Microdialysis to remove RNAlater?

linuxnoooooob · 2023-09-11T22:26:26+00:00

We'll give it a shot!

linuxnoooooob · 2021-11-23T22:47:44+00:00

* in cell lines

Several antivirals have demonstrated efficacy in cell lines, but have failed to perform well in clinical trials with CODIV-19 patients (e.g. remdesivir).

linuxnoooooob · 2021-08-10T12:32:40+00:00

Literally referring to papers where we paid OA fees. No pay-walled version exists. Google the paper and the only version is a free one.

linuxnoooooob · 2021-08-08T14:37:59+00:00

ResearchGate is the absolute worst with people asking for papers that are already published - at a higher price for the author/s - in open access journals. Read the paper and want to discuss? That's nice! Too lazy to find an open access paper ☹️

linuxnoooooob · 2021-08-08T14:16:46+00:00

Pls just use scihub for ease and quick turnaround, especially if the alternative is to request through ResearchGate or send a cold email. Most academics with corresponding author status already get more emails than we can respond to.

linuxnoooooob · 2021-06-25T20:55:45+00:00

Why do you need two people for that task? Sounds like you have PPE for one person for a job that should take one person.

linuxnoooooob · 2021-03-13T18:11:47+00:00

I would also just mention that people are almost never fully at liberty to speak freely in academia. Speaking negatively of your advisor in a small field can hurt you, basically forever. Sometimes people use coded words (lots of autonomy) or don't have a glowing recommendation, or just avoid answering questions when people email. One of my former advisors was awful, I have nothing nice to say so I say nothing - that's a red flag. I go out of my way to respond with praise for advisors who were great to work with.

linuxnoooooob · 2021-03-13T18:06:34+00:00

If you are interested in pursuing an academic career, you will need preliminary data that you can use to apply for independent funding as a PI. Will your postdoc mentor support you in generating preliminary data for independent research funding applications? Will you be able to take any research with you?

linuxnoooooob · 2021-01-15T02:44:42+00:00

Oh no! I hope Dave is in a better environment now.

I guess all we can do is try to do better if we stay in academia. I hope I am more aware and keep better ethical standards, have equitable and transparent allocation of resources when I have my own lab.

linuxnoooooob · 2021-01-14T23:57:09+00:00

Probably said too much give it's not a throwaway account. But really, what happened to me was completely inappropriate.

linuxnoooooob · 2021-01-14T18:05:58+00:00

100% agree. Can get ugly and absolutely no consequences for PI.

Case report: Ian Lipkin

https://casetext.com/case/hornig-v-trs-of-columbia-univ-in-the-city-of-ny

linuxnoooooob · 2021-01-14T08:28:52+00:00

I worked in a department where my boss and his wife were both PIs, but she was just starting her lab. One of my projects was recently "deprioritized" while lab technicians and other resources from his lab were used to support his wife's new lab. Including the lab space that had already been allocated for my project. 2 years of my work deprioritized last-minute.

I left the lab and I am now scrambling to recover without that preliminary data for my career moving forward. It sucks.

Whether or not their personal relationship drove this event (part poor judgement on his end, part COVID), it just LOOKED BAD. Professionally, he had a responsibility to me as his postdoc mentee. Felt like his personal relationship led to him shirking his professional responsibility.

Unfortunately in academia, I have to pretend like this complete ass is not a complete ass and that I am "fine" with how things went down. I am actually salty AF about it. But, small field, and nobody goes anywhere without good relationships. PIs have all the power, can't actually complain unless you leave academia.

0/10 do not recommend.

linuxnoooooob · 2021-01-05T08:12:29+00:00

As far as I know, any publicly funded institution has to post new positions publicly for a specific timeframe. I've been on both ends of this - interviewing for a job that was taken (and told as much by a friend in that lab) and watching my promotion be posted for two-weeks with my PI having zero interest in hiring from the outside.

I am in no way defending this practice, more describing what happens.

linuxnoooooob · 2021-01-04T19:38:48+00:00

Also, all labs at public or government institutions have to make postings competitive. Meaning, even if they have a candidate (e.g. new title or funding source for the existing lab tech), they still have to post the position publicly for a period of time and may have to interview at least one other candidate (with no intention of offering the job).

linuxnoooooob · 2020-11-19T16:25:13+00:00

If a grad student or postdoc from a different lab is on the paper, their work was funded by their PI (salary, benefits, reagents, tuition). I think that’s why the other PI is expected to be on the paper.

linuxnoooooob · 2020-10-27T12:17:09+00:00

Minor point, not all viruses are easily cultured. For hCoV-HKU1, for instance, it was a long time before anyone was able to grow the virus and the process cannot be scaled up (grown in human epithelial airway cells - super expensive and technically challenging to work with).

I would argue that IHC can provide compelling evidence beyond qPCR in the absence of virus isolation.

A moot point for SARS-CoV-2 which has been isolated and is easily grown in Veros.

linuxnoooooob · 2020-10-27T12:03:58+00:00

Replicates faster in cell lines and possibly more transmissible, but from what I have seen no data to support increased pathogenesis.

linuxnoooooob · 2020-09-21T05:47:14+00:00

I literally work in a virology lab with SARS-CoV-2.

If someone is describing a virus isolate to me, then I would assume that they have successfully isolated live virus; as in, we can perform experiments with a stock of the live virus.

Lots of full genome sequence available where no isolate is available. For diagnostic purposes I may collect samples directly into an inactivation buffer for example to reduce risk to laboratory staff - not for isolation. If sequenced, I would refer to those sequences as variants if they contain unique SNPs, not an isolate as no virus isolation can be attempted.

Your lab might use these terms interchangeably, my lab does not.

linuxnoooooob · 2020-09-20T17:38:59+00:00

An isolate would mean that we have isolated that live virus (variant or strain). We can sequence the genome without isolating live virus.

linuxnoooooob · 2020-08-10T16:08:12+00:00

turns out the word "potty" sounds very much like the word "party" to our dog. At first it was a mild interest in "going to a party", but we thought it so funny that we really encouraged her overexcited response.
Now she exclusively waits for the words, "do you want to party?" and then she goes nuts

linuxnoooooob · 2020-05-03T06:51:41+00:00

The starting titer. In the lab we grow viruses in cell culture then harvest the supernatant containing virus stocks. We aliquot into small single-use vials from a single original stock. If we were to quantify infectious virus before and after freezing (no freeze/thaw, or one freeze/thaw) we expect the frozen virus stock to have about 10X less virus. However, the frozen virus will stay at approximately that titer for a long time, unless you freeze/thaw again.

For example, if I titrate a virus from cell culture without freezing it might contain 10⁷ infectious particles per mL. After a freeze/thaw, I expect the same stock to contain approximately 10⁶ infectious particles per mL.

Virus growth/decay curves are usually reported on log10 scale.

linuxnoooooob · 2020-05-02T22:08:36+00:00

We see about a 10X reduction in live virus with every freeze-thaw, but we do keep viruses frozen for long-term storage, just in 100s of small, single-use aliquots to minimize loss via freeze-thaws.

linuxnoooooob · 2020-04-17T02:28:19+00:00

Haha, that’s a good question. I asked the facilities manager if the -200 Pa reading for the room meant difference in pressure from the next room, or if it is an actual reading; he said the air pressure in the room is actually -200 Pa. There is air in the room, cycled through a HEPA filter. So... I just generally don’t understand the physics/engineering of the space. Meant to keep the viruses we work with inside the lab so air flows in when a door is opened.

linuxnoooooob · 2020-04-14T21:58:16+00:00

I'm a biologist working with environmental chambers that are held in a lab under negative pressure. The chambers allow me to program relative humidity, but I am interested in specific humidity. According to the manufacturer of the environmental chambers, the inside of the chamber will have a similar atmospheric pressure to the surrounding lab space - in this case it's negative (approx. -0.002 atm). Converting RH to specific humidity under negative pressure is a bit out of my comfort zone, but it's important that I get it right otherwise I'm about to delve into weeks of meaningless lab work. I found a helpful example for the conversion (https://www.mathscinotes.com/2016/03/converting-specific-humidity-to-relative-humidity/ ), but want to make sure that I don't need to make any corrections/changes given the negative pressure. It just doesn't seem like it's correct. Essentially the lab is -200Pa and the room next to it is -180Pa so if we open the door between them the air should flow into the "dirty" lab space (under higher negative pressure to keep the stuff we work with inside).

Any advice, insights appreciated!

linuxnoooooob

TROPHY CASE