Dr. Jack Auty
Dr. Jack Auty
  • 132
  • 240 699
How can we use RNA sequencing to figure out how a drug works?
RNAseq is such a powerful tool! In this video I discuss how using the awesome power of RNA sequencing we can narrow down the potential mechanism of a novel drug. The key to this method is homeostasis! 
Learning objectives 
Explain the challenges associated with elucidating the mechanisms of action of drugs, considering the intricate nature of drug-target interactions and the limitations of current methods.
Explain and examine utilizing RNAseq techniques to identify potential mechanisms of action for drugs, utilizing transcriptomic data to uncover gene expression changes and pathways involved.
Evaluate the significance of homeostasis in utilizing RNAseq to investigate a drug's mechanism of action. Exploring how biological systems attempt to maintain equilibrium in the presence of a drug - which by definition perturbs biological processes.
Recognize the dual role of homeostasis in regulating inhibited proteins, understanding how it can both upregulate and downregulate the expression and activity of targeted proteins in response to drug treatment.
Переглядів: 400

Відео

How can we use evolution to discover how antibiotics work?
Переглядів 98Рік тому
Learning objectives  Investigate the role of resistance evolution in unraveling the mechanism of action of a drug, exploring how the emergence of resistant strains can provide insights into the drug's target and mode of action. Describe the concept of a morbidostat and its functioning, highlighting its use in studying bacterial evolution under constant drug exposure to better understand resista...
How does Next Generation Sequencing work?
Переглядів 194Рік тому
Learning Objectives: Understand next-generation sequencing principles and technologies for high-throughput DNA or RNA analysis. Explain the importance of fragment alignment in generating complete sequences during next-generation sequencing. Compare DNA sequencing and RNA sequencing methods in terms of targets, purposes, and applications. Explore the use of relative quantity analysis in DNA sequ...
How does PCR work?
Переглядів 244Рік тому
Define DNA as the genetic material responsible for carrying hereditary information in living organisms, explaining its double-stranded helical structure and the role of the genetic code in determining protein synthesis. Explain the process of DNA extraction, including the use of techniques such as chloroform and phenol, to isolate DNA from cells or tissues, emphasizing the separation of DNA fro...
What is AI? The absolute basics!
Переглядів 268Рік тому
Learning objectives Describe how statistics can be used to make predictions by analyzing data and identifying patterns or relationships. Explain the concept of sum of squares and its application in statistical analysis, such as in a linear model. Compare how statistics and AI (gradient descent) would generate a linear model by identifying their respective approaches to the sum of squares. Expla...
What are virulence factors of Bacteria?
Переглядів 987Рік тому
Learning objectives Explain how PAMPs (pathogen-associated molecular patterns) can influence the pathogenicity of bacteria by activating the immune system. Describe the mechanisms by which Exotoxin S and Exotoxin U block immune function, such as by inhibiting phagocytosis. Discuss the type three secretion system, which is used by some bacteria to deliver effector proteins directly into host cel...
Bacteria as pathogens
Переглядів 286Рік тому
Learning Objectives: Describe the gram stain, shape, and pathogenicity of E. coli, S. aureus, P. aeruginosa, and C. difficile. Explain how the dose of bacteria can impact the virulence of opportunistic pathogens. Discuss how changes in the location of bacterial growth on the body can affect the pathogenicity of the bacteria. Identify various environmental sources of bacteria, including food and...
Paper breakdown: Could NLRP3 inhibitors be therapeutic in Alzheimer's disease? (3)
Переглядів 371Рік тому
In these videos were we're diving into this paper: Fenamate NSAIDs inhibit the NLRP3 inflammasome and protect against Alzheimer's disease in rodent models. Daniels MJD, Rivers-Auty J, .... Lawrence CB, Brough D, pubmed.ncbi.nlm.nih.gov/27509... Learning objectives: Gain an understanding of how Daniels et al. conducted experiments to demonstrate the therapeutic potential of NLRP3 inhibiting NSAI...
Paper breakdown: Could NLRP3 inhibitors be therapeutic in Alzheimer's disease? (2)
Переглядів 433Рік тому
In these videos were we're diving into this paper: Fenamate NSAIDs inhibit the NLRP3 inflammasome and protect against Alzheimer's disease in rodent models. Daniels MJD, Rivers-Auty J, .... Lawrence CB, Brough D, pubmed.ncbi.nlm.nih.gov/27509875/ Learning objectives: Understand the experimental techniques used by Daniels et al. to investigate the potential mechanisms of action of NLRP3 inhibitin...
Paper breakdown: Could NLRP3 inhibitors be therapeutic in Alzheimer's disease? (Figure 1)
Переглядів 745Рік тому
In this video series I'm diving into this paper: Fenamate NSAIDs inhibit the NLRP3 inflammasome and protect against Alzheimer's disease in rodent models. Daniels MJD, Rivers-Auty J, .... Lawrence CB, Brough D, pubmed.ncbi.nlm.nih.gov/27509875/ Learning Objectives: Understand the historical context and research question that led to the hypothesis presented in Daniels et al.'s 2016 paper. Gain a ...
What is a Western Blot and how does it work?
Переглядів 539Рік тому
Understanding the Principles of Western Blots: Learn the fundamental principles of Western blotting, including its purpose, procedure, and components, and how it is used to detect specific proteins. Steps Involved in Western Blots: Familiarize yourself with the step-by-step process of Western blotting, from sample preparation to protein detection, and understand the importance of each step in o...
Neuroinflammation in Alzheimer's Disease: How is Amyloid Detected by Microglia?
Переглядів 1,1 тис.Рік тому
Identify the pattern recognition receptors (PRRs) involved in detecting amyloid in the context of Alzheimer's disease. Summarize the research by Stewart et al. that elucidates the roles of CD36, TLR4, and TLR6 in Alzheimer's disease. Describe how activation of CD36, TLR4, and TLR6 leads to the release of prostaglandins and cytokines in Alzheimer's disease. Discuss the hypothesis of amyloid as a...
Neuroinflammation in Alzheimer's Disease: The Role of Neutrophils
Переглядів 766Рік тому
Learning objectives  Understand the mechanisms by which neutrophils are able to infiltrate the brain. Learn how neutrophil degranulation can lead to brain damage through the release of toxic granule contents. Explore the findings and implications of research conducted by Volkman et al. and Zenaro et al. that provide evidence of the involvement of neutrophils in Alzheimer's disease-associated ne...
Neuroinflammation in Alzheimer's Disease: The Role of Microglia
Переглядів 2,5 тис.Рік тому
  Learning objectives Understand how microglia drive neuronal damage through phagocytosis and reactive oxygen species (ROS) creation. Explore the role of flippase and scramblase in microglia-mediated neuronal damage. Understand how annexins can provide insights into the process of microglia-mediated neuronal damage. Learn how primary cell culture can be used as a tool for Alzheimer's research o...
Animal models of Alzheimer's disease explained!
Переглядів 2,2 тис.Рік тому
Understand how insertion of human familial Alzheimer's disease genes into rodents is the foundation of most models of Alzheimer's disease. Briefly explain the process of generating genetically engineered mice. Explain how endogenous promoter regions can be used to target gene expression to specific locations within the mouse. Describe the APP/PS1 mouse model of Alzheimer's disease and list some...
What causes Alzheimer's disease: The pathophysiology of Amyloid.
Переглядів 1,3 тис.Рік тому
What causes Alzheimer's disease: The pathophysiology of Amyloid.
What causes Alzheimer's disease: Amyloid vs Tau
Переглядів 1,4 тис.Рік тому
What causes Alzheimer's disease: Amyloid vs Tau
The brain is immune privileged: What does that mean?
Переглядів 2,2 тис.Рік тому
The brain is immune privileged: What does that mean?
What are microglia and what do they do?
Переглядів 904Рік тому
What are microglia and what do they do?
What cells make up the brain and what do they do?
Переглядів 554Рік тому
What cells make up the brain and what do they do?
Problems in science: Translational failure - why animal models aren't working
Переглядів 145Рік тому
Problems in science: Translational failure - why animal models aren't working
Translational failure: What is it? and what is causing it?
Переглядів 129Рік тому
Translational failure: What is it? and what is causing it?
What is blinding in research? The placebo effect, bias and more!
Переглядів 358Рік тому
What is blinding in research? The placebo effect, bias and more!
What is cell culture and how does it work?
Переглядів 1,1 тис.2 роки тому
What is cell culture and how does it work?
How we know smoking causes lung cancer
Переглядів 9152 роки тому
How we know smoking causes lung cancer
Lung inflammation and disease
Переглядів 6 тис.2 роки тому
Lung inflammation and disease
What do lungs do?
Переглядів 3922 роки тому
What do lungs do?
Inflammation in Alzheimer’s disease: Researching from cells to people and back again.
Переглядів 2682 роки тому
Inflammation in Alzheimer’s disease: Researching from cells to people and back again.
What is silver staining and how does it work?
Переглядів 3,1 тис.2 роки тому
What is silver staining and how does it work?
What is Alzheimer's disease? And what causes Alzheimer's disease?
Переглядів 7962 роки тому
What is Alzheimer's disease? And what causes Alzheimer's disease?

КОМЕНТАРІ

  • @acrustofbread
    @acrustofbread День тому

    12:45 blows my mind a little to think of some ancient human who had everything going for him genetically, except his neutrophils weren't funky and therefore the whole of him is put on the curb for garbage day. but then, i suppose this adaptation and countless others happened way before humans? thanks for the great lectures.

  • @helenalaney
    @helenalaney 4 дні тому

    thank you

  • @helenalaney
    @helenalaney 4 дні тому

    great video. great teacher

  • @nikitacunningham880
    @nikitacunningham880 4 дні тому

    I love your passion for R!! I hope soon I can share the same passion for it 😂

  • @billmulligan4909
    @billmulligan4909 7 днів тому

    If europeans treat asylum seekers as people why are many countries now denying them? Seems like this leftist attitude had changed since this video was originally published. Was getting a lot out of this video until you started injecting politics into it

  • @somidekayode748
    @somidekayode748 11 днів тому

    Your video Is best I have found on UA-cam for the principle of phase contrast I will recommend it to my colleagues thumbs up for the graphic dedication you put but you didn't put the ocular lens in most diagram

  • @yesitsme3054
    @yesitsme3054 13 днів тому

    Are you from New Zealand??

    • @dr.jackauty4415
      @dr.jackauty4415 13 днів тому

      @@yesitsme3054 as kiwi as Razor doing the worm after every Crusader trophy win.

    • @yesitsme3054
      @yesitsme3054 12 днів тому

      @@dr.jackauty4415 Roger 😂😂

  • @user-yz4gw2uo6l
    @user-yz4gw2uo6l 23 дні тому

    Odd E(e)nglish. Is he from New Zealand? He tends to say "conneections".

    • @dr.jackauty4415
      @dr.jackauty4415 22 дні тому

      Us Kiwis have the best English out there! 😅

  • @Emacosa
    @Emacosa Місяць тому

    What the hell is this 😱

  • @inflivia
    @inflivia Місяць тому

    excellent synopsis and enjoyed the delivery

  • @xelionizer
    @xelionizer Місяць тому

    That column graph in the beginning is worth s*** mate! You can't compare grouped results with non-grouped results!! That's basic statistics!!!!

  • @beztroska
    @beztroska Місяць тому

    I love how excited he is talking about it all.

  • @dantedt3931
    @dantedt3931 2 місяці тому

    This makes me love statistics even more.

  • @DraAndreiaTorres
    @DraAndreiaTorres 2 місяці тому

    Amazing class. Thanks a lot.

  • @baileysice2715
    @baileysice2715 2 місяці тому

    Hi Dr where can topical mebendazole be found?

  • @mlawliet6151
    @mlawliet6151 2 місяці тому

    Amazing! Thank you very much for this video, it was very clear and super informative. Will be working with this technique in a couple of weeks!

  • @anonymeironikerin2839
    @anonymeironikerin2839 2 місяці тому

    You are really good! Can you explain reference based imputation?

  • @Daniel-fr8dt
    @Daniel-fr8dt 3 місяці тому

    "Amyloid is not toxic without microglia"? This suggests that overactive microglia are the issue not amyloid. So much pointing in that direction.

  • @Daniel-fr8dt
    @Daniel-fr8dt 3 місяці тому

    How do you equate the fact that some AD patients don't have an amyloid buildup? Perhaps the disease progression doesn't start with amyloid?

  • @MindiKilty
    @MindiKilty 3 місяці тому

    Scratching never felt so good

  • @The-advicer
    @The-advicer 3 місяці тому

    Oh I am teh 800 view and also the 5th comment nice

  • @The-advicer
    @The-advicer 3 місяці тому

    thanks hyou are helpin me in my ee

  • @KamyaChavan22
    @KamyaChavan22 3 місяці тому

    amazing presentation btw..<3

  • @KamyaChavan22
    @KamyaChavan22 3 місяці тому

    i am a Master student want to pursue PhD in these kind of experiments how do i pursue it?

  • @jglennd
    @jglennd 4 місяці тому

    Sounds like the characteristics of cancer. Candida = Cancer?

  • @EH-qb4vi
    @EH-qb4vi 4 місяці тому

    incredible! it's a true skill to be able to explain things like this well - thank you!

  • @piripino9491
    @piripino9491 4 місяці тому

    Hello, what if you accidentally use nominal data type instead of continuous datatype for numerical data? Will the results be different?

  • @DK-tn9lz
    @DK-tn9lz 4 місяці тому

    These videos are awesome!

  • @3_adorableann150
    @3_adorableann150 4 місяці тому

    As a high school student learnin about alzheimer's for a project, Thoroughly enjoyed the video!

  • @Arshak-qy3rt
    @Arshak-qy3rt 5 місяців тому

    What if one of your diseases is th 1 the other th 2?

  • @douglaswatt1582
    @douglaswatt1582 5 місяців тому

    Somewhat disappointing that Jack does not mention that the alpha secretase pathway is actually promoting neuroplasticity while the beta amyloid pathway which is traditionally thought of as pathogenic is also physiologically recruited for synaptic pruning, and for immune defense.

  • @douglaswatt1582
    @douglaswatt1582 5 місяців тому

    Superb review. I've been listening to reviews on inflammation in Alzheimer's disease for decades. This is one of the best overviews. First rate and intelligible

  • @amadeusdre
    @amadeusdre 5 місяців тому

    i must have seen this whole video like 10 times i stg

  • @Lauralopezfed
    @Lauralopezfed 5 місяців тому

    Very interesting and helpful video! You make it so easy to understand, thank you!

  • @lorraineross8748
    @lorraineross8748 5 місяців тому

    Love to know how this information can help people with Autoimmune? So many people suffer and all that’s available are drugs with loads of side effects that suppress the whole immune system. Please make another video if your aware of available treatments that have been successful.

  • @sitharagani9513
    @sitharagani9513 6 місяців тому

    what are the implications of this on immunotherapy and glioblastoma?

  • @wxz1998
    @wxz1998 6 місяців тому

    I hope my doctor learn from you how to break dome the information and present will

  • @atmanmedini3943
    @atmanmedini3943 6 місяців тому

    please can you send the ligne code to import data in R-jamovi. i ved use the same code witch i frecently use it in R studio but it does not work with me

    • @dr.jackauty4415
      @dr.jackauty4415 6 місяців тому

      My advice would be in in Rstudio use write.csv(df, "df.csv"). Then just double click on the new file that is created "df.csv" and copy and paste that into Jamovi. The harder way would be in JAMOVI-R use this code df <- read.csv("C:/Users/Document/df.csv") Note you'll have to change the df and the document address to the ones you are using.

  • @huseyinkocakusak
    @huseyinkocakusak 7 місяців тому

    This is a very good explanation, sir. Thank you

  • @Automobilestats
    @Automobilestats 7 місяців тому

    Nice explanation

  • @user-kk9ec3wp4x
    @user-kk9ec3wp4x 7 місяців тому

    Thank you so much for the explanation. Have you heard of the impact of the enzyme Glutaminylcyclase which produces neuro toxic pyro glu amyloid or N3pE? It it meant to significantly drive the oligomerisation, inflammation and ptau. Also in your last video you did not mention it.

  • @brucestewart3170
    @brucestewart3170 7 місяців тому

    The accelerating and clumping seem to be indicative of prion disease. Some scientist are beginning to equate Alzheimer disease with prions. From what you are saying in this video I can not see the connection. What do you think?

    • @douglaswatt1582
      @douglaswatt1582 5 місяців тому

      Not quite. The seeding and templating process by which small aggregates termed oligomers recruit non pathologically folded forms of the protein to become more problematic is termed "prion like" but it's not fully prion because ingestion of these proteins does not cause templating like a true Prion would enable.

  • @user-hr4jo2eu2b
    @user-hr4jo2eu2b 8 місяців тому

    Production ideas

  • @amreshyadav2758
    @amreshyadav2758 8 місяців тому

    hello

  • @danielhunt3622
    @danielhunt3622 8 місяців тому

    Fantastic stuff! I'm endeavoring to understand how HDAC6 and apoE4 fit into this panoply of genetic chicanery. My understanding is that HDAC6 usually enables efflux of triglycerides and other lipoproteins, while the apoE4 isoform inhibits triglyceride efflux. Thus leading to the amyloid buildup in microglia. Is it the resulting fibroblasts from pyroptosis and channel exiting action that induce neuronal death? Maybe I heed to watch again. Not only do I have to fight AD, but also ADHD apparently. Maybe there's some glial dopamine inhibition going on. Thank you for your work!

  • @user-wr8ih7dw3p
    @user-wr8ih7dw3p 9 місяців тому

    thank you very much for this video, very helpful. I would like to ask whether the silver ions bind because the DNA is acid and so donates electrons, or because the DNA itself is normally negatively charged due to the presence of negatively charged phosphate groups all over the backbone. Thank you!

  • @FreeSpeechblacklistedsmeared
    @FreeSpeechblacklistedsmeared 9 місяців тому

    That actually could have killed me, and it would have if I continued to take the unethical doctors psych abuse

  • @Minisynapse
    @Minisynapse 9 місяців тому

    I don't think many people care about the ability to predict how future samples work, but to learn about the true population. We are interested in parameters, not statistics. At least in science that is, and mainly when we take this statistical modeling to its ultimate purpose: inference about the real world.

    • @dr.jackauty4415
      @dr.jackauty4415 9 місяців тому

      You kind of contradict yourself here. If all you cared about was parameters, then just take the mean of your samples. There's no point doing inferential statistics. If the means of your samples are different, then the means of your samples are different. IF you care about the "real world" then you care about populations, you care if you can repeat your work, you care about if a drug will work in future samples etc. then you need inferential statistics. Your experiment isn't the real world.

  • @Minisynapse
    @Minisynapse 9 місяців тому

    8:21 This is technically not true. If I measure 1 bear, and then measure 1 ant, on almost all metrics I can create an estimation that can classify future instances of bears or ants into their corresponding classes. The bottom-line is that the less true variance there exists between the classifications in your data, the more data you will need to establish a significant difference. But after a certain point, 1 instance of two classes is enough to establish the scale of the expected effect size given we got a larger sample. One datapoint estimates the true mean, just worse than a sample with any amount of variance.

    • @dr.jackauty4415
      @dr.jackauty4415 9 місяців тому

      Only because you have a prior model of what a bear is and what an ant is. If you gave one patient a drug and it cured them and one patient a placebo and they died, you would not be sure about any future efficacy of the drug. The ONLY reason you know that you could classify ants and bears with an N=1 is because you've seen images of hundreds of bears and ants. So your N is actually hundreds. And of course what about the amazing water bear lol.

    • @Minisynapse
      @Minisynapse 9 місяців тому

      @@dr.jackauty4415 "If you gave one patient a drug and it cured them and one patient a placebo and they died, you would not be sure about any future efficacy of the drug." Not "sure", but I would have knowledge. Given that you observe your fellow tribesman die after eating a suspicious plant, would you eat the plant even though N = 1? It's just not AS reliable a sample as observing more people eat that plant, but here we stumble to philosophical territory where the importance of the outcome changes how we should conduct inference. My point is that a datapoint that represents a population is more likely to be empirically similar to other instances of that population than not, and thus even one datapoint tells us something. We just lack variance, which means we can't do fancy sample statistics (because we can't measure error).

  • @Windinthewillows-ct5oi
    @Windinthewillows-ct5oi 9 місяців тому

    I have a FACINATION with VIRUSES AND BACTIERIA..infarct?, I have a FACINATION with anything microscopic, it's a whole different world which truly amazed me!!! 🤔🥸😳