As we continue through our open application window for the Microbiome Awards we are checking back in with some of our previous winners to learn a little more about them and what they have been up to. This week we talk with AndreaTarnecki who is a Postdoctoral Research Fellow at Mote Marine Laboratory in Sarasota, FL and took 3rd place in the 2016 Microbiome Awards.

As we ramp up this year's Microbiome Awards we decided to check back in with some of our previous winners to learn a little more about them and what they have been up to. This week we talk to Dr. Christopher J Stewart who is a post-doctoral associate at Baylor College of Medicine in Houston, Texas and took 2nd place in the 2015 Microbiome awards.

Our journey towards Ficus phyllospheres started at the front gate of the University of Ibadan’s Botanical garden on the 5^th of November 2015.  The garden is rich, diverse and a distance from the working laboratory but I was not tired of going there because the garden was a worthy reward. The garden is fascinating and serene with abundant ‘first class’ fresh air and smooth floor which tempted me to sit for a while. Thank God for the ever-helpful garden attendants especially Mr. Sam for his patience and readiness to provide answers to my questions. I wish I could be allowed a little time out in the garden on weekly basis.

In a recent study, Willmann and colleagues investigated the impact of ciprofloxacin treatment on the intestinal microbiome. Antimicrobial treatments are known to upset the structure of the intestinal microbiome. Taxonomic profiling can reveal the severity and long term effects of antibiotic treatments on the gut community.

If you’ve figured out how to extract high-quality DNA from an elephant, chances are that without too much trouble, you’d be able to do the same from a moose, a mouse or even a meerkat. However, if you’ve figured out how to extract DNA from an Arabidopsis plant, well that might be about all you’ve figured out. That’s because plants have developed something akin to chemical warfare in order to survive a variety of climactic extremes, pathogens, and predators, without the luxury of being mobile. As a result, plants harbor an enormous variety of organic compounds, some with antifungal and antimicrobial properties and some which make them taste bad to herbivores. Other structures are complex networks of polymers that store water and nutrients for both feast and famine.

It’s all good and well for the plants, but many of these substances muck up DNA extractions....

The DNase step is one of the most common causes of degradation or loss of the RNA during your extraction. DNase digestion is frequently performed on the spin column and although this can be a great way to save time on the post extraction processing, it is not an efficient method for samples with large amounts of DNA (for example, spleen, thymus, and even some soils). In these cases, DNase digestion in solution is necessary.

The typical protocols for DNase involve inactivation of the enzyme using EDTA and heat. Both of these things can cause problems in RT-PCR. EDTA can inhibit the RT-PCR enzymes and heating the RNA can cause a reduction in integrity. 

As many of you know, a good percentage of our customers are doing microbiome research. Microbiomes, those localized communities of microorganisms that exist symbiotically with their immediate environment, can be found virtually anywhere; inside human colons, around plant roots, inside coral reefs and even within ant colonies. These little microbial microcosms are a hot topic right now. Recent studies have implicated their role for the wellbeing of people, animals, plants and entire oceans. Variations in microbial numbers and diversity within animals have shown critical involvement in auto-immune disease, obesity, acne, tooth decay, pregnancy and even brain chemistry. Plant studies have shown that symbiotic organisms impart resistance to drought, increase nutrient absorption and prevent attack by pathogens.

QIAGEN is knee-deep in questions about DNA and RNA isolation from stool! One of the most frequently asked questions is how to store fecal samples for shipping and then storage for further processing. We consulted a 2010 paper written by Dr. Rob Knight’s lab¹. Dr. Knight is an expert in the microbiome field working with human gut/stool samples.

QIAGEN is cleaning up...DNA and RNA that is. With the addition of the DNeasy and RNeasy PowerClean Pro Cleanup Kits to our portfolio, we thought it would be a great time to discuss how cleanup kits work and when you'd want to use one. Clean-up kits take dirty nucleic acids and remove contaminants that could interfere with your downstream business. Enzyme-dependent applications like restriction digests, ligations, PCR amplification and sequencing all require squeaky clean DNA and RNA in order to get the best (or sometimes any!) results. 

As part of our research on the best practices for soil microbial DNA extraction, we collect a wide variety of samples for product development. So when we were developing the protocols for the PowerLyzer 24 Homogenizer 24 Homogenizer, we wanted a protocol that worked for most of the samples tested.  Our work on homogenization and bead tubes previously showed that depending on the soil, sometimes a different bead type could give you an increased yield of DNA.  We decided to do a similar study using the PowerLyzer 24 Homogenizer to ask the question: what is the difference in DNA yields and integrity using high powered bead beating between two different soils using the same protocols?  It is not uncommon for people to simply adopt a protocol from a paper for their soil type without doing any optimization.  But, does one protocol really work best for every soil?

One of the most efficient ways to extract nucleic acids from a sample is by smashing it against a hard surface repeatedly under high speed until cell walls and membranes crush from the pressure and release their internal contents. In other words: bead beating.

Bead beating is a great way to do what enzymes take hours to accomplish and sometimes never fully succeed in, which is cell lysis to release DNA or RNA for isolation. While enzymes can be successful for DNA isolation from a limited number of sample types, results are achieved a lot faster if you break down the matrix first. And RNA cannot be isolated in a timely fashion without the use of some kind of mechanical maceration.

The questions inevitably arise though, how hard do I need to beat to lyse my sample and how do I know what bead type to use?

“Just to be clear, and in front of multiple witnesses… you want me to spend my time, at work, designing a microbiome board game?”

“Yes”

Like most projects, it started innocently enough.  Our lab had created a series of educational “trading cards” of bacteria that we were sending the International Space Station. Then someone (jokingly I think) asked if we could gamify them… maybe make something like Pokémon. I thought about it, and decided it wouldn’t work. Then Jonathan Eisen, my supervising professor at UC Davis, said “you know, we really should make a microbiome game” and the rest is history.

This past July, I attended the Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) Workshop at the Michigan State University, Kellogg Biological Station in July 2016 led by Drs. Ashley Shade, Adina Howe, and Tracy Teal. EDAMAME started from the ground up and was a great way to get hands-on experience using cutting-edge metagenomics techniques. Although, I would expect, any one of the organizers to say that a great deal of effort and critical thinking is required to stay abreast on current technologies.

At the interface of land and sea, the coastline is the last barrier before our man-made pollutants hit the ocean. Coastlines in top-notch shape, however, can filter out a lot of these pollutants, cleaning up a pretty big mess in a relatively small amount of space. Impressive, right? Yet, most of our coastlines are so impacted by excessive chemical input, choked rivers, extra sediment, and invasive species (to name a few issues), sometimes we need to help out these coastal zones through restoration.

My dissertation research is focused on the gut microbiomes of lemurs, you know, those bug-eyed primates from Madagascar that happen to be the most threatened group of mammals on earth. I specifically work with indriids, a group of critically endangered lemurs that include the indris, woolly lemurs, and sifakas. Go google them, seriously. They are some of the most exotic and stunning animals on the planet. Ultimately, I hope that my research will not only illuminate the symbiotic relationship between lemurs and their gut bacteria but will also inform conservation strategies for both captive and wild lemurs. 

It was really surprising when I sat down on the forest floor, pressing my knees into the soft organic horizon of the soil, to become quickly enveloped in a foreign mustardy aroma that tickled my nose. Beside each of my legs were emerald green rosettes of Alliara petiolata, a few of which were already beginning to show their delicate white petals adjacent to their heart shaped leaves. As I neared the edge of the forest, A. petiolata had a strong foothold, it was dense, tall, and incredibly aromatic (Image 1). I reached my left hand out and popped off a few leaves, put them in my mouth, and chomped away, enjoying the bitter punch of the invasive plant’s phytochemistry on my taste buds. A. petiolata is closely related to some of my favorite veggies, including broccoli, kale, and radish, but unlike these domesticated cultivars, A. petiolata was introduced into North America from Europe, where it has begun to take over the understory of many deciduous forests in the northeastern USA. If we are to control invasion by A. petiolata, we need to understand how it has become so successful. This is where I stepped in with a sledge hammer soil corer, my PowerSoil® DNA Isolation Kits, a couple pipettes, and an incredible amount of patience! 

My name is Dr Michael Sweet. I’m a lecture at the University of Derby in the UK and researcher who studies aspects of Molecular Ecology. Usually you can find me in the tropics, researching coral reefs and more specifically diseases associated with reef organisms, but this year something different happened. I headed to the poles. 

This will be the last of the #EDAMAME2015 posts for this year, we are sad to see you go!

MO BIO would like to formally thank EDAMAME 2015 (especially green circled Dr. Ashley Shade) for all the interesting science blogs!!  Great group of hardy scientists!!

Last MO BIO guest blog for 2015:

In the last five years, scientists have seen an increased number of papers assessing the diversity of microorganisms.  However, although knowledge of fungal diversity has increased, it is far behind in comparison.  As a mycologist/plant pathologist, I have been amazed by the diversity of fungi and oomycetes in different environments, and their roles in these habitats.  Just here at KBS, we could observe some of this diversity walking around the gardens.

My advisor always says I should ask this question to myself at every step of my research. Your work may be the best in the world. It can be innovative and exciting for you and your lab. However, you must be able to express it in simple terms, so much so that even your parents who may not come from a science background, understand what you did, why you did it, and what is next. Often, we are deeply engrossed in the complexities of our projects that we often fail to take a step back and look at it from a very simple point of view. Asking yourself whether your research makes sense to the random person allows you to critically analyse your own work and address the loose ends that might be present in your research idea, data, analyses, and finally interpretation. I also think that when striving to simplify our own words, we automatically start transitioning into trying to explain our research in a sequential and logical manner.

There is a saying that “You can’t teach an old dog new tricks.” I am a bit of an unusual candidate for EDAMAME2015. I am an older associate professor in the Biology Department at the University of Puget Sound, and can even remember biology prior to PCR! At the same time, I have been following the recent blossoming of research into communities of microbes over the years, ranging from hydrothermal vents, to insect guts, to acidic cave effluent, to the ever present human microbiome.

We are starting a new series of blogs that will include a short synopsis of a recently published peer-reviewed paper. We want to keep you (and ourselves!) up to date on the latest and greatest science news.

Psst, don’t forget about our Published Reference program, you get a free kit for sending us (reference@mobio.com) your published paper using our kits!  Not a bad gig!

This month we picked:

Metagenomic Analysis of the Airborne Environment in Urban Spaces

Nicholas A. Be & James B. Thissen & Viacheslav Y. Fofanov & Jonathan E. Allen & Mark Rojas & George Golovko & Yuriy Fofanov & Heather Koshinsky & Crystal J. Jaing

Hello MO BIO!  My name is Jesse McNichol and I'm a graduate student in the MIT/Woods Hole Joint Program and along with my supervisor, Dr. Stefan Sievert, I study the microbiology of deep-sea hydrothermal vents. These ecosystems are extremely unusual on Earth, since they are mostly supported by volcanic activity instead of the sun's light. The oxidation of hydrogen sulfide and hydrogen gas are probably the ultimate source of food for all the teeming life around these hot springs, including the large fishes, tube worms and crabs. 

There’s been some social media buzz lately about #WomenInScience. No better time than the present to update the list from our previous blog!

Ruth E. Ley is an Assistant Professor of Microbiology at Cornell University in Ithaca, NY. She was trained in ecology and natural history at the University of California Berkeley (B.A.) and in ecosystem science and soil microbial ecology at the University of Colorado, Boulder, where she worked with Dr. Steve Schmidt (Ph.D.). 

Warning ---> If you don't use twitter, this article might give you the extra boost to go ahead start tweeting away..

I met Arwyn's tweet one day and rest is history!  He had posted results from his undergraduate class about how there are essential oils such as lavendar that are actually a more effective bacteriocide than other toxic chemicals such as bleach.  Super Rad result!  I got in touch with him and, over time, learned about his incredible and very global climate change relevent research on microbes that live on ice and snow of the Arctic.

I sent him a few basic questions and voilà!  Enjoy.

My name is Cassie Ettinger and I am a 2nd year PhD student in Jonathan Eisen's laboratory at the University of California, Davis. I am working with Hannah Holland-Moritz, a Junior Specialist, and Jenna Morgan-Lang, the Post-doc in charge of the project, to try to characterize the Seagrass Microbiome, the entire microbial community associated with seagrass.

Why study the seagrass microbiome? Seagrass has an interesting evolutionary history.  Starting out as marine algae, an ancestor of seagrass made the transition from marine to terrestrial with its descendants eventually becoming what we know today as plants.  Some of these plants later returned to the marine home world from whence their ancestors had originated (just like whales evolved from a land-based ancestor that returned to the marine environment!). Seagrasses are the only known flowering plants to have made this return to the sea. This is because surviving in a marine environment poses significant physiological and morphological challenges. We are interested in the role microbes might have played in the adaptation of seagrass to the marine environment and if any co-evolution has occurred between seagrass and its microbiome.

My email dings soon after lunch on Monday, I open the window, and there it is in all its glory. The MiSeq data has arrived! I promptly download the file giddy with excitement…and wait. And wait. The file is huge, and incomprehensible, and somehow contains nearly 15 million sequences.

Luckily, I had signed up to attend the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop hosted by Michigan State University. So here I am at Kellogg Biological Station on Gull Lake taking baby step-by-baby step through the shell, QIIME, Mothur, and R. Many of these I have used in the past, believing that I had taught myself how to run them. But here’s the difference: what I had done was copy and paste some commands, hope it worked, and then compared my results to results from other programs. Very efficient! Now: we are really learning the meat of these programs down to the last –i and / and the knowledge of these details allows the understanding of what happens in each step. My goals while here at EDAMAME 2014 are not to merely analyze this dataset, but to be able to take this knowledge and power and translate it to any dataset.

Hello!  My name is Enid Gonzalez-Orta and I am an Associate Professor of Biological Sciences at California State University, Sacramento, where I teach undergraduate students about the wonderful world of microbes.  In addition, I embed an authentic research experience into my microbial diversity class each spring where we study soil samples collected from CSU Sacramento Arboretum or from local vernal pool sites.  We study the bacterial community of these samples using traditional methods, like culturing samples onto laboratory media, sequencing of the 16s rRNA gene through the Sanger method, and building phylogenetic trees.  However, I began to think about how much the field of microbial ecology has changed and is changing.  I thought about how culture-independent methods allow us to peek into environments seldom studied in the laboratory and how these methods reveal members of bacterial communities that were previously not known to inhabit these niches.  I also thought about how next generation sequencing (NGS) methods are becoming becoming the “tradition” in this field.  And, I thought about how important it is for undergraduate students to have hands-on experience with bioinformatics and computing in order to interpret the volume of sequencing data that is produced through NGS.  But, how I could I do this when I myself had little-to-no experience with processing 16s rRNA NGS data?  Then came EDAMAME to the rescue!

Greetings, Culture Dish followers!

My name is Ashley Shade and I am an assistant professor at Michigan State University in the Department of Microbiology and Molecular Genetics. I am excited to share our first days’ adventures in our new workshop, Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME). EDAMAME is a week-long intensive training in bioinformatics tools and ecological analyses of microbial metagenomics data, held at Michigan State’s Kellogg Biological Station.

I know what you are thinking: Silly new professor! Why dedicate preparation time and a week of your life to a non-credited summer course that won’t count towards your teaching requirements?

Want to play in the mud?  Like the ocean?  If your answer to both questions is “yes,” you may have a tinge of jealousy when it comes to this Where in the World project.  François Thomas, PhD, works as a postdoctoral scientist with Stefan Sievert, PhD, at Woods Hole Oceanographic Institution on Cape Cod in Massachusetts.  His collaborative project* funded by the National Sciences Foundation studies microbes in New England salt marshes. By sampling sediments and roots of the salt marsh grass known as Spartina, he uses both cultivation and molecular techniques to understand the microbial communities in each environmental niche. In particular, he is studying sulfur-oxidizing microbes, which can profit from the release of oxygen from the roots and might play a critical role in linking the carbon, nitrogen and sulfur cycles. To get back to your childhood memories, check out this video from the field.

Last week marked the deep sea submersible Alvin’s 50th Birthday.  This translates to 50 years of unprecedented ocean exploration and discovery!

MO BIO Laboratories, Inc. would like to thank Alvin and the very dedicated folks that make Alvin’s story so historic in scientific discovery!

Thanks to Chris Linder, Alvin and MO BIO's cultivating curiosity were united on R/V Atlantis during the first scientific expedition with the newly outfitted Alvin, awesome sauce!  I can't help but share my own special moments with Alvin, thanks for checking in!

Craig Cary, a friend of the MO BIO Laboratories' family came by to say hello and also updated us on his work. Craig works on soils from Antarctica in a region called the Dry Valleys in Victoria Land.   Talk about extreme!  Imagine glaciers, extremely cold temperatures, very dry air, rocky salty soils, lack of vegetation, “Kadabatic” winds derived from the mountains, 24 hours of sunlight during “summer”, and to top it off mummified seals!  This place has been described as one of the most extreme environments on the planet, and is used as a model ecosystem to better understand the conditions on Mars, a planet akin to this “freeze dried environment”. In 1989, an important treaty called the Montreal Protocol was put into effect banning the use of CFC’s in any commercial products due to its deleterious effects on our ozone layer.  It turns out it this treaty has made a profound effect on positively regenerating the ozone layer which is concentrated in the upper atmosphere of the poles.  This comes with concern about how this will effect the environment in Antarctica, ozone traps heat including the climate changing CO₂ we are pumping in to it.  Will Antarctica continue to warm?  We know that the Antarctic Peninsula, a fingerlike projection sticking up towards South America, is one of the fastest warming regions on the planet.  What will happen with the rest of the continent, will it warm too?  This is what Craig wants to know.

This will be my final blog post as MO BIO Lab's Director of R&D.  I wanted to leave you with some last words as I make the next transition and continue to be a part of the microbiology world, just from another side- as a customer of MO BIO just like all of you.

I have had the most amazing experience being a part of this wonderful family. I am so grateful for the opportunity given to me 5 years and 9 months ago to be the director of the science coming out of MO BIO Labs, for the chance to stretch my brain and be creative every day,   and to work with the most talented people I've ever known.  Thank you for the opportunity to travel to amazing places to represent MO BIO and for all the close friendships with customers that I've made because of my time here.  Many of you I will continue to tweet with and email for mentorship and dialogue and I am grateful.

I am sure that in the back of many a scientist’s mind is the idea that it would be fun or better yet a good career move to start a biotech company. I told myself that very thing many years ago and decided to give it a try. I had recent experience with a startup that some of you may remember if you are old enough. It was called BIO 101 and was the first company ever to sell DNA kits. In fact, I am on the first ever patent for a DNA isolation kit that used silica resin to purify DNA in the presence of binding salts, followed by washing and then eluting the pure DNA into water. This is pretty much the industry standard today for how DNA and RNA get purified.
Wow, it brings back memories of what it is like to have no competition and have the opportunity to sell a product that has a huge impact on the industry. That was 1986. Fast forward to 1993 when I decided to go out on my own with many product improvement ideas I had that did not fit with the BIO 101 plans.

How DOES science fare in the online space? Communication of complex scientific processes is difficult enough one-on-one. With Twitter and Facebook, communication is now not just between two people but hundreds, maybe thousands. This is the topic to be addressed at the next MO BIO Labs sponsored BiteSize Bio webinar.

You may remember our previous webinar with Dr. Joseph Petrosino from Baylor College of Medicine and his talk on Metagenomics and Type 1 Diabetes (T1D).  Dr. Petrosino described the undertakings of an exciting collaborative effort to find the cause of T1D and eventually a cure.

For our next webinar we wanted to do something quite a bit different.  This time around we want to focus on a very important subject that impacts everyone in the community. That is, as scientists, how do we communicate our science and our knowledge of science online.

I would like to meet whoever is responsible for perpetuating the myth that scientists area stuffy and dry bunch and introduce him or her to the amazingly creative and artistic scientists we have the pleasure of interacting with at MO BIO.  This month we invited our usersto submit a poem about their MO BIO experience. The results were quite impressive. The topics ranged from our kit's unparalleled ability to remove inhibitors to our great customer service. In return for their very kind words, we offered up a t-shirt and discount code.

Be sure to check out the video links of MO BIO employee's reading the submitted poems.

We start off our MO BIO Poetry Corner with a poem from our CFO/owner, Liz Brolaski. Mark Brolaski, CEO/owner, reads Liz's poem that gives a shout out to the awesome employees at MO BIO.

Thank you to everyone that submitted a creative piece this month. Have your own poem to share? We would love to hear it, leave it in the comments or e-mail us at customercare@mobio.com for your own shirt and promo code!

Who hasn't pondered the age old question: Which came first, the chicken or the egg?

Debates on this subject have kept philosophers busy for centuries, lending to rich discussions on everything from evolution of chickens to the beginning of life and the universe. One could ponder this question from a literal point of view and discuss the evolution of egg laying species and whether or not this pre-dates the appearance of chickens. Or one could set forth on a metaphysical journey and focus on the possibilities of how one life form can exist without its developmental precursor or how a precursor exist without its original maker?

Here at MO BIO, this discussion led us down a different path. The question we propose to you is: Which came first, the DNA or the protein? You need DNA to know what proteins to make and how to make them, but, you need proteins to synthesize more DNA, to transcribe the DNA into RNA, and to hold it all together.

Jan 24, 2013
69°56.9S X 76°17.2W (Most Southern Point)
West of the Antarctic Peninsula
Sunrise  2:50am
Sunset  12:19pm

We’ve all got our groove on. Sampling and processing seems like a breeze despite it’s challenges.  The flow of efficiency has finally set in and it feels good!

Last week we dropped off the birding duo at Avian Island, a “Antarctic Specially Protected Area” where you need special permits to land.   With the help of a few shipmates, they set up a camp and spent five days researching the massive Adelie penguin colonies breeding there.  During the set-up (which took about a half day), others were able to take the small boat to a deserted Chilean Base for some exploration.  It is a relief to be on solid ground and take an afternoon off, boosts morale especially when you have the opportunity to listen to the sounds of the elephant seals that we encountered.

It's Valentine's Day and love is in the air at MO BIO! To celebrate this special (not so special for some) day, we thought we'd tell you about the cutest and nerdiest proposal of all time. Watch out guys, if your girlfriend sees this and is expecting a ring sometime soon, the pressure's on!

You may have heard some buzz floating around recently about the guy who cleverly proposed to his girlfriend via agarose gel. Yes, we know, it's incredible.  We wanted to ask him a few more questions about this amazing, geeky proposal,  so we tracked down the proposer, Eric (currently a Post-Doc at UCSD) , to get the whole story.

How did you two meet?

We were both graduate students at Stanford. We met at a grad student event and played volleyball together. We ran into each other again later at a department happy hour.

Where did you get the idea from?

Regional Climate Warming: West of the Antarctic Peninsula

Jan 17, 2013
68°00.2S X 69°30.8W
Sunrise  11:37pm
Sunset  9:49pm

MO BIO Labs is going to collaborate with our friends at the popular science blog site, Bitesize Bio to sponsor a couple of webinars for their readers.  Since MO BIO Labs has a primary focus in microbiology and ecology, we want to sponsor seminars that are going to highlight the research and scientists working in this exciting field.

As I was pondering potential speakers, I thought about the women in science I've heard speak, who are an inspiration to me. But my experience is also limited being in the private sector. I don't get to interact with as many women thought leaders as I would like. The question then became: who are the leading women in the field right now?  What women scientists do we have to draw insight and inspiration from?

I attend the Gordon Research Conference in Applied Microbiology every other year where I get to meet so many outstanding scientists from across the globe and of course ISME (also every other year) is a chance to network with many in Europe who don't make it to ASM each year. ASM is a great meeting as well, however, we know many environmental science labs save their money for smaller more intimate meetings and avoid the crowds of ASM.

Boondoggle!
by Emelia DeForce
Jan 10, 2013
66°15.0S X 67°21.9W
West of the Antarctic Peninsula
Sunrise  2:50am
Sunset  12:19pm

I have to pause for a minute to pay homage to and tell you about the humbling power of Palmer Station.  There are only about 30 people that live there in the summer months (Sept-April) but all of them are responsible for running not only a station, but a home.  There are cooks, seamstresses, metal workers, electricians, doctors, scientists, etc. many of them acting in multiple roles on a daily basis.  Each individual plays an integral part to make the station a success even if it means scrubbing someone else’s bathroom floor after lunch.

The Drake Passage

By Emelia DeForce

Jan 4, 2013
64°46.50S X 64°03.00W
sunrise: 2:58am
sunset: 11:42pm
United States Antarctic Program Palmer Station, Antarctica

Honestly, I slept through leaving the dock at Punta Arenas as we forged South towards Antarctica.  The travel, preparations, and constant sunlight have left my body exhausted.  I vividly remember waking up on the ship after leaving and immediately saying to myself, “there is no way we are underway, the ship is hardly rolling!”  It turns out this was a foreshadow of our crossing of the Drake Passage.

 Dr. Emelia DeForce visited us at MO BIO Labs in December after the Plastics at SEA voyage was complete and provided us an amazing presentation of her travels at sea and the important work they are undertaking to determine the effects of plastic in the ocean ecosystem.  It was great to see the effort and passion Emelia and the whole crew has for our precious oceans.

Emelia's next trip takes her to Antarctica where she has the unique opportunity to be a part of the 2013 field season of the Antarctic “Long Term Ecological Research” program. Rather than me tell you all about it, I thought it would be better left in the words of the expert extreme traveler and scientist adventurer herself.  So here is the first post of Emelia's web diary of her trip to "The Ice". She'll be sending us more stories of her chronicles as she has time to write and reflect.  For those of you curious about the life and times of an extreme microbial ecologist,  we hope you enjoy what you read.  If you have any questions for Emelia, let us know!

Enjoy!!

Touch the Toe Before You Go!

A great excursion is about to take place! Thanks to Emelia DeForce, Chief Scientist in the expedition for letting us know about an important research project taking place this month in the North Pacific Ocean. The health and maintenance of our oceans is a subject near and dear to our hearts here at MO BIO, and those of many of our customers. That's why we are excited to tell you about a research voyage embarking this week that seeks to understand the fate of plastic in the oceans and the microbes that make plastic their new home.

A team of 38 scientists, sailors, and students led by PIs, Kara Lavender Law, Erik Zettler, and Giora Proskurowski sets sail out of San Diego, California October 2nd, en route to Honolulu, HI to study the effects of plastic marine debris on the ocean ecosystem. The expedition is called Plastics at SEA: North Pacific Expedition 2012 and is being conducted by the Sea Education Association (SEA). The goals of this research are to better understand the impact of plastic on the ocean ecosystem, while also providing updated estimates of floating plastic concentrations in the region dubbed the “Great Pacific Garbage Patch”.

MO BIO Laboratories, Inc. becomes exclusive sponsor of Nature’s Human Microbiota Special

Carlsbad, CA; August 21, 2012 – MO BIO Laboratories, Inc., the leader in microbial nucleic acid purification, is pleased to announce their sponsorship of Nature’s Special: Human Microbiota, enabling free access to four of Nature’s recent human microbiome publications.

“MO BIO is committed to furthering human microbiome research through the development of nucleic acid isolation kits optimized for difficult samples, including stool and gut material”, Mark Brolaski, President and CEO of MO BIO Laboratories, said. “We are proud to have the opportunity to make these important human microbiome publications freely available to the scientific community.”

I wanted to spend some time writing on our blog to tell you about our exciting new products for high throughput microbial DNA isolation. It's been a LONG time coming.   And it was worth the wait!

How it Began...

We started onthe development of magnetic bead based nucleic acid purification for environmental samples over two years ago. At that time, all of the current technologies available for magnetic bead surface coatings used for DNA isolation were not suitable for dirty, inhibitor containing samples.   Any residual fulvic or humic acids in the lysate stuck to the beads and co-eluted with the DNA.  We knew there had to be a way to make this work and that with increasing sample numbers for the Human Microbiome Project and the advent of the Earth Microbiome Project, a hands-free method for DNA purification from soil and stool was going to be a necessity.

MO BIO is very excited to sponsor a special seminar by distinguished scientist Jim Prosser from the Department of Biological and Environmental Sciences at the University of Aberdeen. Dr. Prosser is on sabbatical for several months in the lab of Mary Firestone from the University of California, Berkeley, so we've convinced him he needs to come down to San Diego and share his knowledge with our local community of scientists.

Don't miss this chance to meet one of the world's leading microbiologists!

The presentation begins at 10 am on Tuesday May 22nd at the Venter Institute. Click the flier to expand your view.

If you are interested in attending, please RSVP to customercare@mobio.com

Seating at the Venter Institute is limited.

A person of great significance to MO BIO Laboratories has passed away.  Michael Moroney, father of our CFO, Liz Brolaski, and one of MO BIO's first employees passed away on October 25th, 2012. He was 81 years old.

Mike was an accomplished geological engineer.  He received his degree from the University of Missouri in engineering and joined the US Army in 1951.  Following his time in the military, he went to work in Calgary, Alberta where he met his wife and spent many years working in the oil industry. He moved the family to San Diego in 1975 where he would eventually retire.

In 1985 when his daughter and son-in-law, Liz and Mark Brolaski helped start one of the first life science biotech companies, called BIO 101,they put Mike to work again.  After 8 years of running BIO 101, Mark and Liz set off to start their own biotech company, MO BIO Laboratories in 1993.  (Bio 101 would eventually be sold to Q-Biogene.) Mike worked alongside them, doing the various tasks that brand new start-up companies need to do.  The UltraClean Soil Kit was under development and Mike observed the R&D scientists trying to work with bead tubes taped down to their vortex and the occasional bead tube flying across the room.

Interested in Soil Ecology and Biogeochemistry?

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• What are the physical, chemical and biological components of soil?
• What do molecular techniques tell us about soil biodiversity?
• How does soil chemistry affect carbon and nutrient cycling?
• How are soil processes affected by global change?

The Summer Soil Institute is designed for graduate students,post-docs, professionals, faculty, and K-12 teachers. Located at the confluence of the Rocky Mountains and the Great Plains, participants will be provided with hands-on experience with lab, field, and modeling techniques including:

...and win a prize!  This month marketing is holding a fun contest that is sure to get your creative minds flowing.  Send MO BIO a video of a song or dance featuring our products by the end of this month and the best submission will get a prize.

The more creative, the better the prize. Prizes will be along the lines of free kits, swag, and anything else we can think up (which probably involves chocolate, coffee, or both).

So get out the video camera, have some fun and make us laugh!

It's getting closer to the General Meeting of the American Society of Microbiology in New Orleans (May 22-25).  We are excited to be authoring two posters this year. 

We are also very pleased to announce that the undergraduate student who is the primary author of the second poster, Joe Lahti, from the University of Minnesota was awarded an ASM Student Travel Grant for his work. Congrats Joe!!

Below are our abstracts. Let us know if you are presenting a poster or were selected for a talk and used MO BIO products. We would love to come visit you during your session and tell other scientists to check out your work!

Poster #1:

Efficient DNA Extraction and Purification of Vegetative Cells and Spores from Sterivex Filter Units 

H. A. Callahan, S. J. Kennedy, M. N. Brolaski
MO BIO Laboratories., Inc., Carlsbad, CA. 

I've had the great pleasure of working directly with this week's featured scientist, Bradley Tolar. I met Bradley at the ISME conference in 2010 and was intrigued by all of the exciting marine microbiology work under study in the Hollibaugh lab at the University of Georgia.  Since then we've been collaborating on projects together.  One of  them involves evaluating a new product planned for launch in May and the other is a potential new method for soil research that would be a huge benefit to the field (when we figure it out).

I have been especially impressed with Bradley's project management skills and his mentorship of the undergraduate student who has been working on the projects. It is clear that Bradley is getting excellent training for a future in academic or industrial science!

MO BIO Labs will be visiting Penn State University in State College, PA this week. We have two seminars planned on April 19th and 20th. Hope to meet you there!

Tuesday April 19th:

Working in Life Science Biotech: A Careers in Science Seminar

What do you know about careers in the biotech world?
Dr. Kennedy will discuss career options in the biotech world and how to prepare for them.

Time: 4 pm April 19
Place: 108 Wartik Lab

Corals are an essential part of a healthy reef ecosystem, providing the biological and structural framework upon which other reef organisms depend. Corals are declining on a global scale due to anthropogenic disturbances and disease. Although many coral diseases have been attributed to microbial pathogens, we now know that corals harbor diverse microbial communities during non-diseased states, many of which are potentially beneficial to the host. However, changes in environmental conditions may cause shifts in these communities, subsequently altering the health state of the coral. Jennifer Salerno, PhD candidate at the University of Hawai’i at Manoa, has dedicated her doctoral research, in Dr. Michael Rappé’s laboratory at HIMB, to studying these highly influential microbes. Her research focuses on characterizing bacterial communities associated with reef-building corals in order to elucidate the roles that bacteria play in maintaining and/or destabilizing coral health.

In our labs, we run a lot of DNA and RNA agarose gels. As you know, my advice time and time again, has always been to analyze nucleic acids using at least two methods: a nanodrop or picogreen reading and an agarose gel.  An agarose gel is the best way to make sure that the Nanodrop reading is accurate and to check the integrity of DNA. As a consequence of running gels all day long, you can imagine that we go through a lot of parafilm and loading dye.

One of the things we dislike in our lab about using loading dye and parafilm is that each dot is usually a different size, since, to be faster, we'll pipette a large volume and then eye-ball the size of the drops. And, the volume of the DNA plus the dye results in needing to re-adjust the pipettor between each sample, or force the pipettor to pipette more than it's actually set it for. Either way, it's a drag.  And I don't know if this has ever happened to you, but what's most annoying is when someone walks by your bench and causes a gust of wind that blows your parafilm containing dye across the bench making the dots roll into each other.

But we put up with all of these things since it is the fastest and easiest way.....until now.

Have you heard about the Earth Microbiome Project?  Led by the laboratories of Jack Gilbert from Argonne National Labs along with Folker Meyer (Argonne), Janet Jansson (LBNL), Rob Knight (University of Colorado), this is a pioneering effort to characterize the global microbial taxonomic and functional diversity from samples collected all over the world.

Similar to the Human Microbiome Project, the Earth Microbiome Project (EMP) is an exciting and massive endeavor that will reveal the vast diversity of microbial species that sustain and nourish planet earth. Withonly a small fraction of the microbes in the environment having been cultivated, this project will expand our knowledge of the "dark matter" that comprises the planet.

To accomplish this project, 200,000 environmental samples will be extracted and the DNA sequenced to produce a global Gene Atlas with approximately 500,000 reconstructed microbial genomes. The project aims to produce 5 million metagenomic reads and 200,000 16S/18S rRNA reads per sample.

OK- great job and creative responses! Let's summarize the results:

There were 21 responses, 62% from men and 38% from women.

The responses for Love or Science were split an even 50-50 (9-9). Three respondants chose both Love and Science. All three of these people were men (14.5%).

46%  of men choose Science compared to 30% choosing Love and 23% choosing both. Let's add the 23% of men who chose both to each number so 69% chose Love and 53% chose Science.

62% of women chose Love and 38% of women chose Science.

Based on this limited sampling of scientists, the majority of scientists (both men and women) say love is better than science!

Thanks for playing. The winning posts are:

Love
Armando- for sharing that great story of meeting his wife.
Denis- very creative!!

Science
Ifuseekbrian- funny answer!

I will contact you via email for your shipping address Valentine's Day.

Welcome back everyone and we hope you had a wonderful New Year celebration.

To kick off The Culture Dish, we wanted to tell you where you can meet and greet a member of the MO BIO Labs team if you are traveling to a scientific conference in 2011.  Here is our list of the biggest conferences in the life and clinical sciences this year where we will be exhibiting or attending.  We will also attend some smaller conferences that focus on specific areas of microbiology so feel free to email us and inquire about any small meetings we may be attending if you want to meet up with us this year.

If you are attending a meeting in microbiology and are looking for a vendor or sponsor, let us know the details and we can consider some last minute additions to our schedule if our budget permits.

Hi Everyone,

I wanted to check in and let you all know that our blog is going to get back to its regularly scheduled updates starting in the new year.  We have some new interviews to share with you, more technical tips, and plenty of primary research articles we can discuss.  The last few months have been spent getting experiments done with our collaborators in time to submit abstracts for the 111th General Meeting of the American Society of Microbiology in New Orleans in May. And, we're very excited to share the news on all the new products we have planned for 2011.

MO BIO Laboratories celebrated 17 years of business this past August.  It is amazing how time flies. It seems like yesterday we celebrated 16 years by sharing with you 10 Little Known Facts about MO BIO.

To celebrate this year, we have compiled questions submitted by long-time MO BIO customers and collaborators, to create a video interview with owners Mark Brolaski, CEO and Liz Brolaski, CFO. We offer this video created by scientists, for scientists, with our greatest appreciation for your continued support.

Enjoy this video of Mark and Liz answering tough questions and sharing their thoughts on how MO BIO began and where it is going, with you.

When I was a graduate student at the Medical College of Virginia, many of the microbiologists in my department were very active in the local ASM.  Our local ASM provided opportunities to graduate students and postdocs to present their work to an outside audience of scientists from the surrounding universities and a chance to set up collaborations with labs working in related areas. 

Now that I am in Southern California, I am glad to see that we also have a local ASM branch (SCASM) that is very active in bringing together our scientific community.  That's why I want to encourage all our of readers and customers who are from the Southern California region to attend this membership drive event hosted by our local branch on Saturday, September 18th at the Stuart Cellars Winery from 11 am- 2pm.

The event will include wine tasting, appetizers, and a winery tour. The cost is only $20 per member and if you bring a new member, the eve

This year at the American Society for Microbiology Annual Conference hosted in our home town of San Diego, MO BIO Laboratories has some fun activities planned that we wanted to make sure you know about and take part in.

Remember MO BIO in your Methods Section of your Poster

If you haven't received a MO BIO t-shirt yet then here is your chance!  Simply mention which MO BIO product you used in the methods section of your poster or during your talk and we will give you one of our new Biofilm t-shirts. 

Send us your abstract and poster details (location, date, time) in advance and take advantage of the opportunity to be included in the MO BIO Poster Guide to ASM.  Don't miss the chance to be featured on our website and at our booth!

We've also planned a lovely evening including food and drinks....

MO BIO Laboratories is an ardent supporter of science education at all levels.  So when we heard about the pioneering soil microbiology classes being taught by Adjunct Assistant Professor in the Department of Microbiology, Immunology, & Molecular Genetics at UCLA, Erin Sanders-Lorenz, we had to know more.

Erin received her PhD in 2005 from UCLA and during that time focused much of her efforts on building programs for teaching microbiology to students in a way that would engage and fascinate them. Indeed, her CV contains a long list of undergraduate teaching and instructional development activities, curriculum development projects, and education publications. Her dedication to microbiology education continues to be her main focus as a academic coordinator at UCLA. Erin is currently the Director of Initiatives in Life Science Laboratory Education and a co-faculty advisor for the Training of Departmental Teaching Assistants program at UCLA.

In an ideal world, we would have time to read every great paper coming out in all the microbiology journals each month.  Instead we have to focus our reading on the topics that directly impact our research. But reading papers from other fields can often help us to find new methods or generate ideas for our projects that we wouldn't have thought of on our own.

To make scanning the monthly journals a little bit easier for you, today's blog is a first in what will be a regular series of articles highlighting some of the exciting research going on in microbiology. After scanning the January and February publications on Highwire, I picked a few headlines that I thought the community would find particularly interesting.

Do you love your work? Does nothing make you happier than a day out in the field collecting soil from the rainforest floor, in a boat collecting Vibrio contaminated water from Puget Sound, traipsing the forest looking for animal droppings from wild birds in Venezuela, or aboard the Alvin collecting biofilms from deep sea floor hydrothermal vents?

It's important to love your work and fortunately for us, there is so much to love about microbiology and the environment. But to find out what is best about working in this field, I asked the question to several of my scientist friends:  What do you love about your work? Why do you study environmental microbiology and what is it that makes it the best field of work?

Wisconsin has lost over half of its wetlands due to urban sprawl.  Entire habitats are filled in due to construction of new roads and wetlands are permanently divided in half by freeways, reducing the amount of space for turtles to migrate and live.  When turtles do try and cross the road, well, you can imagine that their chances of making it to the other side are not very good.

Besides cars and roads, turtle survival is also facing threats from new predators; free-roaming cats and dogs who eat their eggs. 

Hi All,

Welcome back to The Culture Dish! We hope you are all having a great start to your week and to the year 2010.

‘Tis the season to be jolly and at MO BIO Labs, we are a merry crew.  A lighthearted and cheerful atmosphere permeates our halls all year round but it is especially strong during the holiday season.  As we look back on our accomplishments in 2009, with products such as PowerWater, PowerFood, and LifeGuard, we are thankful to all the scientists who played a part in helping us develop these innovations, either by their feedback or with their own hands. And in R&D at MO BIO right now, we are working hard on many exciting new products and helpful tools planned for 2010.

The fourth Thursday of November marks the annual tradition in the U.S. called Thanksgiving. Originally Thanksgiving was a religious holiday that has sinced turned secular and became a national holiday in 1941. Now, for families celebrating Thanksgiving, it is a time to cook a whole lot of food and eat way too much pumpkin pie.

Since everyone is going to be focused on food next week, I thought it would be a good time to go over some important facts about food microbiology and the bacteria that can infect your food if you undercook it, cross-contaminate it, or let it sit out all night. After all, pumpkin pie is full of sugars, protein, and fats- everything that a lovely swarm of bacteria also enjoys as a midnight snack.

First lets discuss what are the sources of bacterial contamination in food.

This month we’re exploring the role that undergraduate scientists play in advancing research.  Dr. Karen Bernd, Associate Professor at Davidson College leads undergraduate searches for the deadly Chytrid fungus in the Western Piedmont region of North Carolina. We had a chance to speak with her in-depth on her research project and how she works to inspire young scientists.

Q:  What is Chytrid fungus and its impact on amphibians?

It's MO BIO's 16th birthday! To celebrate 16 years of creating and producing new products for nucleic acid isolation we'd like to share with you 10 interesting facts about the company and it's founders, and give you, our loyal fans, an amazing discount offer as a birthday present and drop in a word from our CEO and CFO.

First, 10 little known facts about MO BIO Labs

1. MO BIO's first product was the UltraClean 15 DNA Purification Kit for DNA clean up of PCR reactions and agarose gel slices.

2. MO BIO Labs CEO, Mark Brolaski, was one of the original inventors of the first ever commercial product for DNA clean up, Gene Clean, and a co-founder of the company BIO 101.

3. MO BIO Labs manufactures everything right in our own buildings. Every bead tube is made right here.

Welcome to the MO BIO Laboratories inaugural weekly blog, The Culture Dish, introducing what will be the first of many interesting and captivating articles, technical tips, news stories, and interviews with cutting edge scientists. 

The aim of this blog is to give you a better idea of who we are at MO BIO, generate discussion on topics important to you and give you expert technical guidance on the issues that are giving you trouble in the lab.

So please do get involved. We welcome all of your suggestions for topics and scientists you are interested in hearing from.  We will bring you indepth technical answers and share with you our own insights and research experiences using the same products you do.

To receive automatic updates of new articles, simply register by clicking the RSS button on the left. 

Here are ten reasons you won't want to miss our weekly Dish: