MICROBE 2018 recap - Astrobiology: Linking phylogeny, physiology and the rock record

Alright...admittedly the full title of this one was a bit scary for me as the only words, or more accurately, word, I really felt I had a grasp on was 'phylogeny' - yes that was it, 17 words in this title and I was like "I know what a phylogeny is":

Energy controlled distribution of isotopes in biocatalytic systems: A means of linking phylogeny, physiology and the rock record.

But I powered through.

Shawn McGlynn is from the Tokyo Institute of Technology, Earth-Life Science Institute (ESLI) his research interests include - microbial interactions, metalloproteins, early life and it's emergence, stable isotope techniques and microbial ecology. 

To learn more about his research and love of of Japanese hot springs check out his Research Story: Bridging disciplines and continents and check out his google scholar profile.

So we start with the question of:

"How do we elucidate the history of biological catalysis with the material record (sulfur isotopes)?"

MICROBE 2018 recap - Astrobiology: Early Evolution of Photosynthetic Organisms

Dr. Patricia Sanchez-Baracaldo is from the School of Geographical Sciences at the University Bristol. Rather than paraphrase what is already so nicely stated on her of website, I'll just post it here:

"My research aims to understand how cyanobacteria (also known as blue-green algae) have contributed to global nutrient cycles (e.g., nitrogen, carbon, oxygen) through geological time. The timing of diversification of some marine cyanobacteria lineages suggests that cyanobacteria have played a key role in regulating the global environment and past climatic events. By studying cyanobacteria evolution my lab aims to understand how these organisms contributed to making our planet increasingly habitable during the early Earth."

Highlights from the talk:

• Nitrogen is underappreciated in it's role in making our planet habitable.

Check out Patricia's work from 2014 and 2015 which were featured in the presentation:

1. A neoproterozoic transition in the marine nitrogen cycle...
2. Origin of marine planktonic cyanobacteria...

MICROBE 2018 recap - Astrobiology: The History of the World, A Microbial Perspective

So I made it on time to this session...

Before I launch into the glory of astro-micro-biology - I was amused by the starting comments of the session. ASM hands out guidelines for sessions that include the suggestion that you should present learning objectives for the session...so we know what we are getting ourselves into. This was the only session where I saw this presented. It was actually kind of neat; high school student, college student, graduate student, seasoned full professor-die-hard-academic... we all benefit from organizing our thoughts and goals. So kudos to the Astrobiology session for doing this! And kudos to ASM for their app on this meeting - it made tracking and zooming to sessions as well as 'rating' sessions and talks very easy.

Jennifer B. Glass is an Assistant Professor at Georgia Tech with a primary research interest in Biogeochemistry. If we shamelessly stalk her on google we find her interests include: (i) anaerobic oxidation of methane, (ii) greenhouse gas cycling - focus methane/nitrous oxide, (iii) biogeochemical cycling (iv) marine microbiology as it pertains to anaerobic metabolisms (v) integrating omic and geochemical datasets and (vi) coevolution of microbial metabolisms and ocean chemistry over Earth's history - whew!

She's been a NASA Astrobiology Postdoc, PEO Scholar and NSF Graduate Research Fellow and if you'd like to take a look at her lab and research check out her website and google scholar profile!

My favorite part of her lab page -

Failure required, tears optional, please don't lick the science! 

MICROBE 2018 recap - What's New in the Tree of Life?

So I started the meeting in great form...late for the the 'Meet the Experts' Session! DOH! But I did get to hear quite a bit from Barny Whitman and Brian Hedland about the state of taxonomy today.

Notable tidbits:

• We all know that funding is scarce in this administration (insert ugly cry face) but it looks like studies trying to tease apart taxonomy are particularly underfunded despite the interest (and huge debate!) in the topic - about 2% funding for taxonomy.

The huge debate you ask? Yes - I dare you to walk into a bar of microbiologists and yell "OTUs forever, species SUCK!" or "There are no species!!!!" - My guess is you'll start running very quickly from the mob with pitchforks and lighted torches soon.

MICROBE 2018 recap - Keynote: Manu Prakash, "How you are labelled is not where you belong."

For the Keynote at the opening of ASM we got to hear from Manu Prakash a Scientist from Stanford and recipient of the 2016 MacArthur Fellowship with a passion for "Curiosity Driven Science"

I think this tweet from Ana Catarina summed things up well:

How you are labelled is not where you belong - great discussion about multidisciplinarity in Science with @PrakashLab #ASMicrobe

— AnaCatarina da Silva (@7ASilva) June 8, 2018

As well as this one from Jeffrey Maloy:

.@manuprakash - if you care about global health, you have to care about science education. #ASMicrobe

— Jeffrey Maloy (@JeffreyMaloy) June 7, 2018

One of the most notable projects Manu has worked on is the Foldscope bringing microscopy to regions of the world without the need for expensive equipment.

The foldscope at work! @manuprakash points out that these images are unposed - this tool is allowing people around the world to experience that Aha! Moment of science firsthand! #ASMicrobe pic.twitter.com/0QvGV4WCJB

— Jeffrey Maloy (@JeffreyMaloy) June 7, 2018

His talk was inspiring. I have a two year old and you better bet my child will be getting a foldscope!

Foldscope Instruments

If you want more information and to learn about all the neat projects Dr. Prakash has going check out his lab website!

The Prakash Lab

ASM MICROBE 2018

It's that time again, when I go off to learn something new, rub shoulders with colleagues and students and insist that happy hour is a necessary part of the scientific method...

It's been two years since my last posting - those that follow this blog probably aren't surprised. As per usual I only post when I have something to share of intellectual relevance and being a stay at home mom who worked contract intermittently isn't particularly relevant...unless you are counting the times I threatened to swab my daughter to find out what organism is contributing to her foul mood.

But I have reentered the field full-time as of about a year ago and here I am back at a meeting I haven't attended in 9 years. Having trained on the environmental microbiology side ASM was my meeting during graduate school, when I jumped ship to dengue virus ecology and evolution as a post doc my meeting changed to the American Society of Tropical Medicine and Hygiene (ASTMH) for 5 years. Now I have returned to my roots and am back with an environmental focus in my research still continuing to search for my niche...and that illusive tenure track position, or any permanent position really.

I am currently a research assistant professor at St. Cloud State University working in metagenomics and metatranscriptomics of anaerobic digester systems in an attempt to reconstruct pathways and microbial consortia associated with high biogas output. The funding is an energy grant and their interest is the conversion of biogas to electricity. I am still heavily bioinformatics however have delved back into the wet lab as we set up projects and train undergrads and Master's students.

I have some of my own ongoing somewhat funded work in antimicrobial resistance marker detection/quantification and decay. I also have several in silico projects that pile up and get disseminated out as I have time or I find a student interested in the work. I still collaborate with my PhD mentor finishing up some work related to my PhD and I continue to collaborate on dengue work or any other viral work as the need arises with my collaborators at WRAIR. Keeping myself relevant as I can until I land somewhere permanent and can define my focus as I see fit...or, you know, as the grants I get see fit *face palm*.

Finally, in keeping with being the traveling salesman of academic wares I teach within the Minnesota State System as requested at community colleges or any of the universities. I taught Anatomy and Physiology II for a semester at Inver Hills Community College and Advanced DNA Techniques at St. Cloud State. So I take teaching jobs as they come up. I love teaching so while I don't have a permanent home yet, I am quite content with my current activities.

Alright - enough about me - let's get to this years ASM Microbe 2018 meeting. As with large meetings, where you can't attend everything - you will be at the mercy of what I particularly find interesting, but hopefully you'll find something you like within my posts over the week-plus that I am posting on the meeting.

Best,
DrM

New Ventures: Babies, Stats and Python

When I created this blog, I'd set out to have something online where I could dispense what I was learning and I didn't feel the need to post if I didn't think I had something worthwhile to extend to my audience. That's why you are seeing a new post 8 mos after the previous post and the previous post was a newsletter of what I find awesome in the field rather than a written blog post.

Since my last post a lot has changed and I am back after a very long hiatus to have a child, change jobs, move states and attempt to figure out the trajectory of my career from this point on. By way of updates:

• My daughter is almost 11 mos old, awesome, adorable and sleeps through the night - which is great on my sanity. I don't talk personal life on this blog much if at all but if you are the nosy type - head over to my website www.melaniemelendrez.com. This blog is a professional journey, the latter is a personal journey and is updated even less than this one - just saying. I'm pretty busy. Last post on that site was January 2016, same as this one.
• My family has moved to accommodate a job my husband got. I mean seriously, why not? The man moved countries and states for me for nearly 6 years, it was only fair. And while I am still in adjustment mode it was a good choice for both of us.
• I still work remotely for the research institute in Maryland doing data analysis and consulting. It's really a great set up for me right now. Gives me time with my daughter. At least after the adjustment period of having NO WHERE to go on a Monday morning and attempting to be productive at home where household things that need to get done make me twitch as I try to focus and do analysis on days tiny minion goes to daycarae. I think I am getting better *twitch twitch*.
• I am dipping my heels into the academic job market seeing what's out there and developing my philosophies on research and teaching - so real deep soul wrenching stuff. Not really, but reflection is a great practice to have moving forward.

So where do I go from here?

I was looking forward to this 'sort of' break because I knew it would give me a chance to explore my field and how I want my career to play out. If you aren't constantly learning you are falling behind.

"Anyone who stops learning is old, whether at twenty or eighty. Anyone who keeps learning stays young" - Henry Ford

I am determined not to let the gray hairs that are starting to tease me in the mirror get the better of me.

So what does that mean?

I had two main professional goals - to get better at programming (in python), refresh my abilities with stats because I think that last time I seriously did any stats was at Montana State University in 200*-does it matter?! My knowledge is outdated. I also wanted to learn an open source stats program (I've used SPSS and SAS in the past).

Goal 1 - Python programming. I'm not too proud to admit I attempted a formal course around 2013 via EdX administered through MIT...and I failed in fantastic form. I didn't fail the course, I ended up dropping it. At the time (i) I underestimated the challenge level of the course. I liked the challenge but with challenge comes the need to 'meet the challenge' which translates into time! (ii) Time was something I did not have. I was in the middle of building a viral genetics and bioinformatics section at my institute in Maryland which was daunting to say the least especially in light of a million regulations. I made it half way through the course and had to drop as the demands of the job allowed me little time after work to do anything except go home, maybe eat, zone out for a half our then pass out - I'd work runs into the mix when I could. So I conceded defeat determined to conquer the course at a later date; because up til that point I was actually really loving the course. It was (and still is) a well designed online course. I did my epidemiology and biostats certificate completely online, I learn well through an online format. So - now that I find myself with some free time I have re-enrolled in an attempt to actually conquer the course.

So I'm out to start improving my programming from the basics up. If you cannot embrace and learn from defeat you have no business heralding your successes.

Course: https://www.edx.org/course/introduction-computer-science-mitx-6-00-1x-8

Goal 2 - Stats. I actually really like stats despite the heavy math component that can get scary when visions of my high school AP calculus homework start invading my dreams and my stats textbooks. Am I familiar with stats? Yes. Am I a 'pro' with stats? No, but I used to be and I'd like to be again. I'd also like to update my stats programming from the ever so expensive SAS and SPSS to the open source (ie. awesome as hell) R. You can do some beautiful stuff in R.

Oh wait...this is the part where my python programmer/software engineer of a husband serves me divorce papers for not using python pandas/matplotlib and other python visualization tools - doh!

Who says I cannot learn both? Maybe I'll move exclusively to python in the future but for right now in my field R really is the language of choice for data visualization...No! I won't sign those divorce papers. Just kidding, he really is a lovely supportive man who will tolerate my 'hobby' of R.

To this end I could've decided to just do another online course - meh. I think it much more personal and awesome to instead try out a friend/collegue's textbook published in 2014 and I'm really excited about it and that's what you'll be hearing about in the coming blogs on this site - a walk through:

Foundational and Applied Statistics for Biologists Using R by Ken A Aho
Amazon: https://www.amazon.com/Foundational-Applied-Statistics-Biologists-Using/dp/1439873380/

I think I'm the perfect candidate to do a self study on this book and see how it goes. I have stats background and to be frank I really appreciated a sentence in his preface:

"Statistical texts and classes within biology curricular generally ignore or fail to instill foundational concepts...Unfortunately, this problem has been exacerbated by advance in statistical software. These tools do not require any knowledge of foundational principles. However, a poor understanding of the theory underlying the algorithms often leads to misapplication of analyses, misunderstanding of results, and invalid inferences."

How often have I 'preached' about using bioinformatics tools without knowledge to back up why you are using the tool you are using and are you using the best tool (especially in phylogenetics)? Do you even know what a model is? Do you know why you are using that model? You are using Geneious to do WHAT?!! Etc.

Bioinformatics is not about pressing buttons and black boxes. It is not about getting results and taking then with no grains of salt. If you are a researcher I would hope you want to know the fundamentals, what it is doing and what it can tell you when you run your data through it and the caveats associated with it.

I am guilty of pressing buttons in stats, especially of recent - time to back up and practice more of what I preach.

Disclaimer: This will not be a fast process, clocking in at 554 pages, Ken's book is long. But I am looking forward to it. I cannot guarantee every-day postings but I'll get through it! Tune into this blog if you are interested in the journey.

What about the newsletters?

Right - so I spent 3 years running newsletters around my institute via email then started posting some on this blog. I got generally favorable feedback. My newsletters will continue to appear on scoop.it and I encourage you to head there. Though given my goals above I will not be updating them as often as I did before.

Link: http://www.scoop.it/u/mel-melendrez-vallard

Also - Scoop.it is a pay-for service if you want multiple newsletters so I may reduce in the future as readership has been light for over a year now and the service isn't exactly cheap. Just a heads up.

I think that about sums it up.

One final note before I leave you - for those that are in a continual pursuit to improve their abilities in the world of bioinformatics. There are some great reads out there - and here's where I shamelessly plug my bioinformatics justice league - leaders in the field, they will make you think and they will hold you accountable. It makes us all better scientists.

• Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
• An New Online Bioinformatics Curriculum
• Stephen Turner's great list of workshops and training.
• PLoS Biologue: Measuring the success of an online bioinformatics resource
• Todd Harris: It's time to reboot bioinformatics education
• Nick Loman and Mick Watson: So you want to be a computational biologist?
• Greg Caporaso - ya, anything from him: Teaching, Website
• Also refer the number of blogs to the right of this post - all fantastic individuals in the field with a lot of awesome knowledge and opinions to dispense.

For those that read this blog - thanks for your readership, I do hope it's helpful or interesting or both!