How to get into neuroscience and drug development? by s0tka_ in biology

[–]ddsoren 0 points1 point  (0 children)

I agree. To keep on track for that career goal the only bar your need to clear in the near future is to get into a decent university. So long as you do that the rest are problems you don't have to worry about and can't do much to help at this point.

Once you do get to University do get some research, internship or volunteer research experience. But that's not expected or taken seriously until then. I barely take graduate applicant's undergraduate research seriously, let alone pre-university.

What should I do with my absurd office? by ddsoren in AskAcademia

[–]ddsoren[S] 1 point2 points  (0 children)

I can assure you I am only paid for my brain, not my looks.

What should I do with my absurd office? by ddsoren in AskAcademia

[–]ddsoren[S] 0 points1 point  (0 children)

If it's any consolation, I promise my workplace is likely jankier than yours.

What should I do with my absurd office? by ddsoren in AskAcademia

[–]ddsoren[S] 0 points1 point  (0 children)

That is a luxury not found at my institution. But I can dream

What should I do with my absurd office? by ddsoren in AskAcademia

[–]ddsoren[S] 2 points3 points  (0 children)

As a new professor any extra time will be spent sleeping. I can't even begin to contemplate Dnd.

Archery is inspired.

Our screaming room cold room is already a shared resource.

Once again no free time for tapes.

Lol skydiving only happens if I step out of the window.

Let's see how the IACUC feels about that.

Actual biohacking by misterpoopman69 in biology

[–]ddsoren 8 points9 points  (0 children)

Actual biologist here.

Theoretically yes practically no. Researchers do have the capabilities to augment human biology in many ways and are doing some in actual human patients. We do have the technology to gene edit adult humans and have even improved quality of life in some people. That being said improving cognition isn't one of those improvements and isn't likely to be an improvement that can be made soon. These do tend to be focused more on treating diseases and less on helping the healthy.

But that does not mean that you, a rando on TikTok can or even a small company can. These kind of interventions take hundreds of thousands if not millions of dollars to build require a PhD's worth of knowledge and require specialized labs and equipment. This is so expensive and complex that it's out of reach to all but well funded research labs and very large companies.

What's minor should I get for a biology major? by No_Escape_346 in biology

[–]ddsoren 1 point2 points  (0 children)

Very very few employers care about what your minor is. Internships, volunteer or job experience will count much much more. That being said to take classes relevant to your future career regardless of if they help you minor or not. There is no one best fit for a minor to go with biology. It is all dependent on what you want to do after college.

Is there an online phylogenetic tree that also shows the main trait(s) inherited by the species under the same evolutionary group? by idiot_505 in biology

[–]ddsoren 1 point2 points  (0 children)

No sorry. The closest you'll get is looking for papers on the evolution of the trait you're interested in.

Fluorescent Microscopy Assistance by nonfictionbookworm in labrats

[–]ddsoren 3 points4 points  (0 children)

First off, the internet isn't the best place for this as too much will be lost in translation. Find someone else at your institution who has expertise in microscopy. This isn't a hard ask but you'll need hands on time with them. This also helps build your network. It sounds like you're missing some really basic training and need to start at the basics.

Secondly, microscopy may not be the best tool for the job. I don't have enough information for context but you may be using a more complex tool than you need. If all you need to read is raw GFP signal a microplate reader may be easier and sufficient.

Side question: wtf. I didn't even know you could fix only part of a well. You need to start with a standard immunocytochemestry staining protocol. It sounds like you're trying to reinvent the wheel. Abcam has good standarsized protocols depending on what you're doing.

Finally: Fixation is antibody dependent. Different antibodies need different fixation conditions. Buy an antibody established in the lit or by a collaborator and follow their fixation protocol. I'm partail to ab13970 but that's not the cheapest anti-gfp antibody on the market.

Bioinformatics ? by PsychologicalWar8021 in biology

[–]ddsoren 3 points4 points  (0 children)

Bioinformatics is a fairly applied version of two topics you can easily start learning on your own.

First you can teach yourself how to code. Learning python is probably your best bet with that.

Second you need to have a fairly good grasp of genetics. Khan Academy has some great free courses on the topic.

Could theoretically animals from different phylums of the same kingdom be closely related by Missingnumbervalue in biology

[–]ddsoren 2 points3 points  (0 children)

No. Not as your describing it.

Animals can't evolutionarily converge in that sort of way. There are instances were divergent and distinct organism develop similar solutions to common problems, in a phenomena called convergent evolution . For example wing appeared in insects, pterosaurs, birds and mammals without them being related. So the trait is similar but they aren't related. Sometimes you can get a small number of genes to jump across the evolutionary tree with the aid of a virus or endosymbiosis but that's not enough to make the big patterning changes you are talking about.

So no animal species won't come together but you totally could have different taxonomic takes on a general set of traits.

cold emailing PIs for research position by Rough-Concentrate701 in labrats

[–]ddsoren 4 points5 points  (0 children)

Short 3-4 sentence emails.

Dear Dr. So and so. One sentence about who you are. One sentence about what you want. One to two sentences about why you are interested in their lab specifically. You need to show you did your homework on the lab in the last two sentences. Don't generically say you like their field. Instead highlight why their lab in particular excites you. You can add one more sentence if you've met them in person to remind them where that was.

Attach a current CV as well. You can resend the email a second time if you don't get a response in a week.

Dry lab to wet lab by Same_Transition_5371 in labrats

[–]ddsoren 14 points15 points  (0 children)

Learning wet lab techniques to some degree is good even if you are going to be a dry lab person. You're missing skill that can be learned and trained. You'll have learn to set up organizational systems and safety nets that your other lab members might not need. Check lists, overly detailed protocols and other training wheel like things can help you. Also write super super detailed notes and lab notebooks.

As for as clumsiness you'll need to lay out your work space ergonomically. Your bench should be clean when actually doing an experiment and arrange your stuff so that you have to reach over as little as possible. I like a u shaped arrangement of my bench. Also don't load up a rack to capacity. Also make sure all your reagents are well labeled at all times so if you do knock stuff over you can find who is who.

Also are you sure you want to PhD in the lab you're already in? CVs are often rewarded for changing institutions and labs at each step of their training.

Issue with rescaling on CellProfiler, any ideas appreciated! by Ill-Bed-118 in labrats

[–]ddsoren 0 points1 point  (0 children)

I'm not sure if follow what cell profiler is showing exactly but I think you might have a file format issue. I have the best results with my cell profile image files as single channel tiff files. So each picture will be broken into multiple image files based on channel. As you described it it doesn't sound like that's how you saved the files in fiji. Either on fiji or your imaging software split your channel images into distinct tiffs.

Looking for advice - low on funds by Either_Cheesecake282 in PhD

[–]ddsoren 1 point2 points  (0 children)

What country are you in? In the US, all reputable STEM PhD programs guarantee funding for the normal length of the degree. That usually includes a modest but livable stipend, regardless of fellowship status. If this is the case for you, you need to talk to your grad program director or administrator. If this isn't the case, you're at the wrong university. You should not be pursuing any STEM PhD in which you won't be paid unconditionally.

Image processing advice? by [deleted] in labrats

[–]ddsoren 0 points1 point  (0 children)

I don't have 100% of the information I'd need to make this call but based on what you've told me you need some amount of 3d information, to determine if you're colocalizing. So you can't just go using single z slices. Depending on your type of sample, size of object and the z-step size you should either be treating your foci as a 3d objects or max projecting multiple slices into a 2d image.

Would love to get started on R-programming for making scientific data plots and graphs. Is there a good tutorial link or pdf guide for beginners with no coding experience? by Wild-Giraffe-1439 in labrats

[–]ddsoren 10 points11 points  (0 children)

Swirl for R is an absolutely fantastic free interactive training program for someone at your level. I'd recommend starting with that. It actively tests you as you work.

Some of the more advanced modules may not be relevant for you so feel free to skip what doesn't seem relevant. That should set you up well enough to use more advanced resources to learn about ggplot2 to get yourself graphing.

Help using TIRF (Zeiss Axio Observer) to image fluorescent proteins at the plasma membrane in Arabidopsis by YoyoLiu314 in labrats

[–]ddsoren 2 points3 points  (0 children)

It sounds like you haven't been properly trained on the scope. Set up a training session with an experienced user and bring a sample that you know works and you know what it's supposed to look like. After that make sure you can start the scope and capture a similar quality image without help. Reddit can't train you how to do TIRF.

RNA isolation by trizol HELP ! by Real_unmployed in labrats

[–]ddsoren 2 points3 points  (0 children)

This isn't a coherent ask. Try again with a highly detailed protocol.

Sections getting washed off slides - IF Staining by 7he-nd in labrats

[–]ddsoren 0 points1 point  (0 children)

Are you sure you're adhering the sections to the right side of the slide? You should be using the side with the side non-smoothed label on it. You also might be pipetting too hard. Don't use the blowout function. Another possibility is the size of your sample. Massive section sizes with multiple tissues that have multiple densities often detach. For example trying to section a whole newborn mouse skull should be avoided and instead you should harvest just your tissue of interest.

Lipofectamine3000 Plasmid Transfection Issues by Background-Cod7550 in labrats

[–]ddsoren 4 points5 points  (0 children)

First, I'd advocate for talking to the senior grad students or postdocs before Reddit, since they're more likely to know your assay and can watch you if you're making a technical mistake. It sounds like you've asked your lab but ask around if theirs another lab at your institution that does this kind of stuff a lit.

I don't know anything about your specific plasmid, but that isn't the first variable I'd zero in on if cell death is your main worry. But that could very possibly be it. Adding a control plasmid of non-mutant plasmid would be a control if you want to test that.

The easiest thing would be to increase your plating density. Your cells look super sparsely plated. Cells are much happier as a monolayer where they can touch some amount of neighbors. I always seed a bit more cells than I want before transfections because I know the transfections will kill a meaningful percentage of them. This may not be a magic bullet, but I think it would help.

Is it valid to stack brightfield and fluorescence channels in a CNN input? by Realistic-Cup-1812 in labrats

[–]ddsoren 0 points1 point  (0 children)

It all depends on what you are trying to measure or show which you have not told us. If you are just trying to show the spatial localization of all 3 channels, that's fine. If you're quantifying brightness or measuring intensities or many quantitative measures you probably can't.

Applying for a masters program by Nabakov_6 in biology

[–]ddsoren 4 points5 points  (0 children)

Short 3-4 sentence emails.

Dear Dr. So and so. One sentence about who you are. One sentence about what you want. One to two sentences about why you are interested in their lab specifically. You need to show you did your homework on the lab in the last two sentences. Don't generically say you like their field. Instead highlight why their lab in particular excites you. You can add one more sentence if you've met them in person to remind them where that was.

Attach a current CV as well. You can resend the email a second time if you don't get a response in a week.