriction enzymes.
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This is not strictly true. Homing endonucleases such as I-Sce and I-Cre arise from eukaryotic sources, such a Saccharomyces cerevisiae and Chalmydomonas reinhardtii. However, they aren't involved in immunity against foreign DNA, e.g. viruses. They also have much longer recognition sequences than prokaryotic restriction enzymes.
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Dear collogues,
May I ask, What are the best natural herbs for obesity management?
Thanks
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Is it indispensable to receive a vaccine by the COVID-19 recovered person?
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As per my opinion it is advisable to receive complete schedule of COVID vaccine irrespective of past history of infection with COVID-19.
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Immunity rules have always been quite controversial. Many scholars believe that to grant immunity to eg, Head of State or other state officials goes contrary to the fundamental principle of justice and human rights, especially if those state officials are charged with crimes of jus cogens status.
So, does this mean, immunity should be denied as a defence to charges involving of allegation of crimes of jus cogens status (eg, genocide, crimes against humanity etc) regardless of the national or international character of the jurisdiction concerned?
After some research, I have learned that if two parties at disputes are two states, then the other state always has to respect the immunity of the other state (due to the principle of state sovereignty and equality-eg, Arrest Warrant Case). But eg, if an arrest warrant was issued by the International Criminal Court, the answer will be different. Al Bashir Case showed how the ICC denied immunity as a defence by getting around with Art. 98 of the Rome Statute.
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I think a thorough analysis of the elements of the case has to be carried out, considering mainly the material facts and the perpetrator's mens rea. It is very unfair to the victims, and really to the whole of huamnity, that people who are supposed to uphold human rights get easily away with their wrongdoings. This does not, however, mean that they do not have the right to a fair trial.
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One reason for posting this question is to hope that by following this question it is possible to keep up on developments pertaining to this question.
An article in a health magazine, Stat, by Sharon Begley, Experts envision two scenarios if the new coronavirus isn’t contained, suggests the answer for now is, not sure.
An article in Lancet, Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study, by Prof. Joseph T. Wu, Kathy Leung, and Prof. Gabriel M Leung, remarks in the discussion portion of their paper that `independent self-sustaining human-to-human spread is already present in multiple Chinese cities’ including global transport hubs. This suggests that containing, confining and eliminating COVID-19 as a pervasive and ongoing infectious disease might not be possible.
If infected people do not acquire immunity, that affects calculations of the ongoing spread of COVID-19. For example, if 70% of a population catches COVID-19 and most survive and acquire immunity, then the size of the group that COVID -19 could newly infect would be smaller. In that way, over time, as the number of people who survive the disease increases, the rate of new infections might decline because there would be fewer people without acquired immunity. I wonder what epidemiology says? These issues also affect hopes for a vaccine.
Regardless of what the immunity situation is, it seems to be that there should be a permanent cultural shift away from greetings such as handshakes and kissing.
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for sure it's 100% possible even with vaccine
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If a foreign animal protein is adminstrated to the body it develops immunity. Such as kidney transplantation needs immunosuppression. But why the proteins consumed in the form of food don't develop immunity issues?
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Hello Haji Muhammad Umer Memon
For short
Proteins consumed with food do not elicit an immune response, also because they are broken down into tiny, non-immunogenic fragments in the digestive tract.
Larger (immunogenic) fragments do not pass through the filters of the gastrointestinal tract. With aging, the permeability of the filters increases and problems such as foodborne rhinitis arise.
Hope this additional info will be helpful.
Best wishes
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Vertigo is a condition that can make it feel like you or your surroundings are spinning, sometimes leading to a loss of balance, according to the U.S. National Library of Medicine.
Coronavirus 2019 or COVID-19 is a novel entity which had led to many challenges among physicians due to its rapidly evolving nature. Vertigo or dizziness has recently been described as a clinical manifestation of COVID-19.
So, Are dizziness and vertigo COVID-19 Symptoms? and why?
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Dear RG community,
As far as I know, antibodies are different in vaccination and natural infection. While natural infection produces antibodies against different parts of the virus, vaccination produces antibodies against only parts of the virus that are present in the vaccine. For instance, nucleocapsid proteins are not present in the vaccine, so antibodies are not produced against nucleocapsid proteins by vaccination. Is there any authorized COVID antibody test to differentiate a person’s immunity as either natural infection or vaccination? (For instance, a person gains immunity from vaccination not a natural infection, or a person gains immunity from vaccination 70% and natural infection 30%, etc.)
On the other hand, both vaccination and natural infection can produce the same type of antibody. For example, both vaccination and natural infection trigger to produce antibodies against spike proteins. Is there any difference between these two proteins? Can we differentiate antibodies against spike proteins that are triggered by either vaccination or natural infection?
Thank you.
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The very basic aspect to combat ﹰCorona is ﹰHerd immunity . Vaccination may fail very often if natural immunity can be developed to increase the reproduction number it will be better .
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Plan to add a tag with the GOI for the protein-based vaccine. Are there any tags or certain short AAs that can activate the innate immune response?
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Hello, cationic lipids/polymers in general can activate macrophages and DCs so they can be used as a surrogate of a adjuvant. However, I don't know a specific tag that has these characteristics.
Regards
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Immunity can be defined as the first defense line for the body against a lot of infections especially what is known by now as coronavirus infection. So, we need to boost that system in order to make us safe or at least less exposed to catch the disease. How can we do this properly?
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Good and balanced nutrition
enough rest
exercise
peace of mind
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Are resistance (R) genes expressed in response to pathogen attack - or only defense genes - as part of the plant immune response? R proteins act as receptors to recognize pathogen effectors and an interaction between R protein and effector stimulates Effector Triggered Immunity (ETI) which itself involves the expression of defense related genes. However, are R genes also expressed as part of ETI?
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Dear Ruby Metzner Plants have developed a complex defense system against diverse pests and pathogens. Once pathogens overcome mechanical barriers to infection, plant receptors initiate signaling pathways driving the expression of defense response genes. I have attached some PDFs; hope these will provide useful insight regarding answer to your question.
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In your opinion, which country is most successful in control over COVID-19 spread so far? Please share the reasons in favor of your choice.
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Please also take a look at this useful link.
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RNA vaccines follow a different strategy, without using any "real" component of the virus at all. Instead, researchers aim to trick the human body into producing a specific virus component on its own. Since only this specific component is built, no complete virus can assemble itself. Nevertheless, the immune system learns to recognize the non-human components and trigger a defense reaction. So May I ask, What are your opinions about the safety and efficacy of the BNT162b2 mRNA Covid-19 Vaccine?
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please share Immunity boosting Kadha recipes from different regions of the world.
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Please also have a look at the following attached article.
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According to recent study showed that Nicotine may play an indirect role that makes it harder for the virus to gain to access cells AND smokers seem less likely than non-smkers to fall ill with COVID-19.
What is your opinion ?
In my opinion : Nicotine is known to decrease immunity response against infections . So , possibility to develop cytokine storm will be less. I believe this is why it help in COVID-19.
The same thing you will see less aggressive COVID-19 in patients with immunodeficiency e.g. PID or patients on immunosupressive e.g. SLE and RA patients.
I need to hear your opinions regarding this issue.
Regards,
Abdul Hadi Al-Qahtani, MD/MHA
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It is a myth that smokers are protected against SARS-CoV-2 infection.
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We would like see the capability (possibility) of a test substance in enhancing or normalising the expression of TLR2/4. In this context what type of Invivo model or inducing (antigen/ chemical) agent is ideal to test this hypothesis ?
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For the mouse model, FACS, microscopy, and functional testing regarding TLR2 and TLR4 ex vivo view these papers:
These might also be interesting for you:
I do not know a substance to lower TLR expression in vivo. Maybe you could start with the baseline TLR expression, then apply your experimental substance, PBS as negative and maybe R848, or some CpG ODN 1668 as positive control.
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Hi all,
I want to assess the phenol-oxidase activity (PO activity) of bumblebee haemolymph. However, the protocols I found in literature always use a centrifuge step at 4°C to obtain the clear hemolymph without hemocytes.
However, our lab's centrifuge doesn't have a cooling function. Would it be a big problem to use a regular centrifuge without cooling for this step? Or does anybody know of a protocol where this cooled centrifuge step is not needed?
Thanks in advance!
Enya
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Hi Enya,
Melanisation is a tricky reaction, since PO system is activated by various factors, including temperature. However, you can minimise this activation by collecting and diluting hemolymph to ice-cold buffer, keeping the samples on ice and fast work. In this way, you can cetrifuge at lab temperature and still be able to detect constitutive activity of PO.
Nevertheless, I would recommend to measure in paralel the hemolymph treated with α-chymotrypsin. It will activate proPO and you will find out the total PO activity in bumble bee hemolymph, to which you can compare the detected constitutive activity. You can find details of similar PO assay in B. terrestris here: 10.3390/insects11050321. In this experiment, we measured PO activity in hemolymph after its freezing and thawing, which activated PO system to the same extent as chymotrypsin treatment.
It is also possible to measure melanisation in the whole hemolymph, i.e. to omit centrifugation and determine PO activity in the presence of hemocytes. Overall, the design of PO assay depends on a focus of your experiments.
I hope that some of these notes will help.
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Traditional varieties are doing extinct day by day in the race of high yielding varieties. Many indigenous varieties were cultivated past 20 – 50 years. How will allow again the traditional varieties in the situation of climate change? Human diet diversity was played pivotal role during forefather’s life or before 50 years past. Would it be right to say that the native varieties helped to increase immunity? In todays’ situation every person is ready to do something to increase immunity. If today we had food made with native varieties in our plate, then we would not have to run for immunity?
#Climate Change #Food diversity #Immunity #Traditional Varieties
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Manoj Kumar Dash Thanks for sharing the article.
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Many countries of the world particularly United States, Germany, United Kingdom and Italy are planning to issue an immunity passport for COVID-19. How it would be implemented? Is it a good or a bad idea while we do not know when the COVID-19 pandemic will end?
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Immunity passport has again surfaced in to reality after COVID-19 vaccination.
Many countries are issuing a Certificate of completion of full doses of the COVID-19 vaccination to help such people travel.
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Immunity from covid 19 after vaccination
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It will depend on the individual immune system how good it gets trained with the help of the vaccine. The duration of anti-body might also vary from vaccine to vaccine as some vaccines might give longer protection compared to others.
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Should we wait for vaccine against COVID-19 or also look towards other possible options to reduce mortality rate of Corona virus. Can Physiotherapists critically analyze the effect of exercise in Corona patients as exercise has cardio-respiratory effects as well as influence on Immunity.
Need your help and suggestions please?
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Regular exercise or physical activity improves the immunity of the body thus providing protection against the infectious diseases such as COVID-19.
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According to Kirill Dmitriev, head of Russia’s Direct Investment Fund that bankrolled the effort, a vaccine developed by the Gamaleya research institute in Moscow may be approved in days, before scientists complete what’s called a Phase 3 study. That final-stage study, usually involving tens of thousands of people, is the only way to prove if an experimental vaccine is safe and really works.
Scientists worldwide are sounding the alarm that the headlong rush could backfire.
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In phase 3 trial Russian vaccine "Sputnik V" has been found safe and effective against COVID-19.
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I produced Glycerol monolaurate in lab scale, with a melting point of about 37 C. Now I want to use this product as animal feed additives. However the melting point of 37 makes the product difficult to be sold as solid nor as liquid. Now I need to convert this product to be liquid at room temperature, what do you suggest? Kindly put into consideration that the final product is feed additive.
One suggestion is to mix with a another material with very low melting point.
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I need to obtain dendritic cells that are free of macrophages. After the Helft paper (Immunity, 42:1197, 2015), this seems difficult from BMDCs ? Even sorting out F4/80+ cells should not work, because DCs are F4/80med. So how would you get rid of macrophages in BMDCs ?
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Dear Germain!
You look at these articles and protocols for denditic cells, please:
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Worry less about the virus's behaviour (mutation, airborne, immunity, new strain etc) - Because experts are working on that :)
Worry more about personal behaviour - Wear a mask, wash hands, avoid public place and crowds.
We need to focus on what's in our control and keep our lives cautiously.
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Yes. I fully agree with the above thesis. Despite the commencement of vaccination programs of citizens against the SARS-CoV-2 (Covid-19) coronavirus, certain recommended rules and instruments of anti-pandemic safety should still be applied, including, in particular, the use of protective masks and social distancing in public places, and frequent disinfection of hands. Despite the Coronavirus vaccination programs starting now (December 2020), the emergence of new, new mutant variants of the Coronavirus cannot be ruled out. Therefore, it is in the period of the campaigns to vaccinate citizens against Coronavirus that it is necessary to slow down the transmission of Coronavirus in the society, and therefore it is necessary to comply with the rules and instruments of anti-pandemic security. It is a question of social responsibility and intergenerational solidarity. In addition, this issue is particularly important in the context of meeting the strategic goals of a significant increase in the social immunity of citizens thanks to the ongoing programs of vaccination of citizens against Coronavirus.
Stay healthy! Best wishes,
Dariusz Prokopowicz
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Can anyone discuss the claimed efficacy of COVID-19 vaccines (e.g., 80%, 95%, etc.) by different manufacturers (COVAX, Pfizer or others)?
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Outstanding and similar ( so far) for protection.
Bit we need to see:
1. a better breakdown of performance in different age and ethnic groups groups
2. Amy major difference in short term side effects
3. how long protection lasts
4. whether it prevents virus from actually infecting
5. Long term side effects of RNA vaccines In general
6. how they compare to protein vaccines and vectored DNA vaccines
7. AND as noted the impact of production, transport, storage, shelf lives on long term use. and costs.
Lots to learn but ( especially given their designation as EUA) there Is still much to learn. However, they will certainly move us towards herd immunity and a more open economy.
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The reason why is they have specific immunoglobulin to covid-19 since in their past having contracted common colds due to many strains of coronaviruses, they have crossreactivity so they become also immune to the covid-19.
Related 5 websites articles are below:
SMOKERS CONTRACT COVID-19 SIGNIFICANTLY LESS AND MILDER!
Related 5 websites articles are below:
MY HYPOTHESIS:
WHY SMOKERS CONTRACT COVID-19 SIGNIFICANTLY LESS AND MILDER?
Most probably, since smoking is chronic inflammatory process in nasal mucosa and also smokers most often smoke outside or by an open window they contract much more easily common cold and often their mucosa. Due to these multiple contractions of common colds, they have antibodies to both coronaviruses and rhinovirures which are the most etiologic viruses in common cold (coryza) cases. Due to cross reactivity of coronaviruses antibodies they are considerably immune or resistant to covid-19. These coronaviruses antibodies cause significant loss of smelling also. More common colds and less smoking simply means more immunity to covid-19.
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Dear Sinan Ibaguner,
Is it proven fact that smokers are more affected by COVID-19 than non-smokers ?
I don't think so, though I don't have any data .
Thanks
N Das
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Immunity is the ultimate hope in this pandemic. I just wanna to know antiviral immune response in the body. Please suggests some paper which elaborate the mechanism of antiviral response. Thanks in advance.
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Aswagandha (Withania somnifera) is a well known herb which has many medicinal properties. What are the roles of Aswagandha to Boost Immunity?
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Ashwagandha is an efficacious herb, that has various health benefits, that includes its powers to combat diabetes, decrease inflammation, block arthritis, asthma, hypertension, stress, and rheumatism. It is a great immunity booster, that improves immunity due to its anti-oxidant properties. Ashwagandha is good for skin-care,hair care, and has anti-wrinkle properties. Pure Ashwagandha also assists in increasing height and managing thyroid problems.
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Cancer, Immunity
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It is important cancer patients and their caregivers take precautions to lower their risk of getting COVID-19.
take healthy diet
use mask in crowd and social distance is important for them
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Are there any reports on the correlation between the consumption of oseltamivir(Tamiflu) and the incidence or mortality of COVID -19 patients?
what is the effect of Tamiflu on immune system?
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Almost all the microbiology textbooks and relevant research articles mention that Hepatitis B core antigen is not released into the blood of the host. It rather interacts with other core antigen particles to assemble the capsid of the Dane particle. My question is then how the body produces antibodies against HbCAg?
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Most events leading to the immune response, including meeting with the antigen and the production of antibodies does not occur in the blood but in the lymphoid organs
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In the COVID-19 infection, the main issues are not brought by the virus itself, but by our bodies' excessive immunological response to the infected organs - the cytokine storm. This cytokine storm destroys all cells near the focus of infection and kills the respiratory system. So is there any natural non-aggressive way to prevent the cytokine storm from happening in the severe COVID-19 cases?
Thank you in advance for your valuable opinions!
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Dear Dr Ligen Yu ,
Natural non-aggressive way to prevent serious COVID-19 would be to sustain healthy life-style; to justify body weight, blood pressure, blood glucose and lipid, and especially visceral fat, before cytokine storm develops, I believe.
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Sleep is known for its immuno-modulatory and immune strengthening effects. Different sleep stage specific deprivations studies across animal kingdom are found correlated with many patho-physiological, immune-weakening and health detrimental issues. Is the lack of sleep with modern stress and socio-economical changes are driving the immuno-deficiency in humans to combat virus challenges?
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Proper sleep is must for healthy immune system which may help avoid the risk of coronavirus (COVID-19) infection.
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This question relates to the question, Is it possible to catch COVID-19 twice? Acquired immunity might slow the spread of COVID-19 or provide some protection from re-infection for those who survive the disease. The advantages of acquired immunity might be impaired if the rate of mutation, or the kinds of mutation, impair the advantages of acquired immunity.
A March 3, 2020 research article in the National Science Review considers mutation: On the origin and continuing evolution of SARS-CoV-2. The authors are: ang, Xiaolu and Wu, Changcheng and Li, Xiang and Song, Yuhe and Yao, Xinmin and Wu, Xinkai and Duan, Yuange and Zhang, Hong and Wang, Yirong and Qian, Zhaohui and Cui, Jie and Lu, Jia.
The article describes two major strain designated L and S. The authors infer that the S type is the ancestral version, and is less aggressive. The L type they said is more prevalent, about 70% than the S type, about 30%.
The public health advice to follow social distancing is directed to slowing the proliferation of the disease. But I wonder: might social distancing also impair the mutation rate of COVID-19? If slowing the mutation rate is beneficial, then social distancing has advantages in addition to slowing the spread of the disease. Do you know the epidemiology that relates to this question?
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Yes, it helps.
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Is there any reports on the correlation between Vitamin C status and incidence or mortality of COVID -19 patients?
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In my opinion, no research is conducted on the correlation of vitamin C with incidence or mortality of COVID-19. We all know that vitamin C is an important nutrient, and is required in many body functions including immune system. If immune system is strong, there is a very possibility to get infection. Lemon is a very cheap and easily available source of vitamin C throughout the world.The other natural sources of vitamin C include orange, strawberries, papaya , guava, grapefruit, Kiwi, cauliflower, broccoli etc.
I add juice of one lemon in one glass of Luke warm water and drink empty stomach daily in the morning.
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Are there any reports on the correlation between Zinc status and incidence or mortality of COVID -19 patients?
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I am not aware on any scientific study on the correlation of zinc with incidence or mortality of COVID-19. However, zinc is an essential nutrient that helps our immune system.The person with strong immune system are not easily get infected. Zinc is present in a variety of food, such as nuts, seeds, dairy products, vegetables, dark chocolate, shell fish, meat etc.
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In our experimentation, end point is quantification of NK cells after treatment period. Different markers like CD25, CD69, CD16 etc., were given In literature (there is no uniqueness in marker selection for quantification of NK cells). So, here my basic doubt is, what is basis / rationale to select the marker for the quantification of NK cells and what is ideal marker for the same?
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Normally flow cytometry identificaiton of human NK cells depends on staining with CD3 and CD56-specific monoclonal antibodies with NK cells being defined as CD3 negative, CD56 positive cells. If you add in CD16 staining then this will help with defining the two main subsets of peripheral blood NK cells, the CD56bright CD16 negative more immature population and CD56dim CD16 hi-expressing more mature NK cells. If you really want to be maximally precise you could also include CD7 staining (lymphocyte-specific) to exclude a small population of myeloid cells that express CD56
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Is there any method described in any form of yoga to enhance the immune power of human body?
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I'm looking for a protocol to isolate intact antibody:antigen immune complexes from human serum.
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Out of curiosity; is it possible to isolate immune complexes deposits in organs?
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I would like to know a good adjuvant to combine with some peptides of 20aa long to immunize rabbits and after recovery of antibodies.
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Hey,
I'm looking for assays where I can track single cell - single bacterium dynamics, mainly rate of killing. Most methods I find online revolve around finding a single infected cell and following it via live cell microscopy. Are there any other methods, where I can follow the course of infection in a single cell, such that I can measure bacterial killing/survival in macrophages? Thanks!
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Values above 7 can be considered ok? I made the RNA extractions using TRIzol.
I want to quantify the expression of some immune genes in spleen and head kidney of bacterial infected fish. I also tried to extract total RNA from the liver and muscle, but several samples are RIN N/A. Is it necessary to use the TissueLyser for these organs?   
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What has the concentration of the NA samples? Make sure it's sufficient to get a good reading. What did the virtual gel look like? Was it obviously bad, or was there something strange in there? Feel free to post a couple of pics here of the best vs an NA sample.
RIN values may not be calculated for several reasons, like when an unexpected peak is detected, and errors can be considered either critical or non-critical depending on the type. I've attached a document that may help you, if you need it.
You mentioned the TissueLyser. In my experience that is a good way to thoroughly homogenise your samples. What method of homogenisation did you use?
Also think about your sample collection and storage. Could some not be optimal there?
If you have the chance to do some kind of column extraction as opposed to Trizol then it's worth testing a few samples. I've done many many (fish) liver samples with a GE Health column-based kit, and another Qiagen kit with really good results (RIN values typically >8) from RNAlater preserved tissue.
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I am trying to find the list of cells that content endosomal TLRs (TLR3,7,8 and9). Are these TLRs expressed all over the body or there are very specific cells that expresses these TLRs?
Any input is appreciated. Any reading material to find the answer is appreciated.
Thank you.
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Szczepan, thank you for replying to the question. Do you have any reading material that supports your answer? I will highly appreciate if you could share here. Thank you again.
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I am screening products against PBMCs, testing for potential immune activation. I have been looking at CD69 as a good general marker of immune activity, but would prefer something secreted. Does anyone have some good recommendations? Thanks!
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Hi Natascha,
we use in our lab both CD25 and CD26 for CD4+ T cells. They are markers for immune activation, and both have membrane and soluble versións. In addition, the last one is an enzyme, which means that you can measure the amount of this protein with a simple determination of enzymatic activity that uses a Gly-Pro substrate.
Good luck!
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Hello,
I've been (not so successfully) trying to perform basic experiments on dendritic cells to analyze the actions of a fatty acid. I've noticed there are numerous methods to do this and it seems that many people use completely different methods to arise at the same population. I've tried a variety of these methods and have not obtained similar results.
For example, I first tried isolating BM cells (femur flush) and treated them with GM-CSF and IL4 at 20 ng/mL or 10 ng/mL for 5-10 days. I never reached a CD11c% > 60. I've tried taking the adherent cells. I've tried taking non-adherent cells, and now I'm going to try obtaining both. These methods are routinely published and groups get >90% with or without positive or negative selection with beads. It seems that 50% of papers will actually publish the flow results for the DCs before they use them.
Meanwhile Helft et al. 2015. Immnity 42 demonstrated that even CD11c+ cells are 50% macrophages and not DCs. These data were debated (Helft Immunity 2016, Guilliams Immunity 2015, Lutz Immunity 2016) but there still was never a general consensus. More recently, a paper published in J Immunol (Jin and Sprent 2018) demonstrated even newer methods that yielded greater amount of DCs by using less cells and adding IL4 late during culture.
For someone new in the DC field this is very confusing and it seems that there is no tried and true method to isolate DCs. Is the CD11c+ count all that matters? How many markers do I need to show are active upon stimulation? Is CD80/CD86 enough? Do I need to show CD115, CD64, CD24? If so, this is barely ever done. Many groups also just say "We isolated DCs as done previously". This is great except it cites papers from nearly 20 years ago.
I am sorry for the long-winded questions but any help/direction would be very much appreciated!
Best,
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Thank you everyone! It seems that it comes down to sticking to a method and taking care to characterize that model well. Another paper just came out that illustrates this conversation well:
It appears that after stimulation with GM-CSF they again confirm three populations of cells (2 macs, 1 DC) characterized with CD11c, CD11b, MHCII (classical phenotyping). One population can activate inflammasome signaling while the other cannot. This could possibly be confusing without separating these cells into their populations.
I think I am going to try using GM-CSF in culture and then use negative selection (CD3, B220, CD49b, Ly6g, CD115) to isolate DCs and characterize with CD11c, CD11b, MHCII, and CD135 (like both papers above).
Best,
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Good morning all,
I was wondering if it's possible to use CIBERSORT (or similar deconvolution algorhitm) on RNAseq data of gut biopsies from humans?
We are trying to gauge the presence of immune cell types in them, but the biopsies also contained epithelia, fibroblasts and other cells. I am worried that using the LM22 signature set will give me bias due to many transcripts coming from these non-hematopoietic cell types. Based on what I understand, this should be possible, right?
Second part of my question, we get quite high (insignificant) deconvolution p-values. Is there any way to improve them?
My example outcome attached.
Thank you very much for your time,
Adam
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I usually prefer Xcell through UCSF (http://xcell.ucsf.edu). It has several reference datasets available, including RNA-sequencing of both immunologic and somatic cells (64 cell types total).
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I would like to quantify the activation of cell surface antigens, in this case CD69, on peripheral blood mononuclear cells (PBMCs) to screen for an immune response. Do I need to take any special steps or precautions, such as lysing the cells, since the antigens are found on the cell surface, instead of being secreted into the media?
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Hi Natasha Worden , I agree with Shen-An Hwang, I don't know why you'd use ELISA to look for membrane-bound CD69. I would use Flow. I just wanted to add that you need to remember the kinetics of CD69 upregulation - it is among the first markers of T cell activation; it is upregulated in as little as 6 hours (depending on the stimulant), peaks around 24 hours and then down regulates & stays down. Other activation markers such as CD25 upregulate after activation & retain expression over time. However, CD25 does not peak until around 48 hours. So you need to take this into consideration when designing your experiment & measure the presence (or absence) of your marker at an appropriate time point. If you're looking for CD69 1 week after activation & concluding the cells are not activated, your conclusion would be incorrect. Hope this helps :) Melanie
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Hi All,
Small and large intestine are different organs, but have similar structures and functions, here I want to ask,
1) As for intesitnal immunity development, it seems that small intestine contains more immune cells than colon, so small intestine contributes more to intesitnal immunity development?
2) Do small intestine and colon share immune cells? through what mechanism?
Thanks!
Xin
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Hi Xin,
Think you'll find this paper particularly helpful. As mentioned above your questions are currently too broad/ill defined to be answered.
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The differentiation protocol of mouse CD34+ bone marrow cells into dendritic cells is well known. Is anybody familiar with protocols describing the differentiation of mouse CD34+ BM cells into other immune cell types (e.g. T and B cells, NK cells, etc.) ?
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For example, measuring lymphocytes conc. in control gp was 100 ug/ ml while group 1 average was 115 ug/m, performing student t test results were signficantly different. But how to explain this in terms of fold change?
Is expressing the results in terms of fold change a must to prove that there was an improvement (increase) in the group than the control?
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There is no prove. The if t-test is "significant", you conclude that you have enough data to interpret the sign of the mean difference between the groups. In that case you would in some way report that sign. The typically recommended way is to write something like "the mean lymphocyte concentration in group 1 was higher than in the controls (t-test: p<0.05, t=3.25, df=14)". The sign of the t-value also shows the direction of the difference.
You may wonder why the mean difference of 15 ug/ml is not given. Many people consider this very important as being an effect size. However, this is actually a wrong interpretation. We don't know the effect size, and what we have is just some data that is subject to noise, and we may only use this to get some additional information about the effect size. The mean difference in the sample is often said to be an estimate (of the effect size). This not not completely wrong, but a much weirder kind of estimate than one would think: it is the assumed mean difference (in some assumed statistical model) under which the observed data is most likely. It does NOT say, by itself, that the value of the estimate is good, probable, or credible value for the (still unknown) effect size. Data alone is not sufficient to give us an estimate (however, the relevance of this argument decreases with increasing sample size).
As this is likely to be a quite controversial point for many people (including statisticians), it's common practice to give the sample value (+15 ug/ml in your example) as an estimate of the effect. However, such a value should never be given without some indication of the (un-)certainty that is associated with this value. Many people give the standard error, but (and this is far less controvesial) the better alternative is to give the confidence interval (usually the 95% confidence interval).
Should you show the mean difference of the fold-change? - this depends on what you tested. If you used the concentrations in the t-test, you tested the mean difference, and then this should be reported. If you used log concentrations in the t-test, then you should report the mean difference of the logarithms what is equivalent to report the log fold-change (LFC). You can anti-log the mean LFC and the limits of the confidence interval of the mean LFC to get the mean and the confidence interval of the fold-change.
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Once triggered into action, an immune cell overhauls its metabolism, making changes that could be exploited for treatment.
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Caution is always important in today's fast-paced research environments.
Dennis
DennisMazur
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I was told that survivors of tetanus do not generally acguire natural immunity to the disease. However, does it happen at least sometimes? Or, if not imuunity, do they have tetanus antibodies after they survive the disease ? Obviously, I mean the circumstances when nobody gives them a toxoid booster.
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Hi Barbara, most foreign proteins (non-self) will generate an antibody response in a healthy individual.
I am not an expert in immunology or toxicology but it is pretty obvious that all of us have been exposed to many pathogens at levels that would kill immuno-compromised individuals.
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It has been shown that the treatment with ruxolitinib, which selectively blocks JAK1/2-dependent signaling pathways, resulted in a high response rate exceeding 80% among corticosteroid-refractory GVHD patients.1 It is notable, however, that IL-2-JAK3-STAT5 axis is also considered to be responsible for the therapeutic effect of ruxolitinib. IL-2-JAK3-STAT5 axis is essential for the development, survival, and proliferation of regulatory T cells (Tregs).2 The conversion of FoxP3-negative Treg-progenitor-cells into mature FoxP3-positive Tregs in the thymus occurs mediated by TCR-independent but IL-2-STAT5-dependent process.3 Ligand binding by the high affinity IL2-receptor complex results in the phosphorylation of three key tyrosine residues localized in the cytoplasmic domain of IL2-receptor-beta by both JAK1 and JAK3.2,3 Furthermore, it has been also shown that ruxolitinib suppresses the differentiation of donor T-cells into Th1/Th17 cells, while increasing the differentiation into FoxP3-positive Tregs.4 Importantly, ruxolitinib is reported to inhibit IFN-gamma signal transduction in donor T-cells, which is required for those cells to infiltrate into GVHD target organs via chemokine receptor CXCR3.5
References
1: Zeiser R, Burchert A, Lengerke C, et al. Ruxolitinib in corticosteroid-refractory graft-versus-host disease after allogeneic stem cell transplantation: a multicenter survey. Leukemia. 2015;29:2062-2068.
2: Mahmud SA, Manlove LS, Farrar MA. Interleukin-2 and STAT5 in regulatory T cell development and function. JAKSTAT. 2013;2:e23154.
3: Burchill MA, Yang J, Vang KB, et al. Linked T cell receptor and cytokine signaling govern the development of the regulatory T cell repertoire. Immunity. 2008;28:112-121.
4: Spoerl S, Mathew NR, Bscheider M, et al. Activity of therapeutic JAK 1/2 blockade in graft-versus-host disease. Blood. 2014;123:3832-3842.
5: Choi J, Ziga ED, Ritchey J, et al. IFNγR signaling mediates alloreactive T-cell trafficking and GVHD. Blood. 2012;120:4093-4103.
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Hello Go J.
In use of drugs, they permeate and diffuse within the cell. One of the ruxolitinib- or similar-targets is the Jak signaling pathways. However, every drugs cause toxicities in every corner of the cell. The excessive or diffused drug would influence healthy state of cellular activities, including intervening metabolism, accumulation radical oxygen species (ROS) and delaying or arresting cellular processes and etc. Increased ROS could cause hypoxia, leading many cellular responses in addition to the specific inhibition. Thus, non- or specific drugs are all foes of the cells in every aspect. So the machinery? It includes everything you might think of cellular activities on top of the Jak pathways. In particular, the ROS-caused cellular response.
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Dear Sir/ Madam,
I am doing research on feed additives (prebiotic, probiotic and synbiotic) for fish and need a clear very concept about pro-inflammatory cytokine genes (TNF-α, IL-1β, and IL-6) expression. From internet and some researcher working on cell culture said “if the relative expression level of pro-inflammatory cytokines is higher than control means inflammation is in the body which is bad for immunity” and they thought feed additives will be used for decreasing the relative abundance of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6). However, my research result showed opposite of their thinking and the following 1st three articles showed significant higher expression and 4th one showed significantly lower expression is good for fish immunity.
1. “B.T. Standen, M.D. Rawling, S.J. Davies, M. Castex, A. Foey, G. Gioacchini, O. Carnevali, D.L. Merrifield, Probiotic Pediococcus acidilactici modulates both localised intestinal-and peripheral-immunity in tilapia (Oreochromis niloticus), Fish. Shellfish Immunol. 35 (2013) 1097–1104”
2. “A. Abid, S.J. Davies, P. Waines, M. Emery, M. Castex, G. Gioacchini, O. Carnevali, R. Bickerdike, J. Romero, D.L. Merrifield, Dietary synbiotic application modulates Atlantic salmon (Salmo salar) intestinal microbial communities and intestinal immunity, Fish Shellfish Immunol. 35 (2013) 1948–1956”
3. “A. Panigrahi, V. Kiron, S. Satoh, I. Hirono, T. Kobayashi, H. Sugita, J. Puangkaew, T. Aoki, Immune modulation and expression of cytokine genes in rainbow trout Oncorhynchus mykiss upon probiotic feeding, Develop. Comp. Immunol. 31 (2007) 372–382”
4. C. Qin, Y. Zhang, W. Liu , L. Xu, Y. Yang, Z. Zhou, Effects of chito-oligosaccharides supplementation on growth performance, intestinal cytokine expression, autochthonous gut bacteria and disease resistance in hybrid tilapia Oreochromis niloticus♀× Oreochromis aureus♂, Fish shellfish immunol. 40 (2014) 267-274.
If anyone can provide, clear concept about pro-inflammatory cytokine expression and its relation to immunity will be very much helpful for me. If you have any good document please send that to me.
Thanks in advance..........
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Hello,  
When it comes to the immune response; we cannot distinguish them as “good” or “bad”, because several factors can be involved in fish condition and immune responses. Maybe a feed additive boosts the fish immune responses and increases the expression of some genes like IL1B, but it does not necessarily mean that it can change fish resistance to the pathogen. Considering the pro-inflammatory markers, it depends on your purpose; they might positively influence fish health in a short time (e.g. therapeutic feeds), for example, resistance against possible infections as results of poor environmental conditions (density etc.). However, prolonged expression of pro-inflammatory cytokines has different effects. The increased expression of these cytokines is expected following immunostimulant administration, but the results are species-specific and also very time-dependent. They usually boost immune response strongly in shorter (1-3 weeks), but then the expression and stimulatory effects go down due to the negative feedback loops. Having different short and long time point in an experiment gives a good idea about their performance.
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Immunoglobulin class switching, also known as isotype switching, isotypic commutation or class-switch recombination (CSR), is a biological mechanism that changes a B cell's production of immunoglobulin (antibodies) from one type to another, such as from the isotype IgM to the isotype IgG.
#space #iss #humanspaceflight 
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The goal of this investigation was to analyze total blood IgE levels, specific IgE-antibodies and interleukin-4 in blood of Russian crew members before and after space flights to the International Space Station (ISS) and during a long-term isolation study. For this purpose, authors used the ELISA assays as well as other special kits. It was noticed that four out of nine cosmonauts had high total serum IgE (more than normal clinical values of 120 IU/ml). At the same time, there were no statistically significant changes in serum IgE levels before and after long-term space flights (128–195 days).
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Hi Dear colleagues, We want to know which herbal extract may have efficient effect to increase antibody production and immune response in fish were experimentaly i.p. injected with a vaccine containing bacterial lysate plus herbal extract
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I would consider adding melatonin to the bacterial lysate. If you do a rapid search in PubMed you'll find  many reports conferming that melatonin may have an immunoemnhancing effect even in fishes. On the other hand, melatonin is also contained in plants.
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Hello Everyone! I wanna make some actuators based on PAMPS gel. I am not chemistry backgroup. So what I can do is just buying PAMPS water solution on Sigma-Aldrich and trying to cross-link it. I saw various crosslink method on papers. But I am not sure which one should be the best one for actuator application. Could anyone of you give me some advice or references? Thanks a lot!:)
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  Hi Lingju
Find  article  attached   might help you
Best regard
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My lab would like to perform an immune cell killing assay using activated T cells or PBMCs on miRNA treated ovarian cancer cell lines. Ideally, we could like to see if there is a difference in immune cell induced apoptosis of the cancer cells between treated and untreated cells. However, as a lab we have no experience in working with immune cells so it would be great if someone could highlight the important points to consider while designing such an assay.
Thanks in advance
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Thank you so much for that information Anna!
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Hi, I am doing an adoptive transfer study in which I transfered splenocytes from immunocompetent to immunosuppressed mice. I am wondering, for those with experience, how long does it take until you see the transfer to take effect?
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Hello
See link here . hope help you 
Good Luck
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I am going to use Immune complex for testing my antibody binding to FcgRIII on NK cells. The immune complex consists of the whole virus. But I want to get rid of unbound antibodies from IC solution. Has anyone used MWCO columns for getting rid of free antibodies? What KDa? And what company?
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Thanks Gerco!
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I am currently looking into reviving T-cells or B-cells from frozen human tissue. Is it feasible? If yes, is there a specific way on how to freeze the tissue in the first place to get the best possible outcome?
This is for immunotherapy-based studies, so in general how a human tissue sample can be stored?
Thank you in advance
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Dear Ioannis
Yes you can isolate T/B cells from frozen tissue but they won't be viable unless they were frozen in liquid nitrogen. So if you are after cells for immunocytochemistry or immunohistochemistry, you can do it from a frozen tissue (-20-80C) but if you are after viable cells for functional assays, the tissue should have been stored in correct conditions. Hope that answers your question. Good luck. Siva
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Can anyone suggest me the suitable normal cell lines to study TLR immune pathway? The cell lines that can produce the cytokines?
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You can use HEK293 cell line
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Hi everyone,
Perhaps this is a stupid question but it came across my mind that it is much easier to evade immune recognition of antigen derived from immune privileged sites such as the brain, the bone marrow and the placenta. How do these sites not having higher chance of developing tumor than other organs? Please share with me your idea. Thanks so much
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Dear Dung,
a recent discovery of lymphatic vessels lining the dural sinuses and directly connecting the nervous and immune systems strongly supports a tight molecular exchange between the brain and the immune system. This new anatomic finding brakes the classic assumption of the blood–brain barrier, and allows new hypothesis on the pathogenesis of conditions involving the immune and nervous systems
Louveau A, Smirnov I, Keyes TJ, et al. Structural and functional features of central nervous system lymphatic vessels. Nature 2015; 523: 337-41. PMID: 26030524
Best Regards,
Cristina
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I wonder whether anybody has been able to detect exosomes from an MHC knockout/knockdown lymphoma cells(or any kind of immune cell line) or not?
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Can anyone suggest me immune cell line for in vitro cancer co-culture studies studies?
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May be this article of some help:
Cytotoxicity and infiltration of human NK cells in in vivo-like tumor spheroids
Ulrike Carolin Müller-Quernheim, Lars Potthast, Joachim Müller-Quernheim, and Gernot Zissel
J Interferon Cytokine Res. 2012 Apr; 32(4): 169–177.
doi: 10.1089/jir.2011.0020
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I recently identified significantly increased levels of phosphodiesterase type 5 (PDE5) in the serum of sick patients relative to normal control patients. While I think this is interesting, I have little experience with phosphodiesterases and am wondering why this would be increased? What might it be doing in circulation? and how is it released? I'm trying to gain an idea about whether or not this is relevant to study, given that I am a new postdoc!
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If you find cardiac specific PDEs biomarker, that will be Nature paper for you!
I am wondering about the same Qs you have mentioned. PDEs biomarker role will be very interesting to look into. I am little worried about it, given the fact that PDEs are fond in all muscle groups, it would little difficult to specify which exact muscle group PDEs are coming out from? There might be the entirely new role of circulating PDEs which we don't know yet.
All I can say is best of luck, may the force be with you! :)
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Interested to know, In TLR pathway, myd88 or Trif contribute to anti-inflammatory response?
Thanks
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per se, both are pro-inflammatory. But there is an inhibitory splice variant of MyD88 that can get activated and shuts down the signalling. And it also seems to depend on the ligand invovlved. For example: Int J Mol Sci. 2015 Mar 26;16(4):6902-10. doi: 10.3390/ijms16046902.
Anti-inflammatory effect of Streptochlorin via TRIF-dependent signaling pathways in cellular and mouse models.
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Stick floating cells to glass cover slip, any specific reagent, their concentration, and your experience. 
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I applied BSA on slide and then poly-K. It seems working. Thank you very much again.
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I am trying to identify submucosal immune cells in samples of rat gut tissue via IHC, but need a good marker/antibody for these cells. Does anyone have any suggestions as to which marker may be appropriate? Thank you.
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Dear Madeline Lewis
Pls. find the attached files, may help in your research, good luck
Nicholas S. Jakubovics, Robert J. Palmer, Jr.. 2013. Oral Microbial Ecology: Current Research and New PerspectivesEBSCO ebook academic collection Horizon Scientific Press,Pp.232 ISBN 1908230177, 9781908230171
Committee on Biologic Markers, Commission on Life Sciences, Division on Earth and Life Studies, National Research Council. 1989Biologic Markers in Pulmonary Toxicology National Academies Press, 0309039908,Pp196. ISBN 9780309039901
Regards
Prof. Houda Kawas
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I know experimentally the percentage of CD4, CD8 and NKT cell equivalents I 'm getting from my guinea pigs but would like to know if it is comparable to murine and human, or if substantial proportional differences exist.
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Hi Julianna,
Here is a reference on relative  % within the mouse spleen from Stemcell.
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Is there any data on Rhesus prophylaxis for women with weak or partial D types?
Which weak D types would be in danger of immunization, and how much Anti-D (dosage) should they get, as their red cells will surely react with the antibody?
What do you do?
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Hi Julian,
Although most guidelines recommend anti-D prophylaxis for all Rh(-) women who are pregnant, it's true that according to the current stand of knowledge, one should additionally test for D antigen variants (weak D) even if the immediate spin results D negative. To my knowledge if a woman tests D(-) at immediate spin but positive for D variants an anti-D prophylaxis is not recommended, since weak D can act like D(+) when it's the recipient blood and this can endanger the mother.
But it would certainly interest me as well if you run into more detailed information on this topic! 
Best, Zeynep 
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Generally a lysogen will protect the bacteria from a super infection by a similar bacteriophage. However does this immunity extend beyond the family level ? Is anyone aware of any example ?  
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There are well described cases of such superinfection exclusion/inhibition in the old and recent litterature (see doi: 10.1038/ismej.2016.79. [Epub ahead of print] for instance!) !
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It is possible that a heterozygous mutation in JAK3 can cause immune deficiency in humans?
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I was diagnosed (Boston Childrens Hospital) last year "heterozygous for a mutation in JAK3 (3096 +18A greater than G)". I am 61 years old. I have had a lifetime of immune related problems. 1. Lifelong T-cell deficiency & chronic lymphopenia, 2. pediatric pulmonary Tuberculosis (age 4), 3. Regional Enteritis - Crohns, 4. MGUS, 5. Severe EBV infection in college, 6. Chronic Low IGA & IGM, 7. Barratts Esophogus to name a few.  Thank you.....any comments?
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Have come across a strange lagged response to an infectious agent where females seem to respond far more rapidly than males.
Is there anything in the literature regarding profound differences in immune response between the two genders or anything about gender and immune lags or immune feedback loops?
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Many thanks Willem. After some more analysis it looks like the time lags may also have something to do with different routes to infection between males and females, however, the differential immune responses are of vital importance.
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I want to study the relation between the dose of antigen and liver immune status.But I don't know how to judge the live‘s immune status.Is there a criterion that differentiate liver’s immune status?
Thank you!
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A quantitative measure you could use would be plasma/serum levels of ALT and/or AST. Release of these enzymes occurs during acute inflammation in the liver because of hepatocyte cell death, so it's an indirect measure of an active immune response in the liver. This wouldn't tell you anything about the nature of the immune response though. You can also digest liver and enrich your cell prep for lymphocytes or myeloid cells using a Percoll gradient - you could then perform flow cytometry to look for different cell populations (such as effector T cells) or isolate RNA and look for changes in inflammatory gene expression, etc.
For example:
"Liver lymphocytes were isolated from the liver after perfusion and digestion. Briefly, mice were perfused via the inferior vena cava using digestion media (RPMI-1640 containing 5% FBS; 0.2 mg/ml crude collagenase, Crescent Chemical; and 0.02 mg/ml DNase I, Roche Diagnostics). Livers were forced through a 70-μM filter using a syringe plunger, and debris was removed by centrifugation (30 g for 3 minutes). Supernatants were collected and centrifuged for 10 minutes at 650 g. Lymphocytes were isolated using a 60:40 Percoll gradient"
J. Publicover et. al., Age-dependent hepatic lymphoid organization directs successful immunity to hepatitis B. J Clin Invest. 2013 Sep;123(9):3728-39
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Why cannot we use an algorithm of physical means - temperature, pH, salinity, pressure etc, and even time - which is survivable by every human cell type but unsurvivable by pathogens? The big question is not how to create these conditions within the body, but would it work, if we could create them?
So far I haven't found anything in the literature to tell me why this would not work.
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