r/Biochemistry

PAGE proteolysis? help!!
▲ 4 r/Biochemistry+1 crossposts

PAGE proteolysis? help!!

TLDR I ran a gel for a his tagged protein I'm expressing in E. coli and I'm really not sure what to make of the smeared band I observe where I expect to see my protein, looks to me like proteolysis or (hopefully, tbh) just a gel running issue?

My target (his tag, SUMO for tag cleavage, "Rex3" is a 20AA IDR of interest, and 2x nanoluciferase) ought to be 52.2 kDa, and there's clearly something around that range but it doesn't look like it's coming out in one piece. My first (terrifying) thought was proteolysis despite the inhibitors (Roche cOmplete, EDTA-free) in the lysis buffer, but I also wonder if it could just be overloaded in a funky way or running weird or even modified in bacteria (looked to me like ubiquitination almost, if it wasn't e coli). Any help much appreciated!!

u/First-Amphibian1118 — 20 hours ago
▲ 79 r/Biochemistry+36 crossposts

Hey guys, if you missed it, CytoDyn just settled $500K with investors over claims it misled the market about its drug leronlimab some time ago. And they have already sent the agreement to the court for final approval.

In a nutshell, in 2021, CytoDyn was accused of overstating the effectiveness and regulatory progress of leronlimab. In short, the FDA later said the company’s claims were not supported by data, revealing no clear benefit. 

After this news came out, the stock dropped 25%, and investors filed a lawsuit for their losses.

The good news is that the company recently agreed to settle $500K with them, and already sent this agreement to the court for final approval. So, if you invested in $CYDY when all of this happened, you can check the details and file your claim here.

Anyway, has anyone here invested in $CYDY at that time? How much were your losses, if so?

Biochemistry related articles that are NOT peer-reviewed?

I'm trying to find popular source articles related to biochemistry to see how they describe topics to a general audience and gauge their overall accuracy, but it's surprisingly difficult to get search results to filter out the actual good, peer-reviewed stuff, and leave behind the blogs and news stories to dig through.

Are there any popular sources out there that people have noticed post biochemistry related topics before? Doesn't matter how trash or not-trash they are. Anything helps!

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u/RainCatB — 1 day ago

Do any plants Incorporate Sodium and/or Chlorine into compounds?

I'm somewhat familiar with the "usual" plant chemicals ie. Carbon, hydrogen, ozygen, nitrogen but it has left me wondering, can any plants make usage of reactions with salt/sea salt. I know there are plants like mangroves that can survive salty environments but im unsure if they merely protect themselves from it vs if they can make use of it. Are you aware of any plants that produce compounds from salt? What other "atypical" elements can feature in plant compounds

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u/pine64enjoyer — 2 days ago

Issue dissolving catalase

Hi everyone! I have a bit of an annoying issue in the lab and I'm hoping someone might be able to share some insight that helps

I purchased 50 mg of catalase enzyme and need to prepare a stock solution of 0.8 mg/mL - the purpose is to use it in an imaging buffer for single molecule localisation microscopy, catalase is used alongside glucose oxidase to reduce oxidative photobleaching.

This afternoon, I tried to dissolve 12 mg in 15 mL of my buffer (10 mM HEPES, 150 mM NaCl, 10 mM MgCl2, pH 7.4) but found it didnt dissolve very well at all. I tried heating at 30°C for an hour or so but that didnt seem to help. I then tried centrifuging, discarding the buffer and attempting to dissolve in distilled water, to no success.

The internet tells me that it should dissolve easily up to 1 mg/mL in water and neutral buffers (specifically mentioning phosphate buffer, which I will try next if nothing else)

Does anyone have any experience or advice? Thanks in advance!

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u/dettySJD99 — 3 days ago

rant

hi, im not really passionate in this field, but im passionate towards forensics, that’s why im doing this degree because i heard it was a gateway to the forensics world, i was interested in pathology until i learned you had to go to medical school and i don’t have it in me so im kinda lost. What i really want to do is music production and art, but i want to move out of my dads house as quickly as i can (hard relationships in fam) i guess im just a bit sad. i cant do what i really want to do because i just cant tell the future or how jobs will look. i have no portfolio for music and i know the music scene is portfolio based and not degree based, i keep trying to tell myself i can always learn music on my own, but that just makes me even more depressed. i tell myself im doing stem to fund my hobbies, but its taking a toll on me. this isnt career advice, this is just a vent post

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u/WrongdoerEnough5531 — 4 days ago

What is the actual form of 'bound niacin' in unprocessed corn?

I am trying to find out how the niacin is 'bound' in unprocessed corn as in what chemical form. In detail, I want to understand how processing the raw form of corn such as nixtamalization and boiling 'unbinds' the niacin into more easily absorbable form for humans and animals. In another words, I want to know the chemical form of 'bound form of niacin' which turns into the chemical form of 'unbound form of niacin' via some type of post-harvest processing.

I read through Maize in human nutrition (Food and Agriculture Organization oF the United Nations, 1992: https://www.fao.org/4/T0395E/T0395E00.htm) to find out what I want, but I could not really find the information I want.

Does anyone know about this?

Thanks.

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u/shcrimps — 3 days ago

I made an evidence map of 200+ biohacking compounds

hey guys, I built this:
https://bio-atlas.vercel.app

It's an evidence map of over 200+ biohacking compounds either I've come across or found in the communities that I'm a part of. I then had an AI agent go and find relevant papers. I haven't been able to fact check everything so keep that in mind. There's so much out there and I needed a way to view things clearly. I hope other people might have use in this.
The more critical eyes on it, the better.

I think this grey science space is getting a little too "vibes" based and not science and I wanted to create a resource for people to actually start their research with evidence.

I know it’s not perfect yet, so people poking holes in it is exactly what would make it better.

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u/jawnwick3 — 4 days ago

Consuming Kale and its Effect on pH of the Body

What would be the effect on the pH of an average human body by eating 16 oz of chopped kale in one sitting, by virtue of kale being an alkaline food?

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u/Novel-Device-9237 — 5 days ago

Need good recs for a laptop

I want to pursue my career in structural biology and I want to purchase a new laptop. My budget is upto 60k rs.(625$) So can someone guide me which laptop I should buy? I mostly want to run pymol, chimera, chimera x and maybe sometimes coot and even blender

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u/averageperson_69 — 6 days ago

Grad Cap Ideas - Protein Structure

I’m hoping to include my research into my grad cap design, but I’m stuck on how to represent the protein itself. Was thinking of those curly ribbons? Would love to see what ideas everyone has

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u/shineyshines — 7 days ago

protein refolding from 2M to 1M urea

hello, i'm working with a novel fusion protein. it's highly aggregation-prone, and right now it's in 8M urea-containing buffer. When diluting it stepwise from 8-->4-->2M, the protein remains mostly soluble. however, i'm having issues maintaining solubility when dropping from 2 to 1M. i'm diluting my buffers very slowly (over the course of an hour with constant mixing in the cold), but the proteins still are crashing out. My buffer components are: 50mM tris-HCL, 100mM KCl, 10% glycerol, pH 8 (PI of protein is 9.7). i've tried adding arginine and increasing the salt concentration, but my proteins still crash out. if anyone could help, that would be greatly appreciated. thank you!

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u/hana-maki — 9 days ago

May 13: Education & Career Questions

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

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u/Eigengrad — 8 days ago

For the Chemical Biologists

Hi everyone, if you are a chemical biologist, I would love to know what a day in your life looks like! I am super interested in understanding arrow pushing mechanisms and even more so in biology! Do you guys study this in your daily lives? do you think about this electron tracking across peptides and so on? like nucleophilic additions to amino acids, carbohydrates and so on?

I would love some advice on where to put my love for this.

If you could reach out to me or comment, I would love to know.

Thanks!

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u/Historical-Kiwi-1280 — 8 days ago

Metabolism is Scary, but It Shouldn't Be: New Free, Comprehensive Metabolism Chart for Students (Pre-Med, Med Students, Educators, and Everyone Else)

tl;dr new, comprehensive metabolism chart for students and educators here:  https://www.dropbox.com/scl/fi/ngnjczhee586v6espfry3/Metabolism.png?rlkey=apz99xchnczdfa0d19qif8kjc&st=9g5622u9&dl=0

Hey everyone! I'm a rising M1, and I have a strong passion for education. Over the past few months, I made this comprehensive metabolism chart because I wasn't satisfied with some of the other options online. It's completely free to use and share, so please do! My goal is for this to be something students all across the U.S. (and maybe even other countries???) can use. I recommend starting in the bottom left to see the intro and diagram key.

Please let me know if you see any typos or mistakes. While the bulk of it is done, I need a team effort to make this as perfect as possible!

Comment here, DM me, or email me at metabolismshouldnotbescary@gmail.com if you have questions, suggestions, error corrections, or just wanna chat!

u/MetabolismRevamped — 9 days ago

MCAT Biochem Self-Studying

I started self-studying biochem earlier this week and was hoping for some guidance. I’m a little lost. I finished reading the first 3 chapters of the UWorld Biochem textbook and only have metabolism and metabolic reactions left. However, I haven’t been memorising just reading, understanding and trying to grasp everything. I was wondering what steps should I take now? Ik the metabolic pathways is the most difficult section so should I go back first and start to really memorise and comprehend everything or finish reading and understanding then going back and really understanding everything. I would really appreciate some guidance on how I should schedule my time because I am devoting this summer to MCAT and want to make the most of my time. Please help, thanks!

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u/Embarrassed_Let6188 — 9 days ago
▲ 15 r/Biochemistry+1 crossposts

ACS Certified… but not?

I’m graduating next week with a BS in biochemistry, and our class was told about becoming ACS certified (if we took inorganic and a chemistry research credit), which I think 90% of us (including me) never did. However, last week, I got an email from ACS sending me my credentials for becoming ACS Certified! I asked my professor about it, and she was confused. None of my friends got it, either, even though we all never did any of the ACS-required classes.

Did the requirements change to get certified? Or has this happened to anyone else? TIA.

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u/Extra-Key4088 — 10 days ago
▲ 2 r/Biochemistry+1 crossposts

Troubleshooting a Protease Activity Assay - Why r my halos coming out blue instead of clear? HELP A PORR STUDENT

Hi everyone, I’m a Master's student studying leaf senescence and I’m sufferying trying to estimate protease activity using an agar diffusion assay, but I’ve hit a wall.

So, the method was simple:

  1. Medium: 1.5% Agar enriched with 0.1% BSA.
  2. Procedure: I pipette a protein-rich extract (lyophilized leaves in phosphate buffer, normalized to 0.1 mg of protein) into small pits in the agar.
  3. Incubation: 24 hours at room temperature.
  4. Staining: 2 hours with Coomassie Brilliant Blue (CBB), followed by a destaining solution.

The Problem: In my head (and my supervisor’s), the proteases should digest the BSA, leaving a colorless/clear halo around the wells. Instead, I’m getting the exact opposite: darker blue halos around the pits.

What I’ve tried so far:

  • Adjusting the exposure time for both the Coomassie stain and the destainer. (not better)
  • Moving to a colorimetric method using Azocasein, but the substrate doesn't seem to dissolve completely and is very difficult to work with.

I feel like I'm the only person I know doing this specific method for coffee leaves. Has anyone dealt with these "reverse halos" before? Could it be protein-protein interference or the high concentration of my extract proteins staining more than the BSA?

Any advice on how to fix this or a recommendation for a more reliable protease assay for plant tissue would be a lifesaver!

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u/Sensitive_Goose1093 — 8 days ago

How many additional chem options (beyond required chem classes) do undergrad biochem honours/majors students usually take?

My question is in the title. I’ll be starting university in September. Just generally wondering because I was looking at possible useful/recommended/related electives to take in the later years of my degree. Also, what are the most common ones (besides more chem)?

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u/Aggravating-Drag6064 — 10 days ago

Anybody experienced in monitoring Tryptophan fluorescence to track protein conformational changes?

I am trying to do something similar. I would need your help. Please DM. Thank you very much.

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u/a_knownstranger — 10 days ago