Dr. Jack Auty
Dr. Jack Auty
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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: 506

Відео

How can we use evolution to discover how antibiotics work?
Переглядів 149Рік 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 398Рік 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 324Рік 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 321Рік 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 1,5 тис.Рік 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 358Рік 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 467Рік 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 539Рік 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 960Рік 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 1,3 тис.Рік 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 1,6 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 1,1 тис.Рік 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 3,9 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 3,1 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 1,9 тис.Рік тому
What causes Alzheimer's disease: The pathophysiology of Amyloid.
What causes Alzheimer's disease: Amyloid vs Tau
Переглядів 2,3 тис.Рік тому
What causes Alzheimer's disease: Amyloid vs Tau
The brain is immune privileged: What does that mean?
Переглядів 3 тис.Рік тому
The brain is immune privileged: What does that mean?
What are microglia and what do they do?
Переглядів 1,3 тис.Рік тому
What are microglia and what do they do?
What cells make up the brain and what do they do?
Переглядів 790Рік тому
What cells make up the brain and what do they do?
Problems in science: Translational failure - why animal models aren't working
Переглядів 1652 роки тому
Problems in science: Translational failure - why animal models aren't working
Translational failure: What is it? and what is causing it?
Переглядів 1562 роки тому
Translational failure: What is it? and what is causing it?
What is blinding in research? The placebo effect, bias and more!
Переглядів 4582 роки тому
What is blinding in research? The placebo effect, bias and more!
What is cell culture and how does it work?
Переглядів 1,3 тис.3 роки тому
What is cell culture and how does it work?
How we know smoking causes lung cancer
Переглядів 1 тис.3 роки тому
How we know smoking causes lung cancer
Lung inflammation and disease
Переглядів 7 тис.3 роки тому
Lung inflammation and disease
What do lungs do?
Переглядів 4123 роки тому
What do lungs do?
Inflammation in Alzheimer’s disease: Researching from cells to people and back again.
Переглядів 3273 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 3,7 тис.3 роки тому
What is silver staining and how does it work?
What is Alzheimer's disease? And what causes Alzheimer's disease?
Переглядів 9193 роки тому
What is Alzheimer's disease? And what causes Alzheimer's disease?

КОМЕНТАРІ

  • @antara9
    @antara9 День тому

    Bottomline which dtugs helped??? Your excitement masked clarity, please clarify? Watched 2 vids, same story. Thanks in advance.

  • @cjstevens6405
    @cjstevens6405 11 днів тому

    Great videos, really great. Have to say that the playlist order of "The immunology of Alzheimer's disease" is a little confusing though, it would be very helpful if you could reorganize it a little.

  • @fareedahmedkakar8219
    @fareedahmedkakar8219 28 днів тому

    can i get your Help,how may you help me ?

  • @laithmoushib6748
    @laithmoushib6748 Місяць тому

    Thanks for the lecture ! Cheers

  • @evansattaasamoah2985
    @evansattaasamoah2985 Місяць тому

    Thanks for this video! Many doubts of mine have been clarified

  • @Nefertiti0403
    @Nefertiti0403 Місяць тому

    The Reason I stopped and listened to your Video is…I got Pancreatitis and on the blood work I could’ve sworn it said my Neutrophils were up high pretty high. Then I got to wondering why not the other white blood cells? So why those and not the others? So if my pancreatitis is inflamed why would it go after my own body? No germs or bacteria?

  • @stevendonaldson3090
    @stevendonaldson3090 Місяць тому

    Why are you laughing???? You are meant to care!!!!!!

  • @petercplau
    @petercplau Місяць тому

    Thank you. You make statistics fun and understandable

  • @JuliaGephart
    @JuliaGephart Місяць тому

    I got it from a motel room it was on the bedspread My head scalp and hair I have been dealing with for months,been on Ivermectin,permethrin and Malathion nothing is working . I got online sulfur cream 5 percent seems to be helping me.I had to shave all of my hair off and Apply Veet hair removal on my scalp twice. It's been a nightmare for me.

  • @scotia-drewshields1067
    @scotia-drewshields1067 Місяць тому

    Better than "This Week in Parasitism" with those idiots never getting to the point. You cut right to the chase, totally awesome.

  • @scotia-drewshields1067
    @scotia-drewshields1067 Місяць тому

    that was awesome! Keep doing these man, everyone has Ascaris. You'll get 1000s of views of you stick to it.

  • @gautamsethi3751
    @gautamsethi3751 Місяць тому

    Nice intro to Jamovi. Thank you!

  • @gautamsethi3751
    @gautamsethi3751 Місяць тому

    There is no explanation here. You just mechanically transposed the same formulaic approach you criticized in the opening part of your video and translated it to "cells." You never really explained what dof is (hint: it is the amount of non-redundant information in a sample) and what this concept is used for (hint: It's used squarely in the inferential statistics world to obtain unbiased estimates of population parameters). A full explanation would require explaining what inferential statistics is, what unbiased estimators are, and how to obtain them from sample data.

  • @MA4TU2
    @MA4TU2 2 місяці тому

    Thanks Dr. Jack for the clear and easy to understand education.

  • @GladysNakiguli
    @GladysNakiguli 2 місяці тому

    How comes that you treat it and it keeps coming back

  • @ariannahmendoza2640
    @ariannahmendoza2640 2 місяці тому

    6:02

  • @ariannahmendoza2640
    @ariannahmendoza2640 2 місяці тому

    3:45 4:45

  • @seanc9839
    @seanc9839 3 місяці тому

    Little did I know, but I had scabies on and off for 18 months. I saw a dermatologist and despite checking me all over with his magnifying glass he did not diagnose the condition. I had very few rashes or bumps, but had intensive itching (particularly at night), occasionally sensitive skin when in the sun and often had goosebumps and chills. Strangely enough, the only thing that provided temporary relief from the itching was a very hot bath!? In the end, I took 2x treatments of Permethrin, 2x treatments of Ivermectin, but the game changer seemed to be 2x treatments of Malathion. In addition all clothes were changed daily, bagged up for 3x days or washed at high temperatures. All bedding was changed every other day - believe me this felt like some sort of super variant that made my life hell, so don't underestimate it!

  • @patriciatatem2725
    @patriciatatem2725 3 місяці тому

    Ive had em for 5 yrs u can plainly see the burrows under my skin. And most of em shows dark round bug at end of burrow and they dnt itch they burn like my skin on fire

    • @sevic333
      @sevic333 2 місяці тому

      Had them for 6 years and spent big until I got the cure from a food. I live in Australia. FDA has banned it. I wonder why. They are Satanic.

  • @tmesian
    @tmesian 3 місяці тому

    Could you not (in theory) still use slices of potato if you wanted to do, for example, mycological mycelium culture? I know that there would be no benefit, but I wonder if you lightly steam-sterilized the potato, then under a flow hood you carefully cut away the outer "cooked/steamed layer of the potato, then put thinly sliced sections of potato into petri dishes, would that work as a culture medium? I suspect that the interior of the potato (if fresh and skin intact) is free of contaminants (otherwise it would rot straightaway). So long as contaminants aren't introduced in the preparation, I think it might work...

  • @Fafdi-s6i
    @Fafdi-s6i 3 місяці тому

    😢i found live scabbie mite when i ittichng too much 😢

  • @geralddurkan6966
    @geralddurkan6966 3 місяці тому

    Excellent

  • @gerardcagney1578
    @gerardcagney1578 3 місяці тому

    Very good, very clear

  • @gargik
    @gargik 3 місяці тому

    How does the virus get into the phagosome of a macrophage? I though the macrophage will engulf the virus, if it can attach to some molecule on the virus surface. What is the macrophage attaching to on the virus surface?

  • @angelestrella35
    @angelestrella35 4 місяці тому

    Candida is like King Ghidora, oxygen independent, no need oxygen to survive, it could go to space.

  • @akhileshpuranik175
    @akhileshpuranik175 4 місяці тому

    I read that anterior eye is immune privileged now does that mean that the anterior eye proteins are never shown to maturing T cells in the thymus ?? Or cells are negatively selected in thymus but some cells which escape the negative selection may then get into eye following trauma and Damage the eye Another thing I read somewhere, injury to one eye can make another eye susceptible to activity of immune cells how is that so if the immune cells can not reach eye ?

  • @BolBolGai
    @BolBolGai 4 місяці тому

    Very interesting presentation I love that.

  • @luispereira-ss6yw
    @luispereira-ss6yw 4 місяці тому

    I am studying the chi-squared goodness of fit hypothesis test to compare a histogram of a set of samples to the normal distribution with some mean and standard deviation. Some literature says that to calculate the amount of degrees of freedom we must use the expression: n_of_bars_of_histogram -1 - n_of_parameters. If I understand your explanation well, in the expression of the literature the parameters will take out 2 degrees of freedom and there is a number which cannot vary given some mean and standard deviation. Is this correct?

  • @CraigvonTuebingen
    @CraigvonTuebingen 5 місяців тому

    Hi there, you're a bit turned around. Phase contrast changes the phase of the non-diffracted (surrounding) light, not the diffracted light passing through the tissue. This light passing through the tissue has already been (-λ/4) phase-shifted by virtue of passing through the sample. The area you're depicting as the openings on the phase plate is actually a ring of material that changes the phase by either advancing background light by λ/4 (positive phase contrast) or retarding it by -λ/4 (negative phase contrast) in order to cause interference. It is not the middle of the plate as you show... that part just lets the diffracted light through. Light coming from the annulus ring and being focused into the phase plate ring has not been diffracted by the sample. The phase plate then makes the light out of phase (with the diffracted light, reducing the amplitude after it converges. That's why nuclei are really dark compared to the medium: there are a lot more diffracted waves that interfere with the background light significantly more than the medium. So just to clarify it is not how you show it, that the diffracted, phase-shifted light is being further phase-shifted. This would work poorly because the diffracted light passing through the specimen already has a low amplitude. Changing the phase of this light by passing it through another material would lower the amplitude again and actually reduce the contrast because the background light would flood the image.

    • @dr.jackauty4415
      @dr.jackauty4415 5 місяців тому

      We are both right, but you are focusing on a different effect of the phase contrast which explains why the nucleus is dark. Because phase contrast is not really used to look for nuclei and is mostly used for cell counting and cell morphology, I focused on the bright halo we see around the membrane. This is because of phase shifted and diffracted light causing positive interference. In this paper, this phenomenon is called D-leak. www.ncbi.nlm.nih.gov/pmc/articles/PMC3372640/

    • @dr.jackauty4415
      @dr.jackauty4415 5 місяців тому

      Oh I think I get what you are saying! Yeah we are saying the exact same thing. I wondered what you meant by "advanced". Glass doesn't advance a wavelength. It does the opposite. But I do see that Zeisus describes it your way too. The phase ring is actually a thinner piece of glass, while the body is a thicker piece of glass. So you could say that the thin glass ring advances the wavelength (+lambda/4) relative to the thicker glass of the body of the phase plate, or you could say that the body retards the wavelength relative to the light that passes through the ring (-lambda x 3/4) . The important thing is that these perturb the wave timing differently to eachother. Glass cannot "let diffracted light through". Glass will always effect the wave timing. So it is all about relative effects of the different thicknesses of the glass. In my mind thinner equal less purturbed makes sense. I did also leave out that the phase ring normally dims the light with a metal layer.

  • @josie955
    @josie955 5 місяців тому

    Great video

  • @miasmic100
    @miasmic100 5 місяців тому

    I pulled out an Ascaris, thanks to Mebendazole tablets.

  • @victoriamcleod-tardiff5321
    @victoriamcleod-tardiff5321 5 місяців тому

    Dr. Solomon Carter Fuller

  • @DougCarr-rk7dc
    @DougCarr-rk7dc 5 місяців тому

    Got infected by going to a dirty barber's

  • @karensioux1244
    @karensioux1244 6 місяців тому

    Can eliminating breads and sugars stop it?

  • @helenalaney
    @helenalaney 6 місяців тому

    thank you

  • @helenalaney
    @helenalaney 6 місяців тому

    great video. great teacher

  • @nikitacunningham880
    @nikitacunningham880 6 місяців тому

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

  • @billmulligan4909
    @billmulligan4909 6 місяців 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

  • @kaythescientist1
    @kaythescientist1 6 місяців 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

  • @LukeWarmLiving
    @LukeWarmLiving 6 місяців тому

    Are you from New Zealand??

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

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

    • @LukeWarmLiving
      @LukeWarmLiving 6 місяців тому

      @@dr.jackauty4415 Roger 😂😂

  • @MaxPommer-h6d
    @MaxPommer-h6d 6 місяців тому

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

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

      Us Kiwis have the best English out there! 😅

  • @Emacosa
    @Emacosa 7 місяців тому

    What the hell is this 😱

  • @inflivia
    @inflivia 7 місяців тому

    excellent synopsis and enjoyed the delivery

  • @xelionizer
    @xelionizer 7 місяців 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 7 місяців тому

    I love how excited he is talking about it all.

  • @dantedt3931
    @dantedt3931 8 місяців тому

    This makes me love statistics even more.

  • @DraAndreiaTorres
    @DraAndreiaTorres 8 місяців тому

    Amazing class. Thanks a lot.

  • @baileysice2715
    @baileysice2715 8 місяців тому

    Hi Dr where can topical mebendazole be found?

  • @mlawliet6151
    @mlawliet6151 8 місяців 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 8 місяців тому

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