Any and all biological disciplines welcome. Share stories, facts, research or ask questions. I'm a microbiologist with a focus on immunology.
Here's a white blood cell (neutrophil) chasing and phagocytosing Staphylococcus aureus bacteria. Neutrophils are the most abundant white blood cell in your body and are typically the first responder against invading pathogens.
Here's ATP synthase, the enzyme that converts ADP to ATP.
How does that bacteria know he's about to be eaten? I really think the microscopic world is just fascinating, it's amazing to me how living things can be so complex and tiny all at the same time
This footage of amoeba eating a paramecium always freaked me out
Is vet med allowed? Because there is some cool shit going on inside peoples pets.
I'm still only dealing with dead ones right now, but it's still very interesting to see how everything works and shit.
*sigh* The amoeba boys are at it again
>mfw all of chemistry is based on the work of glass-blowers.
>manually counting cells with a bürker chamber on first lab exam
>three out of 40 succeed
>second attempt a week later, nobody succeeds
>third attempt, 1 succeeds
Why do I fail? I'm so bothered about it... Are our eyes bad? Can we not determine the difference between cells and error/crap? Advice plz.
>second lab in uni
>we're going to cut rat open for [x] certain tissues
>we do it
>i stay for fun
>i cut its head open, sees brain
>teacher seems pleased
nobody talks to me anymore
>How does that bacteria know he's about to be eaten?
As far as I know it doesn't, bacteria just react to chemical stimulus, if they have flageles or cilia or something that let them move they will move randomly until they find something that attracts them or not.
The microscopic level seems like a place for an engineer, everything seems to work more like a simple biochemical machine than a living thing as we understand.
Im guessing that the ameba surrounded their prey without touching it or throwing anything around that could be detected(like Im also guessing that the reaction of the paramecium was due the ameba throwing lisosomes at the poor bastards) but then it means that the ameba could detect the paramecium before the paramecium detected the ameba... how?
They don't move randomly. Chemotaxis is movement in response to chemical stimuli. The surface membranes of cells are packed with a variety of receptors. When a receptor binds with its ligand (some molecule specific for that receptor) it elicits a response via intracellular signaling.
Think of it like following a trail of bread crumbs, or better a dog sniffing out something or someone. That bacteria is leaving a trail of molecules specific to it that are binding to surface receptors on the neutrophil, leading to intracellular signalling and directing the cells movement.
god damn, thats some smart AI. What if you were to flood your blood with those same scent chemicals so that the bacteria is confused as fuck and unable attack anything ? Or make traps that are scented with those chemicals so they go to your trap and die ?
ehh. I don't know any possible way you could set a trap. Microbes don't attack you per se. To them your body is nutrient wonderland. Killing its host is rarely in a pathogens interest. Symptoms from infection are caused by your immune system in response to the pathogen. The pathogen itself does not cause them.
Flooding your blood with some chemical would most likely effect many more cells than whatever you're after.
>They don't move randomly.
I might not have expressed this well... I said that they move randomly -untill- they "detect" something that makes them go in the direction of that stimuli or the oposite(getting away)
>What if you were to flood your blood with those same scent chemicals so that the bacteria is confused as fuck and unable attack anything ?
The bacteria that enters your body don't usually "attack" anything(some does, but even that is somewhat unintentional) what they do is get in, find a place comfortable(full of nutrients and protected from the inmune system) and live their lives in peace. The problem is that they will either take nutrients from you, will obstruct pathways or they produce chemicals to defend themselves from the inmune system.
And for the part about being confused see down...
>Or make traps that are scented with those chemicals so they go to your trap and die ?
Not all bacteria react exactly the same to the stimuli, there is always a small part of "retards" that have deficient receptors or they simply didn't catch the signal and these "retards" are truly the problem because while their "smart" brothers will go blindly into the trap, the retards won't and they can reproduce. so you would have artificially selected those to survive and transmit that information to their offspring or other near bacteria(bacteria can share "information" with each other).
Of course being deficient into the detection of an "attractor" is just one way to protect themselves. These bitches can even become inmune to wathever you throw at them,they only way to be sure that there is no artificial selection is to completly kill them all witch is not easy task either.
seeing that image, makes me wonder.
Are virus alive?
I know this is the same shit as usual, but I haven't found anyone to discuss this. As far as I know viruses are more like "inteligent molecules" more than anything else. If you could simplify them in two it would be like "DNA/RNA containers" and thats it. They lack any form of metabolism, if they are not flying around they can cristalize like they're made of rock, viruses don't move, don't eat they're just lying around like needles everywhere wating for a certain cell to get stung by what could only be describe as an unfortunate accident.
And when they perform their "biological" functions, they act more like biochemical machines not a living thing. Everything they do was a product of pure natural selection, from binding to injecting the RNA works like pulling the trigger from a pistol, it happens because it couldn't happen otherwise with the mechanism involved.
And yet, they can completly surpass a shit load of protective systems. Our defenses can't go into a virus haunt since they're too small and too "irreactive", what they can do is expect for a cell to get infected and "warn" the others. More like a physicist knowing that there is a black hole out there by its effects around not by looking into the black hole(although I remember that is part of the past) and we humans can't do a lot either.
I recently found the theory of living systems and it only pushes foward the idea that viruses can't be alive. But as as we know they actually perform biological functions with organic elements in its structure, they just do it in a more abstract manner(they reproduce, and since they must take the cell resources they are technically eating the cell for example)..
>Not a biologist, but I always wondered what all of these enzymes I read about at a level looked like.
Imagine an atom.
Now imagine 10000000 atoms composed by C,H,O,Fe,Cl...organized in planes and helixes moving around constantly.while keeping themselves as much compact as they can.
All representations out there are just colorfull variations of this.
not the OP of the previous post, but I am inclined to think that the distinction between living and nonliving is rather contrived, or at least has a great deal of development to do before it becomes accurate in any real sense. Biology is ultimately the sum of many smaller molecular mechanisms, thus there is no reason to believe that the addition of larger and more complex super structure to these mechanism somehow changes their nature from "nonliving" to "living" I may be a minority opinion, but its just my 2 cents on the matter. Biology is ultimately a kind of machine, deterministic and predictable, merely very complicated and often difficult to study and understand.
Where do you work? How much do you get for it? Is the job market being flooded by people like you or it will grow steadily before all positions are occupied?
I'm just considering a master in bioinformatics coming from a biology background.
I am self employed, my pay is determined mostly by the contracts i get from other labs around the state, or by the grants my team and i propose to..as far as the job market goes I do not think i am at liberty to say much, except that bioinformatics is a highly specialized and challenging field and there are some very exciting things going on out there, especially in the neuroscience department. I highly recommend it, although i came from a physics and computer science background and expanded in biology and biochemistry so it may not be the same experience for you.
It's honestly just semantics. Calling viruses alive/not alive has absolutely no impact on how we study them and what we do to prevent infection.
I agree with the term "obligate intracellular parasite." This includes some bacteria, fungi, and all viruses.
Saying we can't do a lot is very wrong. There are many ways our immune system combats viral infection. Viruses evolve much more rapidly than us, and employ mechanisms to evade host immune responses and then hijack cellular machinery.
Viruses are very dynamic group of organisms that are intimately involved with most, if not all other organisms.
from what some of my friends tell me, and what i pay my own team, you can expect to make anywhere from 65 to 130k annually if you find the right place to work in your field. I work mostly with computational neuroscience, so it may be different for you specifically but i hear the university of washington is offering some good graduate programs for CompNeuro.
Do you work with medical doctors?
I took a course in computational medicine. What mathematical models do you use to predict disease progression and patient prognosis?
Is your work involved with tumor progression in the brain/disease or something different?
> but I am inclined to think that the distinction between living and nonliving is rather contrived,
the problem is that there is a line somewhere to say whats alive and whats not, we would never call water alive just because its formed by some atoms or potassium because it reacts to other atoms or molecules, and so on with enzimes and proteins(although we have prions)
In supracomplex system(althought after reading the theory of living systems Im not so sure) we don't say that countries or towns are alive, and so on. And if we draw the line between mammals and bacteria then viruses become the hardest challenge to that view.
>Saying we can't do a lot is very wrong. There are many ways our immune system combats viral infection
Not by far in the same way you deal with bacteria, as I said the inmune system reacts to the effects of the virus not the virus itself, but it can react to the presence of bacteria or more complex parasites and destroy them actively.
you may also find Mitre corporation and North Shore LIJ are hiring right about now. Bioinformatics seems to scale a bit with computer science jobs, more so than the other STEM disciplines (barring comp sci. of course).
I see what you mean, but i have to wonder about stars then. It may sound a bit odd, but stars carry out many analogous processes to biological organisms do they not?
It's actually quite similar.
Antibodies can bind to viruses and prevent infection of cells. These are termed neutralizing antibodies.
Complement proteins that circulate in the blood can bind to viruses, which allows phagocytic cells (such as macrophages) to engulf and destroy viral particles. This is called opsonization.
Virus infected cells secrete cytokines that serve a number of purposes. They can increase that cells own resistance by shutting down it's machinery, alert NK cells and others. These immune cells will destroy infected cells.
All of these mechanisms can be employed during a bacterial infection.
The part that I still don't catch(under the classical definition of life) is:
How stars reproduce?
I get the idea that the stars can form a nebula and that nebula might form another star later, but thats not exatly reproduction but rather more like a form of inmortality where you reorganize all the atoms that conformed while you were alive and use them to create a knew individual.
sponges do something similar, but its not reproduction but rather a form of protection when the enviroment becomes unstable or dangerous.
>It's actually quite similar.
Aaarm... I learnt about interferons but not about opsonization used to kill viruses. Now I just feel stupid.
>They can increase that cells own resistance by shutting down it's machinery
When does the cell "realises" that it has been infected by a virus?. As far as I know the virus binds into the receptors like its just a normal molecule, then the DNA(or RNA+inverse transcriptase) enters and binds to the nucleus
uniport- drives single ion or compound across membrane
antiport- drives two compounds across a membrane in opposite directions simultaneously
symport- drives two compounds across membrane in the same direction
There are intracellular receptors that recognize highly conserved structures common to pathogens.
Toll-like Receptor (TLR) 7, for example, recognizes single stranded RNA. The subsequent signaling cascade leads to production of cytokines that can alter the behavior of the infected cell or warn other cells.
There are a number of cytoplasmic proteins that can prevent infection almost instantly if they interact with the virus DNA/RNA. It all comes down to recognition of pathogen specific structures.
Yes. They are not attached to one another though.
jelly fish have their polyps, why not stars....i suppose the extra stars and systems forming from a nebula after a stars death are essentially polyp forms of the parent star. in the case of black holes, perhaps some kind of strange end of life scenario?
of course, I was only really interested in illustrating how a larger system can be made of many smaller mechanisms and still not be distinct in nature from those mechanisms...It is unnecessary to differentiate between living and non living as "living" systems are essentially nonliving systems in their own right. I would even, for the sake of argument say, that a carbonic rock and a human are comparable as far as structure and mechanics are concerned.
I am currently working on hematopoietic stem cell differentiation. My lab is looking to find the regulators at play in myeloblast differentiation.
It seems OP, that our research is connected.
I'm currently working on a paper, so I don't have one quite ready for reading. My first paper on the subject will likely be on laboratory optimization of experimental methods in regulation research. Next I will be testing the actual hypothesis (results predicted by our differential model) to improve and perhaps remodel the differential process depending on newly discovered factors.
But I do have a couple that have been published on similar research by the PI of the lab.
my biochemistry classes made me feel freaking fortunate for not having any genetic diseases, like I pulled somekind of "life lottery" and won. Goddamn, it seemed that there were as many or more as proteins we had in our body.
I disagree, there are many areas that we don't study viruses that we could if the were considered "alive". As research continues to build, it seems that viruses have evolved from less developed viruses, yet many researches are not willing to enter this area of study because of the alive vs non-alive stigma that is attached to it.
I suppose i am obtuse in this matter, as in computational biology, we tend to be unconcerned with whether something is "alive" or "not alive" merely that it is a system with defined mechanics that can be understood and simulated at a resolution sufficient for our study but not so detailed as to be computationally intractable. I do not understand why one would be put off from a subject of study by something so, in my mind, contrived.
I don't either, but a scientist like any person is the slave of his reputation. If an area of research will harm their reputation, they are very unlikely to go into it. This is the case even if there are advancements to be made in said area.
I'm of the firm belief that it's every scientist duty to explore unbound by the social conventions of the ancient past and move into whatever area interests him.
hmm...indeed, it is unfortunate that social perception of a given researcher and his field has such skewed effects on the viability of research therein. Though, this is anecdotal, I am finding that running my own lab affords me obscurity and thus some degree of protection from social forces, barring grant applications of course.
Nice. I'm just about to get into the lab. My advisor's lab is working on isolating and studying a T cell progenitor.
Do you enjoy research? I see /sci/ shit on it a lot. I just started working towards my masters to see if I will enjoy research.
I'm an undergraduate actually. But most of my time is spent doing research after I tested out of my biology reqs. I love research, but i've known since I was a little boy that this is what I wanted to do.
If you like solving problems, and can handle frustration, research might be for you. It is very rewarding, i'm currently working on getting published.
I've also decided to add the mathematics major to add some course. Not to mention that I love mathematics.
You are my idol
I am currently an undergraduate studying computer engineering/science. I am thinking of taking a masters in AI and cognition but I also love mechatronics. Now Bioinformatics is the fucking thing, however the courses required for that masters are some subject classed under medical faculty like cellbiolog, immunology etc.
How many biology courses did you read before entered the field of computational biology?
I am flattered, but I would hardly consider myself a good role model.
I took cellular biology, biochemistry 1 and 2, immunology, and our 200 level and 300 level neuroscience classes, as well as one odd ball molecular neurochemistry and a odd neuro-psych course. i finished my major with a 400 level Neurobiology and 400 level biophysics....I am 32, i would hardly say all the schooling was worth it, most of what i payed so much for and spent all that time on i probably could have picked up in the field in the intervening years since i left school....
What's more is that bacteria are too small to detect changes in concentration in real time across their membrane, like our bodies' larger cells do.
They rely on a kind of chemical 'memory' relating to phosphorylation state of receptors. Extremely interesting subject, not to mention the biomechanics of rotating flagella.
Biology really does integrate all the traditional sciences to figure things out. I highly recommend the signaling and movement chapter in White's Biochemisty and Physiology of Prokaryotes.
It's simple :
The cell is both alive and the basic unit of any living organism.
Viruses are neither a cell nor composed of cells , so the viruses are not alive.
Got into an immunobiology research program as a trainee that researches intestinal microbiota, might even get a job for the summer out of it unless I fuck up royally.
Any tips from someone that has experience in research programs?
having cells is an arbitrary metric for saying if something is alive or not
the definition works fine until you find something which appears to be alive but is not comprised of cells
at which point you can stick to the old and arbitrary definition or you can rethink the line between living vs non-living
there is merit to either case. but who cares if we call it alive or dead? does it change anything?
Naw dude, naw. All living things need to be enclosed in a lipid membrane and take up energy from the environment to maintain a disequilibrium from the environment, and contain encoded information to build all the structural elements of itself, and be able to reproduce.
What you're saying is like:
>"well I think physicists need to expand their definition of energy man. We all got our psychic aural energies vibrating inside our chakras to the harmonics of the kundalini maan. It's all energy maaan."
Also why are doctors so autistic? When I tell them my symptoms and keep quite they are impassive and wont help me. When I complain louder and make my own disagnostics that I got by reading the interwebs they condemn me
Normal procedures, you don't do anything invasive unless you think is something serious and for that you do exams first.
People come with a lot of diseases, its not common that a lot of pacients come witht the same disease.
People (normally homosexuals) come with a lot kinds of shit in their anuses. From dildos to broken glass.
One time a guy came with another man with his hand deep down his asshole... he got stuck and the other one couldn't relax his shit. He got his pinky finger broken. There was blood and shit everywhere but students and nurses are there to clean.
Another man came with a latch in his butthole and he couldn't reach. He said that he was drunk and "wake up" like that.
>he got stuck and the other one couldn't relax his shit. He got his pinky finger broken
Let me get this straight. He got his pinky broken by the other mans asshole?
you said earlier your specialty is internal medicine.
wouldn't a hang in anus situation be an emergency medicine thing? Maybe bring in a proctologist and a gastroenterologist for reference?
Or is a hand stuck in anus a lets bring everybody in and look at this kinda thing
Internal medicine sees coloprotology too. All the proctologist go early because they don't have a lot of work.
Also it was my night shift and I was in charge.
Aparently the guys waited until early morning to go to hospital, because the shame.
And yes, I called everyone to see that shit, it has hilarious.
but with new evidence biology books are soon going to be classifying viruses as alive or making up a new classification for them.
some virus latency period has been discovered to be controlled by the genetic material of the virus. Apposed to it being controlled by the host cell.
some viruses choose to have a latency period to protect themselves from being noticed too quickly
Viruses aren't alive, they doesn't have the caractheristics of a living being.
It definition is "small infectious agent". Their genetic material doesn't function without a host and its full of errors and holes that makes them irregular. They dont choose to have a latency period because they are not alive, they just mutate in order to replicate.
Just because there are very complex viruses doesn't mean all of them are like that and they dont have the complexity of a living cell.
>some virus latency period has been discovered to be controlled by the genetic material of the virus
Hurr. Being alive means you have an active metabolism, you retard. Viruses can only replicate using host machinery.
Anybody else interested in human genetic modification?
I had the idea recently that we should insert gfp connected to eye promoters/enhancers into our genome, so we could get some sick ass glowing eyes.
Maybe we could take different colored variants of GFP and connect them to various promoters/enhancers, so you could have eyes glowing green, semen glowing blue etc.
Would be really sweet.
whats a good online or offline resource to get a grip on basic bioinformatics? failed the course last semester because i barely attended and i cant retake it now. still need to take the test, so i guess i have to teach it to myself.
It's not about usefulness, it's about awesomeness. If you do a quick google search you'll see many pictures of of various organisms with gfp in their eyes and they seem completely normal.
op here. I was interested in bioinformatics too but I have zero cs knowledge. I feel like it would be much easier to get into it starting from cs and moving to biology.
Can't really help you. I have asked /sci/ and /g/ for bioinformatics advice and gotten nothing. If you already took a class you should at least have some basic idea where to start.
i'm into computational biochemistry and I recently did a simulation of an enzyme that breaks esters. you can analyze how close the ethyl propionate gets to the active site of the lipase (it's from a fungus) and how much the protein fluctuates during the diffusion. the idea is to design drugs by such molecular dynamic simulations. here's a little video of the process in crappy quality because of the file size limit
Some viruses can hide from a host by turning off expressions. Is it possible to deliberately activate them so your immune system can kick their butt until they go into hiding again and then activate them again, repeat until virus free or virus is too diffuse to cause problems?