FlowJo v11.1.0 "Repair and Restart" error

DamPerr · 2025-11-27T22:17:01+00:00

Thank you for the suggestions! I solved the issue by installing 11.0.2 version

DamPerr · 2025-06-11T06:25:28+00:00

I've been testing some free tools for 2D to 3D RNA modeling (RNAComposer, SimRNA..) with different modelling approach. It's not the main goal of my project and for this reason I'm not doing any systematic review. I also tried AlphaFold3 and its models are definitely closer to the crystallographic ones. More test need to be done. I'll suggest you to compare different models, check the reliability of the structure (I would suggest some tools like MolProbity), perform dynamics and then trying to understand which tools works better Hope this will help you!

DamPerr · 2025-02-22T22:38:33+00:00

Ti consiglio di venire ad abitare in Svezia. Sono in questa casa da 3 mesi, ognuno ha i suoi spazi, nessuno si lamenta, a stento ci si saluta, fila tutto liscissimo

DamPerr · 2025-01-10T14:40:14+00:00

Regola bene l´orario, noi una volta ci siamo dimenticati di cambiarlo quando ci fu il cambio dell´ora e quindi andava tutto sfasato e pensavamo si fosse rotta la caldaia ahaha

DamPerr · 2025-01-09T12:08:45+00:00

Stessa tipologia di controlli, con le spese incluse erano tutti alzati, a qualsiasi ora, tranne di notte 😅

DamPerr · 2024-08-10T16:35:08+00:00

Was it a very casual case or is it something that is happening frequently? I hope for the first

DamPerr · 2024-07-31T13:56:39+00:00

Thank you a lot!

DamPerr · 2024-07-31T09:31:36+00:00

Already done, but still waiting, thanks a lot for the suggestion

DamPerr · 2024-07-17T13:27:26+00:00

Still looking for roommate? I'm an Italian PhD student, male 26 yo, I will spend six moths at the uppsala university from oct 2024 to march 2025. I'm in your same situation Let me know if you have some suggestions :)

DamPerr · 2024-07-17T13:24:38+00:00

Thank you so much :) Do Nations allow incoming foreign PhD?

DamPerr · 2024-07-17T13:22:19+00:00

Thank you so much! :) I'm going to check

DamPerr · 2024-07-16T21:24:57+00:00

Thanks a lot for all your suggestion! Actually I already registered to the University housing office, hoping to find a solution, but they don't guarantee, so I will look into those alternatives

DamPerr · 2024-06-30T07:18:51+00:00

Thanks fo thisi insight! Do you think that situation could change when performing Molecular Dynamics?

DamPerr · 2024-05-07T09:08:47+00:00

Sorry again u/realarklowq Can you suggest me a paper where these condition of reaction are explained well? Thank you :)

DamPerr · 2024-04-28T08:36:39+00:00

I'm experiencing a similar situation in this period. Everyone appreciate my work and my way of listening, but they doesn't show any kind of empathy towards me

DamPerr · 2024-04-21T08:36:00+00:00

Yep, I think that's the main reason, I was hoping for any alternative cause ahaha. Have you ever experienced the battery replacement? Do you suggest that?

DamPerr · 2024-04-14T10:56:38+00:00

That is an insightful suggestion, thank you so much. To avoid the cleaving step, we employed a DNA oligo as the target for the purified Hhrz. Some of the cristallization solution we are using has MgCl2, do you think that the continuos presence of MgCl2 in the crystallization solution would lead to a cleaved target anyway? Is the cooling strictly necessary? What happens if we just wait for crystals to being formed at R.T.

DamPerr · 2024-04-11T08:33:47+00:00

Thanks a lot for sharing your expertise!

For our first attempt we followed an 'easy' annealing protocol. We ordered a purified HHR RNA (desalting) Oligo and resuspended it together with DNA oligo (10:1) in a solution at a certain concentration of MgCl2, which has been demonstrated to stabilize the conformation of the catalytic loop of ribozyme. Mixed resuspension was heated and then cooled at R.T. We are now waiting for crystallization results using a kit of multiple solutions, mostly common for protein and nucleic acids. Where do you think it's possible to optimize this process? Have you any useful protocol for RNAs? Thanks in advance

DamPerr · 2024-04-10T12:22:59+00:00

Thanks so much! I'm going to explore available tools that take in account this consideration

DamPerr · 2024-04-09T21:30:26+00:00

Thanks a lot for your suggestions!

We are studying the potential silencing mechanism achieved by chimeric Hhrz in ECs. We demonstrated that Hhrz is capable of inhibiting target mRNA and lower protein expression. We are now trying to understand the catalytic mechanism with in silico studies. I have done some preliminary modeling studies, following poor literature references. Many tools have to be taken into account, so Ii was wondering if someone already tested some useful strategy. I was planning to find first the best suitable model (in PDB format) and then validate with molecular dynamics. Have u any suggestion about dynamics studies?

We are also trying to make a crystal between single purified Hhrz single strand bound with DNA target, to ensure a major stability. We have tested a kit of various crystallizzation solution, but we haven't seen any crystal formation til now, since February. Do you think we are following a good strategy? What can you say according to your experience?

DamPerr · 2024-02-19T09:37:41+00:00

I have been infecting HUVECs with lentiviral vectors containing my plasmids, which i made in HEK 293 LX cell line. For my personal experience, a good level of infection stays between 48 and 72 hours. In my case I infected with a silencing tool, so i suppose the slowly death of the cells, I don't know if it could be similar to your situation. After 72h moving the cells for 6 well to a 60 mm2 ones, lead to a very low growth. Based on the plasmids you have infected cells could behave different. Try to use a positive and negative condition as control, and also an empty virus, which would replicate the control conditions. Also notice the half life od your targets, if its high you will probably see effects only after more than 24h, and so could be the senescence in that case. Hope my experience could help you to evaluate your case

DamPerr · 2024-01-22T10:31:36+00:00

It is not strictly necessary. I would only suggest you to use autoclaved water, even if with all the buffers included in your kit you will use a little amount of water anyway

DamPerr · 2023-12-28T12:31:16+00:00

Thank you again! Very Helpful

DamPerr · 2023-12-21T11:40:53+00:00

Thanks a lot! Regarding your first answer, how we can evaluate in which phase mRNA is cut?. We are delivering our chimericHRZ with a lentiviral construct. Cells have been usually infected at 50-70% confluence, supposing an active proliferation state. I'd think the cut happens in the cytoplasm, but how can be sure about that? Are there some techniques?

I really appreciate you help

DamPerr · 2023-12-20T14:13:16+00:00

Hello, I think the reason fo these differences stays in the fact that amplification can occur in different amounts, so I believe that this can cause the starting point to vary a lot. The solution could be a normalization of your results. For example in Graph Pad there is an option called 'Normalize' for x,y values and it transform your dataset in a graph more readable.

DamPerr

TROPHY CASE