This IS ME

At the end of my summer, (just a few weeks ago) I had the privilege to visit Montreal, Canada.  I have wanted (for almost 6 years) to attend the national conference for the science I like to do, microbial ecology! Studying microorganisms can be tedious or overly technical to describe, but the research is awesome and improving our daily lives and resource management at many scales.  While at the conference, I decided to use twitter as a way to convey what was happening at the conference as well as increase my focus for a concise ‘take-away’ from each of the presentations I attended.  My summary of the conference follows with the subject of my tweets (~20 #ISME16 @MicroNYC tweets) in bold text.  As you read (or just scroll down), there are photos of the bits of time spent outside of the conference center.

The ISME conference is the meeting for The International Society for Microbial Ecology, where ~2000 attended from 52 countries!

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The view from the rental apartment, towards new Montreal and the cross on Mount Royale

The week started with a great performance from a local, traditional dance group. So, for us, the audience, some with many years of experience, I had a funny thought about traditional elements of the performance and microbial ecology: Mouth harps & mouth pipetting. The traditional music and dancing of Montreal featured a mouth harp. Mouth pipetting is an old traditional form of collecting or transferring a liquid in a laboratory setting.  Even though this is a rare practice today we still have to remind students that it is not allowed and is particularly dangerous in a microbiology lab.  Now know that microorganisms are all around us playing important parts in our lives a lot of the research is going to the general public (as citizen science) to collect samples from the environment or their bodies, it’s for science!

Many science presentations happened through the week and there were many concurrent sessions! I chose extreme environments (traditionally thought of as not supporting life) as my starting point.  This was because microorganisms in deep-sea hydrothermal vents was a first science crush for me.  There are other extreme environments and I enjoyed two talks about them and their microbes: saline lakes in eastern Europe with Nitrospira bacteria learning to live with the salt as well as the strong influence from pH (Daebeler) then a ‘science rockstar’ presentation about dirt actually being an extreme environment for microorganisms (I’m not so convinced yet, Fierer).  Regardless of calling dirt as extreme, it does host a complex community of microorganisms that is awesome and is even better to study when it is old frozen dirt such as the deep in the tundra (Mackelprang).

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It wasn’t always sunny skies, but it was a beautiful run along the Saint Lawrence River.

One of the challenges of studying microorganisms in the setting of the surrounding environment and plants or animals is that the ideas that organize similar work for plants or animals were developed before we knew about microorganisms (they were just a ‘black box’ in concepts or formulas). Therefore, another set of presentations I went to were focused on making the connection between microorganisms and the early ecology ideas. However, the challenge for any ecologist, is still to think out of the ‘box’ (Curtis) of any existing ideas. An example of big ideas at the small scale, is how the Neutral Theory does not apply to marine microbial communities in many cases (Furhman). When looking for new ideas or applying these old ideas in new ways, often the simplest answer is the best answer, parsimony (Curtis).  This is true when trying to figure out how the power house of our own cells, mitochondria, have their own genome or set of genetic instructions.  If the mitochondria left it up to the nucleus then the materials it needs to run may be delivered to the wrong area in a cell, so their genome is a way for them to make sure they get what they need (instead of the greedy endoplasmic reticulum; Anderson).

Many techniques to understand microorganisms focus on knowing the genes and what genes do. Such as how core genes revealed more about the bacteria and additional genes clarify the role in the environment (Young). The diversity and abundance of antibiotic resistance genes in microorganisms suggests selective roles (pressure from exposure that only allows microorganisms that can resist the pressure to survive) of antibiotics on all microbes (Wright). Sometimes the loss, rather than gain, of some genes can also make bacteria more dangerous to other organisms (Anderson). Antibiotics produced by microorganisms are ‘at the end of the day’ more of a weapon than a form of communicating (Wright). Applying these weapons microorganisms are predators and when preferred prey overlap, the predator that has a variety of preferred prey lessens the impact on the community from another predator that has specific prey (Chantinotas). Then something to think about for microorganism communities is that most (91%) of the world’s best predators, viruses, infect a specific host and 84% live in a specific area (Kyrpides). These dynamics illustrate how microorganisms are highly diverse and scaling models, or formulas that describe all the elements that promote diversity, predict >1 trillion microbial species on earth (Lacey).

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Old Montreal was breath-taking and quiet at night.

To understand more about this potential trillion species sampling technology is improving. Often the traditional method of travel, sailing, can support innovative methods, such as the Tara expedition. This expedition traveled the world and has now contributed to finding 80% of the marine microorganisms we know (in the genome catalog; Bower).  Some of their conclusions are interesting in the context of community ecology – they found that in the plankton network that the neighbors were more important than the neighborhood (environment) and cooperating with them is more important than competing with them (Bower). Additionally, having equipment move through the ocean the same exact way the water is moving keeps the equipment with the same marine bacteria. Then this equipment can regularly sample and learn what the bacteria are doing in their environment (by looking at which genes are being used, transcriptome; Delong).

One important role of bacteria in the environment can be bioremediation.  After the Deep Water Horizon oil spill in the gulf much research has been in progress and completed on the best way to remove the oil.  A common response to oil spills is to apply dispersants to disperse or reduce the visible sheets/globs of oil.  With some ideas that these now smaller particles would be more available to bacteria to breakdown the oil then removing the oil from the environment.  However, there is counter evidence that while the oil is invisible to us it is not gone, the bacteria are not consuming it, which creates a greater risk of our exposure (Joye)While the marine microbes have a minimal natural role of oil bioremediation they are essential for moving nutrients through the system, such as Nitrogen. Though where there is limited oxygen at great depths in the ocean, there are only a few microorganisms that can move the Nitrogen around, which increases their environment or system to be vulnerable to changes in climate (Sachdeva).  In shallower environments, like wetlands, microorganisms have a mixed roll in influencing climate changes. The methane, a ‘greenhouse gas’, produced in wetlands is directly related to the amount and type of microorganisms producing methane (Tinge). In environments with less water, drought or long periods without rain or snow can alter what the microorganisms do in the environment, such as decomposition.  Overall microorganisms are highly resilient and are back to their normal roles after a 1-3 years of change (such as drought; Allison).

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In old Quebec City, is this amazing palace as part of the fort that strategically overlooked the water protecting the territory.

In the theme of scaling up from what microorganisms are to what they are doing there are also the symbioses of microorganisms living with other macro-organisms (plants/animals).  My favorite of these symbioses is the microorganisms that live with corals and sponges. These symbioses, particularly with coral, is so interwoven that the term holobiont is used to describe all the living organisms as a single unit.  The bacteria are essential to the survival of coral and the bacterial community regulates the algal symbiosis (Medina). The genes of the algae (a dinoflagellate, symbiobinium genome) are connected with physiological or the way it lives affects its symbiosis with the coral (Aranda-Lastra). This complicated, intimate symbiosis of macro- and microorganisms regulating each other while supporting the growth of each other is why the term holobiont is necessary. Then not all bacteria are welcome to live with corals or sponges, especially for sponges they are food.  Therefore, there are bacteria that create proteins, which sponge cells produce, to fool the sponge into ignoring or not eating them (Thomas).

Thank you for reading to the end.  I hope there was some science points that were a fun ‘take-away’ for you too.

 

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In the south of Quebec, there are a few vineyards with hardy grape varieties.  The Vignoble d’Orford winery was a nice detour on the way back to NYC.

 

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The Upward Trend

What creates a trend? Is it just one more event behaving like the previous? When should a series of events be credited as a positive trend?  Well I have a few exciting positive trends lately…

I am starting a metagenome project in the nearby estuary through a summer fellowship with the Science and Resiliency Institute at Jamaica Bay. A soil microbiome project is well underway to describe the bacterial community of the different urban soil series. Soon the dissertation coral microbiome project will be submitted! All in addition to the AREM urban microbiome, as defined by the city undergraduates. So much data and analysis, with more coming, trending in greater time spent at a computer but learning about our daily environment (that we built or influence)!

The number of campuses and students participating in the Authentic Research Experience in Microbiology (AREM) is growing!  We have now about 15 campuses across the U.S.; in 2014/2015 there were 922 students participating then this academic year (2015/2016) 1228 students! That is amazing growth trend in the number of students able to participate in research!

The most surprising trend, is that the nicer aspects of Brooklyn and NYC are standing out more. The mild winter weather may be one contribution (even though it was a forced snowboarding season, avoiding the patches of dirt on the slopes). Many friends and family have visited and moved to the area, opening the JLee B&B more often. This summer is set to be busy, while in NYC there are plenty of BBQs and dining outside planned as well as trips to the beach.

For my decade birthday this year, an epic trip to Peru was accomplished. Over 30 miles in the back country was traversed with the amazing destination of Machu Picchu. More than 7 miles or 7 hours of trek’ing would result in an aching body but the next day is a new start and that this and more can be accomplished when only consuming soup for meals. Therefore, tomorrow is always a new day, a fresh start and that the good/bad in life can be better when experienced with a partner (#itsbettertogether).  Visit Flickr for the abbreviated list of photos from the trip.

Despite the decreasing trend of how much free (unplanned) time each week, hopefully this post is actually a positive trend of updates occurring more than once a year.

Onwards and upwards!

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An open door that leads up. Ollantaytambo, Peru

 

 

 

A year already!

It’s incredible to look at today’s date and see that it has been a year since my last post, which also means I’ve lived in NYC for more than a year!  I certainly was optimistic that I could stay awake on the subway and use the time to write.  I did learn how to get around the center of Brooklyn quickly by biking to Prospect Park and Lincoln Terrace Park for yoga and tennis (MeetUps.com was a great way to have something to do the first few weeks in the city).  Audiobooks from the library have also been great for the long subway rides and walks; lately, I love the Maisie Dobbs series.

The first apartment was not the lovely oasis from the busy city as I had hoped.  A water leak in the first month became a 2nd floor skylight 10 months later when the weakened ceiling collapsed.  For pesticide treatment (after being there only 3 months), I had to pack up my apartment into bags  and even at the end of the lease 9 months later, I was still living with my clothes still in plastic bags.  However, I am now in a lovely studio in a better neighborhood and I hope that those issues (& the others) don’t repeat themselves.

NYC may have about 8 million residents but everyone is incredibly busy.  Childhood and old friends are no exception to the busy city lives.  I am grateful for the opportunity to reconnect with friends even though so many have too packed social calendars.  The graduate students at Brooklyn College have been great to spend time with building friendships.  Though I am extremely happy when a friend comes to visit and we can to ‘play tourist’ together and I get to host them at the J.Lee B&B. During one of these visits and after imbibing some good red wine, one friend suggested online dating as a way to meet new people.  After a few weeks, maybe months, only one person stood out as a great guy and someone worth getting to know.  It is about 8 months later, he and his family have made Brooklyn feel more like home and it has been so special for him to meet my family just across the rivers in Jersey.

The postdoc has been interesting – learning to balance teaching, research, and managing the AREM undergraduate program (arem.cuny.edu).  Through the year, I have learned how to work with a diversity of campus personalities of faculty and students.  This summer has been my first full exposure to the field of Pedagogy and learning about the tools and methods at the forefront of Biology undergraduate education.  The Fall semester should be interesting as I teach a section of Microbiology lab for the third time and implement more program updates for AREM projects.  I hope some externally funding comes through so I can get back into the field and doing water quality/marine disease research.  I really enjoy being outside more than at a computer and where I am now is a great opportunity to bring city students into their local environment that most don’t even realize it exists let alone the value.

Overall, it has been a long year with no shortage of opportunities nor experiences.  I would never wish it on someone to have the year I had, but I made it through and most things are looking even better as we go into Fall.

 

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The short…long ride

I remember when traveling 30 minutes was too far or required special planning because it was a ‘day trip’.  I’m over that now.  There aren’t many places I can go, except the nearby grocery store, in <30 minutes.   So what does this mean?… I’m already good at figuring out the subway. I love audiobooks more, because they don’t take up more space/weight in my bag. I’ll be printing articles that need a careful read and they’ll regularly take up space in my bag. I’ll now have 2 snacks in my bag in case the 30min trip becomes >1hr. And maybe more blog posts as I’ll have more time to jot down thoughts on my phone.

I did say I would share a little more about the move and the apartment.  I’m still uneasy to be out at night but I’m getting to know my neighbors and where to go to buy certain groceries.  (I actually know more people in my building in the month I’ve been here than my new labmate knows in his building of 6 months.) The apartment itself is a good size for NYC (even though my couch didn’t fit in the entry way) and I love how I have it set up.  I really look forward to the Fall when I can cook more, especially some pizza (I’m not used to a gas stove that heats up the whole apt!).

What should have been a normal ‘short’ hiring process has now taken longer, almost 6wks. The Fall semester is about to start and that means work will really start to get busy for awhile.  Since the move, I’ve been meeting with different faculty of the City University system of New York (CUNY) campuses and learning more about the pedagogy side of the project. My postdoc is with the CUNY Research Foundation for the Authentic Research Experience in Microbiology (AREM) program.  I’ll have to balance a lot but I’m excited to see all the different projects as part of AREM!  Once I feel comfortable with these responsibilities, I’ll start applying for other grants to do some marine microbial work in the nearby areas, such as Jamaica Bay.

I’m soon off for another short distance trip but it’ll take longer to make because of city traffic.  However, it is so worth it! I get to celebrate with grad school friends the wedding between two amazing people!

 

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A fun adventure

I am bound for Brooklyn, NY.

When I tell friends and family or a stranger, almost everyone recognizes the adventure that lies ahead of me. Hopefully it is this sort of adventure that will get me to post and update the website more often.

For the next few days I am on the road to the city.  I left Athens on Friday with my mom and the days in between apartments will be spent in the Shenandoah mountains. I look forward to the peaceful few days hiking. We already did 6 miles to a waterfall! Today will be a shorter hike then going to the valley to see the caverns.

My replacement bedroom set should arrive sometime next week and the rest of my furniture showed be delivered by the movers sometime next week as well. I do not get to the apartment until the first of the month so I hope that their arrival doesn’t fall too late or on the same day. The apartment is smaller than what I had in Athens but it is walking distance to all the life essentials (ie, Laundromat and grocery store). Next post I will share the apartment with hopefully the minimal chaos of moving into the city.

 

Three extra letters…

PhD. The defense is over!  Wow! It has been a journey.

I have learned more than just what is in my dissertation.  Made some great friends and have watched many of them start lovely families.  I created my first home and Athens will always be a special place. I am grateful for the full life I have had as a graduate student.  At my defense, my final slide was packed full of names of those who have helped with the countless hours of field work, lab work, and data analysis.  Many of them became an extended family to spend happy hour with and holidays.

My previous post was while I was traveling, before the last crazy weeks leading to the defense.  I was wondering about what will be next and where I will be moving.  I wish I had a better update.  I still know that what I do next will be an adventure but it will be sad to leave Athens. 

Currently, my favorite phrase is about dandelions: that ‘Some see a weed, while others see a wish’… 

I have had many side projects and experiences that almost were weeds, something pretty but in the wrong place at the wrong time. I really look forward to bringing more attention to these areas and maybe something more will come of some of them. That is what I hope part of my post-doc will be, spending more focused time on the projects that didn’t make it into the dissertation. 

Now there are three more letters after my name, Jessica Joyner, PhD. To earn these letters it has been a good 6-years learning about corals, bacteria, and myself.  I wonder what they will really mean for me in the future…

 

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Weather… Whether…

I have had a wide range of weather events over the past few weeks. I think the ice storm in Atlanta marks the beginning and I’m not quite sure where the end will be. I already mentioned the winter weather experiences that continued through my visit to Brooklyn. Then it is only best to say that the following week, last week, was in Hawaii and it was nice to not have closed toed shoes and heavy coats. Interesting enough is that it was still winter for Hawaii and I thought it was still chilly and windy. For most of the time in Hawaii, I was at a conference learning more about ocean sciences and biology. I really enjoyed making new friends and catching up with old friends! Only through these friends did Oahu come to life. I enjoyed the sunshine kayaking and good food! with family friends I hadn’t seen since a kid. The hospitality of a friend from college made my week at the conference easy and was more of an introduction to life as a local. Following the conference was an extreme low pressure weather system that kicked up epic waves on the North Shore. We couldn’t go surfing but it was sweet to see the waves get up to forty feet! My friend from grad school was traveling with me and we were glad when the sun came out for the morning of our last day of being ‘tourists’.
Whether or not to take a job is the other current event. There are a lot of decisions to be made that contribute the final one. Whether or not I can move North? Whether or not I can still have a marine microbiology project? I made my mind up and weather may become a greater part of my daily life. Now there are new decisions to make. Whether this… Whether that…
Whether or not there is a variety of weather to enjoy in the future I think there is an adventure ahead for me. I will try to write better posts that are not just my rambling thoughts as I take a red-eye back from Hawaii.
North Shore Weather