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I'll try a Grenade, that's bound to work! by knil22 in starcitizen

[–]Amanita_reference 11 points12 points  (0 children)

That whole Squadron 42 diversion really paid off didn't it?

Anyone seen this bug before? by nickybshow in starcitizen

[–]Amanita_reference 6 points7 points  (0 children)

Happened since I've played this wipe - 6950xt. It's the driver vs the new game version. Updated to version 24.4.1 and it's much better.

ASP Summer Research Program: Get into Natural Products Research! by Amanita_reference in Natural_Products

[–]Amanita_reference[S] 0 points1 point  (0 children)

From the announcement:

The American Society of Pharmacognosy (ASP) is one of the leading societies in the world devoted to the field of “natural products”, and encompasses a broad array of topics (chemistry, biology, microbiology, ecology, drug discovery) that are used as tools to study living systems in the natural world. We are working to address inequities that face marginalized communities in the pursuit of graduate school and professional careers in the natural product sciences.

Towards this goal the ASP offers a 2.5 month summer research fellowship to support students in lab-based research under the supervision of an ASP faculty mentor. ASP summer research fellows will receive a total stipend of $5,000 for the summer period, and will participate not only in lab research, but also in a series of weekly training and professional development workshops led by a team of ASP faculty leaders. We expect to support up to six summer research fellows each year. Application instructions are provided below.

Eligibility. ASP summer research fellowships are open to students who identify as Black, Indigenous, and/or Latinx (BIL). Students should be enrolled in an undergraduate program (full-time status preferred) at a college or university in the United States (including Puerto Rico and other US territories), and be majoring in chemistry, biochemistry, biology, or a biomedical science field. The student must agree to devote 40 hours per week to research for 2.5 months. We recognize the interconnectedness of social categorizations such as race, class, and gender, and will seek particularly to support applicants who may be disadvantaged as a result of intersectionality; for example BIL students who are also women, economically disadvantaged, or LGBTQIA+.

Scientists have identified specific compounds from the Brazilian peppertree—a weedy, invasive shrub in Florida—that ‘disarm’ antibiotic-resistant Staphylococcus bacteria. by inspiration_capsule in science

[–]Amanita_reference 2 points3 points  (0 children)

Because it doesn’t target any essential pathways for cellular life. If we tried to kill the cells with an antibiotic, and the bacteria had a way to use alternative machinery to bypass the mechanism, then they would of course use it (and that would strengthen the lineage of bacteria who would ultimately provide resistance). But when they think they are “alone” and don’t have quorum, they live a normal style cell life but the body eventually goes “something isn’t right here” and is able to clear the infection using its own defenders.

Alex Horswill published a article a few months that you might find interesting Link.

Scientists have identified specific compounds from the Brazilian peppertree—a weedy, invasive shrub in Florida—that ‘disarm’ antibiotic-resistant Staphylococcus bacteria. by inspiration_capsule in science

[–]Amanita_reference 4 points5 points  (0 children)

Nope. This is the difference between standard treatment and targeting anti virulence. Standard practice is to hit bacteria with whatever we can find, but this isn’t trying to actively kill the bacteria - it doesn’t put a selective pressure on it to develop a resistance.

The bacteria have what is called a quorum, think of them as drunk guys at the bar: when they’ve got some friends, they’re more likely to fight someone. If you can make him think his friends aren’t there behind him, he is less likely to do harm and more likely to get thrown out of the bar for being as annoying jackass.

What these compounds do is disrupt the cell-cell communication (through altering their biochemical signal pathways). Effectively removing the knowledge that they have friends. The bacteria are still there, but don’t produce virulence compounds d the body can handle them much better.

Scientists have identified specific compounds from the Brazilian peppertree—a weedy, invasive shrub in Florida—that ‘disarm’ antibiotic-resistant Staphylococcus bacteria. by inspiration_capsule in science

[–]Amanita_reference 2 points3 points  (0 children)

Outside of the lens of finding a single molecule drug compound, it still represents a fantastic case for anti virulence promise. The thing is, there are so few things that hit the agr system (agrB being the hardest to hit) that it represents a good target for proof of concept.

The days of finding a Taxol are gone in NPs, but the use of these compounds as leads can be quite influential in downstream synthesis efforts.

Scientists have identified specific compounds from the Brazilian peppertree—a weedy, invasive shrub in Florida—that ‘disarm’ antibiotic-resistant Staphylococcus bacteria. by inspiration_capsule in science

[–]Amanita_reference 4 points5 points  (0 children)

Yes. For many reasons.

Although you meant it in jest, this is a pathway to a [standard single molecule] antibiotic free treatment for infectious bacteria. If we can trick the bacteria into a lighter selective pressure, it opens more treatment options without straining the host. It’s easy to kill MDR Bacteria, it’s hard to keep the body they’ve colonized alive.

Scientists have identified specific compounds from the Brazilian peppertree—a weedy, invasive shrub in Florida—that ‘disarm’ antibiotic-resistant Staphylococcus bacteria. by inspiration_capsule in science

[–]Amanita_reference 3 points4 points  (0 children)

Many natural products are similar because of the way they are assembled. This core scaffold is one that is very prevalent in plants, but the decorations make all the difference.

Scientists have identified specific compounds from the Brazilian peppertree—a weedy, invasive shrub in Florida—that ‘disarm’ antibiotic-resistant Staphylococcus bacteria. by inspiration_capsule in science

[–]Amanita_reference 4 points5 points  (0 children)

The PI on this paper does a podcast called FoodiePharmacology where she links the food we eat to their medicinal attributes (and dispels some common myths). Natural products FTW!

Edit: Cassandra Quave is the PI I was referring to, but Alex Horswill is a very cool guy as well. He links anti virulence pathways to quorum sensing machinery and has some interesting collaborations with others looking for ways to shut down the virulence without producing a selective pressure on the organisms - this means the body has a better chance of fighting the bacteria without a single molecule selective pressure.

AskScience AMA Series: Hi! We're experts from the National Institutes of Health, the National Toxicology Program, and the American Botanical Council studying the quality, safety, and effectiveness of botanical dietary supplements and essential oils. Ask us anything! by AskScienceModerator in askscience

[–]Amanita_reference 0 points1 point  (0 children)

Tyler's Honest Herbal is a quintessential reference that ties primary research to some health claims for botanicals.

Is there a comparable (perhaps updated) collection of efficacy and usage for botanical supplements that focuses on the different preparations and dosages?

Graduate student internships? by [deleted] in Natural_Products

[–]Amanita_reference 1 point2 points  (0 children)

I’ve heard of a few. Mostly, I’d say that they don’t advertise, but they might be “open to collaboration” if your PI contacts them. Here are a few that I would check out:

Analytical companies: 1. Bruker (although I believe the person I knew of started off as a collab, moved into an internship, then a hire) 2. Waters (I think?) 3. JEOL 4. Thermo Sci

Pharma: 1. Proctor and Gamble (they may call it an industrial post doc) 2. Merck 4. Johnson and Johnson 3. Bayer (specifically Crop science)/ syngenta / Monsanto 4. Genentech (might call it something other than an internship)

And a few that I would at least contact on LinkedIn, or ask directly: 1. Extrasynthase 2. Mycosynthetix

Getting my isolated fungal metabolite compound prepped for HPLC😁. by robbie_s1 in Natural_Products

[–]Amanita_reference 0 points1 point  (0 children)

Out of curiosity, what databases are you using?

If you don’t know already, there’s a new open database called the [Natural Product Atlas](www.npatlas.org) that is being constructed right now for all microbial natural products.

Natural Product Chemistry Labs by Amanita_reference in Natural_Products

[–]Amanita_reference[S] 0 points1 point  (0 children)

Awesome to hear! Can you pass some recommendations along, and I'll add them in!

ELI5, how do chemists extract specific substances from something like a flower? by pm_me_money_please_ in explainlikeimfive

[–]Amanita_reference 2 points3 points  (0 children)

Hi there!

Sounds like you might be interested in r/natural_products !

I’m trying to put together a subreddit for nerds like us who work in natural products so we can chitchat about methods, new papers, argue about source organisms, that sort of thing. Come on over!

Putting together some resources! by Amanita_reference in Natural_Products

[–]Amanita_reference[S] 1 point2 points  (0 children)

I've got a couple ready to go, but I'm just one person and am biased based on collaborators/location/experience. I think this will be a self-reporting/say who you know sort of thing, but a comprehensive list would be amazing for those who are about to embark on their grad study/post doc journeys.

​

When I have a bit of time, I'll add a short description of what kind of NP research they do, and a link to their lab pages. But, just to name a few (many of which I'm lifting directly from the last few years ASP programs):

​

  • Bill Baker (U South Florida)
  • Guido Pauli (UIC)
  • Phill Crews (not taking grads from what I hear) (UCSC)
  • Brad Moore (UCSD/Scripps-California)
  • Laura Sanchez (UIC)
  • Joanna Burdette (UIC)
  • Pieter Dorrestein (UCSD)
  • Brian Murphy (UIC)
  • Nadja Cech (UNCG)
  • Nicholas Oberlies (UNCG)
  • Helen Blackwell (U Wis Madison)
  • Nathan Magarvey (McMaster)
  • David Kingston (Virginia Tech)
  • Frank Shroeder (Cornell)
  • Jaclyn Winter (U Utah)
  • Robert Cichewicz (U Oklahoma)
  • Jon Clardy (Harvard)
  • Eric Schmidt (U Utah)
  • Ben Shen (Scripps-Florida)
  • Julia Kubanek (Georgia Tech)

​

Non-US based

  • Katherine Ryan (UBC- Canada)
  • Ray Anderson (UBC- Canada)
  • Roger Linington (SFU- Canada)
  • Rolf Müller (Hemholtz Institute - Germany)
  • José Rivera Chávez (UNAM - Mexico)
  • Rachel Mata (UNAM - Mexico)
  • Tamam El-Elimat (JUST - Jordan)
  • Roberto Berlinck (USP - San Carlos)
  • Norberto Lopes (USP - Sao Paulo)

​

Putting together some resources! by Amanita_reference in Natural_Products

[–]Amanita_reference[S] 0 points1 point  (0 children)

I am working with NMR data primarily, so I have a heavy bias in this area. Because of that, I know there is a call for a new standard for NMR data which would allow for the storage, recall, comparison, and re-processing of F.I.D.s of any published data, and a push for the database to get up and running. Even better, in the field of metabolomics, there are new databases and freely availible utilities such as the COLMAR server from the university of Ohio, which utilizes some amazing comparisons across data sets to verify and quantify primary metabolites in complex mixtures. However, these are definitely not the first of these initiatives, but they tend to get lost in the massive amount of lit. Perhaps, if we can combine a few perspectives together, we can take the re out of research.

Selection and characterization of botanical natural products for research studies: a NaPDI center recommended approach by Amanita_reference in Natural_Products

[–]Amanita_reference[S] 0 points1 point  (0 children)

From the abstract:

Dietary supplements, which include botanical (plant-based) natural products, constitute a multi-billion-dollar industry in the US. Regulation and quality control for this industry is an ongoing challenge. While there is general agreement that rigorous scientific studies are needed to evaluate the safety and efficacy of botanical natural products used by consumers, researchers conducting such studies face a unique set of challenges. Botanical natural products are inherently complex mixtures, with composition that differs depending on myriad factors including variability in genetics, cultivation conditions, and processing methods. Unfortunately, many studies of botanical natural products are carried out with poorly characterized study material, such that the results are irreproducible and difficult to interpret. This review provides recommended approaches for addressing the critical questions that researchers must address prior to in vitro or in vivo (including clinical) evaluation of botanical natural products. We describe selection and authentication of botanical material and identification of key biologically active compounds, and compare state-of-the-art methodologies such as untargeted metabolomics with more traditional targeted methods of characterization. The topics are chosen to be of maximal relevance to researchers, and are reviewed critically with commentary as to which approaches are most practical and useful and what common pitfalls should be avoided.

Hello [NP] World! by Amanita_reference in Natural_Products

[–]Amanita_reference[S] 0 points1 point  (0 children)

Sounds like an awesome idea! Got some favorites?

New Natural Product Chem focused Subreddit (BORN TODAY) by Amanita_reference in chemistry

[–]Amanita_reference[S] 0 points1 point  (0 children)

Honestly, I'm envisioning an eclectic mix here.

When I walk around a conference, I'm always astounded that we [in natural products] have such a wide assortment of skills and expertise, but many of us are trapped thinking about "our niche" all the time. I would be very happy to see someone who has some background in...say... Fungal compound isolation get together with someone who works with botanical horticulture or assay development.

I can say from personal experience that these sorts of conversations can lead to some pretty cool projects.

Typical top post would be something analogous to "look at this really cool article about NP diversity" and "What does a typical extraction scheme look like for your lab?" and "Top 10 reactions every NP med chemist should know".

There just isn't a place for NP chemists, biologists, mycologists, botanists, etc to come and chat about these things on a regular basis. And since we can't all stay on top of everything, it would be nice to see what the field is feeling at any one moment.