Let’s take Glutamate for an example. In its native form it is said to function as a neurotransmitter. If thermally degraded in a hydrophobic solution will thermal degradation destroy its functional capabilities?

So, to start, I'm a layman when it comes to anything biology or chemistry, I only know the very basic buzzwords that get thrown around. Still, I kinda developed the stupidly ambitious goal of attempting to write my very own protein folding algorithm (Don't judge me).

The problem is that for that to ever be remotely plausible, I need to learn more about how proteins are constructed.

As far as I managed to guess, I need to find sources where I could learn about the following topics:

• How are proteins assembled, as in, how each amino acid connects to each other to form a chain. I'm assuming there's a
• What defines bond angles, and can it be accurately calculated? Or is there some quantum boogery that makes that particular task hard. I see the theory about how the valence electrons repel each other, so the angle could be approximated by a polyhedron with the same number of vertices as electrons, but there seems to be many exceptions, why? and how?
• What intermolecular forces direct protein shape? I learned from Foldit that hydrophilic and hydrophobic interactions play a major role but what about electrostatic forces Temporary polarizations and van der Waals force? Could dipole moment propagate across the protein, turning it into a big state machine?
• Are there any resources about hydrogen bonds and how they form and break?

Any info about these subjects that is not paywalled is appreciated.

Hi everyone! I’m finishing my master’s degree in Genetics and Molecular Cytology next year. In addition, I’ve gained experience in microbiology, parasitology, immunology, and also zoology and botany (the latter two during my bachelor’s).

In my home country in Europe, salaries in this field are extremely low, and I’d be lucky just to find a job at all. That’s why I’m seriously considering moving abroad. I’m still unsure whether to stay within Europe or aim for something further, like the USA.

I know people here come from all over the world, so I’m curious—what are the approximate salaries like in your country for someone in genetics, molecular biology, or related fields? I’d appreciate examples for entry-level positions (fresh graduates) as well as average salaries for people with some years of experience. Thank you! 😊

Malignant ascites, cancer

I am looking (preferably for a commercial single plasmid system) for Cas9 base editor to induce C to G in a cell culture. Thanks a lot!

I used assembly my sanger sequencings with genious prime or CodonCode aligner. But those are not free. Would anyone happen to have a suggestion??

Hello I 27F work in a cell culture lab and was trying to grow fish cells but after they start growing, they die after few days. Both me and my supervisor are currently trying to find a solution by changing the media supplements and also the conc. Of antibiotics but not sure what exactly is happening. The incubator so far runs ok and other organisms grow well. Then what's the matter with fish cells?

Anyone has experience or has any idea please share

Hey everybody.

I work in a small community college lab researching deinococcus. Personally I work with D. ficus but have many, strains available. We are starting to pitch spring conference poster ideas and im super freaking stuck on a hypothesis and general idea, this is my first year presenting and I've only been doing this for about 2 years. I've done things like chemical and electroporation transformations, ep gels, and some other basic lab protocols.

I was going to do a overall pH tolerance description of a strain just below d. Rad in terms of current use and research, there is little to no pH data on this othet strain,, however my PI says this is more descriptive science and not the kind of exploratory novel research we aim for.

So now my PI is thinking I could do something bioinformatically by looking at say the catalase genes in D. ficus. I could spend 2 days on UniProt and NCBI and get no where, this is all so new and there is so much to learn.

I guess what im asking is, how do you tune your brain and find these, what my PI calls, pinholes in research that need to be explored?

I just don't know where to start, and trying to comprehend all this genetic information, tools and protocols.. it just overwhelming.

Thanks in advance.

Mine is growing fine in a normal lb plate. But when i inoculate it in lb low salt broth it doesn't grow unless a large inoculum is inoculated

Hi there, I have a very specific problem in establishing southern in our lab. I am using this semi-dry electrode system for transfer of DNA from agarose gel to nitrocellulose membranes, but when I use denaturation buffer from a protocol I found online I basically "contaminate" the agarose gel with NaCl, which makes the gel way too conducive. Therefore, my transfers don't work when I try and denature the DNA samples.

TL;DR Did anyone here ever work with southern semi-dry transfers and how did you denature the DNA in agarose gel?

Hello,

I am trying to optimize an RNA extraction protocol from bone tissue. I am homogenizing the sample mechanically in Trizol, separating the nuclei acid phase with a density gradient (by adding chloroform and centrifuging) and then loading the aqueous phase onto a column for clean up (Qiagen columns). Only after I loaded the material on the column I can do the gDNA digest with DNase I. So, I was thinking: would it be better to do the gDNA digest before loading the material onto the column to reduce the competitiveness between gDNA and RNA to bind to the column? Any lab rat has idea on this? Anything would be helpful! Thank you very much!

🐁🐀

Hello folks! Do you guys have any tips for high quality DNA extraction from seeds of Bétula péndula? My supervisor wants me to extract DNA from each seed separatly and do a long fragments PCR to determine mitochondrial DNA stability . Previously i only worked with animals tissues with significantly more material per sample. Am i cooked :D?

Hello everyone,

I got some funding to sequence and assemble the Absinth genome (Artemisia absinthium L.). The genome is quite large (4.324 Gb) and I was thinking about doing long read sequencing (such as PacBio HiFi or Nanopore). Both methods need high quality, molecular weight DNA. I have very little experience with such DNA extractions in plants, and would like to have some suggestion for recommended kits and protocols.

Thank you!

I am in a bit of a fix. I have a gene which expresses two transcripts, both of them are expressed in all cells. Lets consider these two transcripts as EI (exon inclusion) and ES (exon skipped). Both the transcripts are expressed in all cells, EI higher than ES. EI makes a protein which can be detected and ES protein has not been detected yet. We cloned ES with a flag tag and found that it expressses when transfected to cells and doesn't interact with any known EI interactors. To know more about ES protein interactions, we performed a co-IP and sent the samples for mass spec analysis. There are a small bunch of proteins which interact only with ES. One common interactor of EI and ES is UBB. Any ideas what this could indicate and how do I go about making a paper describing a function these interactions. I am just completely clueless right now. I need to finish up this story ASAP! Grateful for any suggestions!

I need tips to study molecular biology.

For context, I'm a sophomore studying biotechnology. One of my courses this semester is cell and molecular biology.

I unfortunately stopped with bio right around grade 10, choosing to focus on chemistry- it was my love for biochemistry and organic chem that led me to majoring in biotech.

To say that this course goes indepth is an understatement. It just is so detailed, that I feel clueless 75 percent of the time. We were told that grade 12 bio was a good enough precursor to this course, but that just is the metaphorical tip of the iceberg. This is such an interesting subject, but my fear of failing this course somehow works counterintuitively and i just don't know how to study it.

I've decided that I'm gonna pass this course with atleast a B-, and I'm ready to put in any point of effort for the same. I have copies of Campbell's biology to bring up my bio knowledge, and I've also gotten a copy of genes by Lewin for additional information. Also have the prof provided material. I don't know where to start tho, could use some tips. From students, professors, working professionals of this subreddit. Thanks a lot.

Ps: I'm really sorry about invading the subreddit with this post. I see the calibre of discussions here, and i don't mean to interrupt it, but I felt the beet advice would come from this subreddit.

The collaboration will utilize molecular biology techniques for better cancer detection. Molecular biologists, what are the scientific prospects and challenges of this approach?

I am told to analyze my data using -ddCt, and I have already complete this and have the converted this data to bar plots. However when I am reading (going down the rabbit hole) I have also notice that people just keep it as -dCt calculation and conversion, so I did this as well. Now I am conflicted. Both offer the same indication but -ddCt represents my data because I can fit the results into one bar plot.

To be honest I am not a big fan of "it looks/feels better" so I am wondering if anyone also had the same thoughts as to this.

Or am I missing the point because -dCt and -ddCt are vastly different and provide differences in prospective when conveying the same data/result?

Hi guys so I have a list of genes that I want to check if they are expressed in the brain, not concerned about region. My list consists of 1000 genes and I wonder is there’s a tool to check transcriptional expression with bulk input. I’ve tried GTEx but many of the genes aren’t identified (I’ve tried gene and ensembl names). Human protein altas and Allen brain atlas don’t have bulk inputs. FUMA gwas is good but doesn’t give TPMs.

I’m at a dead end and refuse to think that someone hasn’t made a good website to check this without painstaking searching genes individually. Any help or direction is appreciated.

(Note: As I am posting similar messages in other relevant subreddits, you may encounter similar inquiries if you participate in biology and chemistry-related subreddits.)

Recently, I came across James A. Peters' "Classic Paper in Genetics". Obviously it was a much more curated and professional selection but if you were to compile a list of the most significant and pertinent papers in [subject], which ones would you select and why?

Hi guys I am molecular biology student, I have in this semester Molecular Biology of Plant lecture. There is a good source to study for phytohormones. It is called Teaching Tools in Plant Biology.

Our professor has recommended it, however our institute not allow to take the lecture note zip file for free.

The price for only 24 hours is a lot for a student for my country. Could you please help me , how can I find it ?