Biochemistry and Molecular Biology

Dear CHIPers, I have just started optimization for CHIP in my current lab since we don't have an optimized CHIP protocol in our lab. I am currently following the Abcam protocol (see attached). A) I have started with optimizing sonication cycles. I used a Diagenode Bioruptor (with water bath) for shearing chromatin from non-crosslinked 0.4 g rice leaf powder: 3 times of 10 cycles (30 sec ON, 30 sec OFF). Please find the gel picture attached. Next will start with crosslinking and reverse-cross-linking optimization. I will perform crosslinking of the cold tissue powder instead of whole tissue and without vacuum. Thereafter proceed with nuclei extraction, l…

Hi there, Are there any transmembrane receptors (metabotropic or ionotropic) which have their ligand-binding domain located inside the membrane, and (if metabotropic) has G-proteins, kinases or other signalling proteins on the extracellular side? I guess that it is possible for cells to 'misplace' their receptors and put them backwards or reversed inside the membrane. But are there any proteins which function regularly by having intracellular ligands bind and then mediating a signal to outside the membrane? Thanks in advance, Dagl

I was wondering how one would find what part of a protein is bound by antibodies in the body. I would assume it's not the entire protein but a certain amino acid portion, or am I incorrect?

Why do people with Her's disease (liver glycogen phosphorylase deficiency) have more lactate in the blood?

Hello, I'm looking to design randomized oligos obeying certain rules (e.g., similar Tm or GC content, but differing in at least X nucleotides). I could write a script to generate these oligos, but I'm guessing somebody already wrote one and I'm just too dumb to find it (I tried). Can anyone help? Thanks!

I have recently started looking back at the function of the Golgi complex and am now aware not all proteins pass through the Golgi Complex (cytoplasmic translation). However I was always under the impression that most post-translational modifications (PTM) happen in the ER (co-translational) or Golgi complex. Additionally, some types of PTMs happen in the mitochondria or at other organelles (transmembrane receptors come to mind). My questions are fourfold: 1. Are there specific PTM's exclusive to the Golgi complex. 2. By what mechanism can proteins translated by cytosolic (floating) ribosomes be folded and modified (in the ER the concentration/…

Hi ! I just wanna know: how PEGs are grafted onto 2nd generation liposomes and an example of a cancer cell receptor. Thanks =)

Hi there, Please see the following paragraph of the Book [I don't want to bias anyone so I can't post its name, will do after a few answers], and the relevant radiation-related claims in the research article (https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1432-0436.1991.tb00872.x): I tried looking up sources for gamma-radiation-mediated enucleation, but can't find any. And in the articles he/they don't talk about "absence of genes' or 'DNA destroyed'. I think I have enough (lack) of evidence to say that the Book is misinterpreting/spinning the story, but wanted to check here just to be sure, before I accuse the Author of doing so.Because this…

Hi, In the winter the air is dryer so there is less water in the air. I wonder how water can keep the skin on hands from getting dry and crack.

Hello everyone I would like to detect the aggregation of newly synthesized proteins, but in the process I have encountered some problems. My strategy was to label the newly synthesized protein in vivo with 5ug/ml puromycin for 30 min, then through the differential centrifugation to isolate the aggregated proteins. Finally, anti-puromycin were used to detect newly synthesized proteins in aggregated proteins. Question 1. I found that each time I do this experiment, it was difficult to keep the same amount of aggregated proteins after centrifugation. I mean that there were sometimes more or less aggregated proteins in the same strain. Is there any way to…

In my experiment, I use a HepG2 cell line for a cytotoxicity assay with Alamar Blue dye, to test toxicities of different metal ions on the liver cells. HepG2 is a liver carcinoma cell line from a Homo Sapiens (human) origin. I know that usually liver cell is used for cytotoxicity assay, however, I wonder what will happen if I use brain cell line instead? And what if I use rat cells instead of human cells? I noticed a study comparing a mouse neuroblastoma line (neuro-2a) to primary neurons found that neuro-2a cells were much less sensitive to neurotoxins, possibly due to a lack of important membrane receptors and ion channels. It means that some neuronal cell lines produce…

Hi People, I want to purify my peptide from other byproducts. I chose Ion exchange because my peptide (Fluorophore-KARK(modficiation)SAGA) its positively charged (Lysine and Arginine). I guess that the isoelectric point is around 11 and therefore cation exchanger is more suitable than anion exchanger. The thing is that my peptide is dissolved in Tris Buffer pH 8.2 and I would like to use it also as elution buffer (Tris buffer with NaCl). Nevertheless I read that for Cation exchanger is high recommended to use Phosphate buffer and Tris is more suitable for Anion exchange. My question is Why and if the use of Tris buffer represent any problem in the cation exchanger chr…

Dear Science Forum, Question: How do you explain that the TB skin test that uses PPD does not serve as the sensitization phase agent of DTH, thus causing subsequent positive TB skin test results when using PPD? Disregard the question. The PPD inoculum is too small induce sensitization.

Yesterday I received the reviewers comments from an editor of "Journal of clinical biochemistry". The paper was rejected but what upset me most was the fact that it took almost four months to reach this decision and one of the reviewer wrote a total of 4 lines (!!!!!) and this could have been done in one day. I can accept that a paper might not be good enough for a journal, what I can't accept is that it takes 4 months to do that. The scientific work is based on publications that are needed to raise funds and for career advancement. I think it is unbearable that we are hostages of editors of scientific journals who can decide if, and when a paper can be publishe…

Ordinarily the polyacrylamide gels are rubbery, but the ones I poured last week were very stick, and the stacking gel did not seem to solidify. I was able to run a pre-stained standard, and it looked almost normal. However, the gel stuck strongly to the glass plates and was unusable. I made new acrylamide using a different manufacturer's bis-acrylamide, and the new gel behaved normally. Either it was the bis, or I made some other mistake in making the acrylamide solution. Has anyone ever seen something similar? Any guesses about what could cause a gel to become sticky and less of a solid?

What other possible hormones are involved in the cholodny-went theory in which auxin is responsible for phototropism?? Plz help!!

Hi, This is from user Lawrence over on Longecity. "Early in 2014 a group of 7 males, aged 45 to 66, decided that we would do a group buy of NMN. Our designated lead guinea pig is a molecular biologist and he began taking NMN late in 2014. In the beginning we monitored his blood work with monthly full panel blood tests performed by LabCorp. We believed that inflammation levels were a good indicator of health and aging, so we added two inflammation tests to the standard panel. The inflammation markers that we tracked were; C-Reactive Protein, (CRP), Tumor Necrosis Factor-Alpha (TNF-α) and Interleukin-6 (IL-6). As he began the NMN dosing (3,500 mgs of NMN twi…

I have followed the kit instruction, however, after I added the elution buffer to both of the 2 samples (from the same stem of the plant) for DNA extraction, I find out one of the AC column contains more liquid than the other one, so I pipette the excessive liquid from one AC column (for one sample) to another one (for another sample). It seems to be not a good idea, but does it mean that the two samples cannot be used? In another DNA extraction, I added the elution buffer not to the centre of the AC column (suggested by the instruction in the kit), does it mean that I better discard these samples? I only tried DNA extraction for three times... so... Wish …

Hi, I have always been interest by quantic physic even if I don't have the mathematic or physic knowledge allowing me to really understand it. So a question came into my mind: do we find any impact of the physic quantic theory on the relation ligand receptor? Does some people research on bio-quantic stuff? I have the same question about protein reploiement and quantic effect. Thank you if you can help me, and I hope I'm being clear.

Is the further study of molecular biology the to find safe and effective cures por cancer, for example lung cancer? If it is, which approach should be taken or what specific processes should scientist explore in future researchs?

I’m currently studying about collagen. And i have a couple of questions i can’t find in the litteraturen. I’m sorry for my Eng, it’s not my nativ language. I understand that the H-Bonds betwine Alfa-strands in tropocollanin occurs with hydroxyproline, but to what Other aminoacid does it connect to? Is it betwine another hydroxyproline in the next strand ? is the h-Bonds betwine tropocollagen aswell? Or is it only allysin- lysine covalent bonding? what happens with the bonds when the cell gets Old? Does it increase or decrease? My guess is that the more interaction the more bonding occurs, thats why old ”meat” gets so chewy. ? Or?

I would be interested to hear what your thoughts are on the role of mitochondria in longevity (specifically in humans but it doesn't have to be.) I have drafted an experiment procedure that could potentially deepen our understanding, but I want to find out what already know as a collective. Thank you for your time!

Hi. Does skin and muscular cells do mitosis? If so, why they stem cells? Why heart muscles cant regenerate?

Hi Everyone, I am looking for a relatively large protein (more than 100 kDa) that has known stable conformations. Changes in conformation should be switchable chemically or using light for example. Basically something similar to the photo-active yellow protein but 10 times bigger. Any suggestions? Cheers

Hi. I want to ask, why in anaerobic conditions piruvate is converting to lactate or alchol? Where oxygen is used in aerobic conditions? What it do?